Encryption A cryptosystem is a way of encoding and decoding messages so that only certain people are able to read them. This case presents a cryptosystem based on matrix algebra and implemented using Matlab. It is much more secure than simple systems you may have seen, such as replacement of each letter by a different letter. As per MATLAB it is not possible to reverse engineer it back to m file. Decrypt Files Without Key; Decrypt File Online; Matlab P File Crack; Decrypt P File Matlab.
@Jan: Jan, I think you missed my point. I already said that the encryption was put in place on purpose to protect intellectual property, which is what I like.
I meant to say that hacking P-code is possible but probably very difficult. I probably had a smirk on my face when I say 'hey, if you find a way, please let me know!'
He positioned the figure—its upright stance reiterated by the vertical orientation of the canvas—in a descending diagonal from upper left to lower right. The Armory Show also had the unfortunate effect of showcasing the provincialism of American artists who seemed to paint as if nothing had changed since the Realist and Impressionist movements of the nineteenth-century. 2), 1912, oil on canvas, 57 7/8 x 35 1/8 (151.8 x 93.3 cm) (Philadelphia Museum of Art)As the exhibition toured the country, Duchamp’s painting captured widespread attention for its unconventional rendition of the nude. In the face of this realization, the American artist, one of the exhibition’s organizers wryly lamented, “we have not yet arrived at a National Art.” 1. Dude descending a staircase rar. Detail, Marcel Duchamp, Nude Descending a Staircase (No.
I didn't know hacking P-code is not a real challenge and I still believe it is going to be very hard. Are you afraid that math98 will take my word for it and go cracking the encryption? He said he 'heard from an old MATLAB user that there are some ways to decrypt a pcode'.
Is that 'old MATLAB user' referring to you? Walter didn't want to take that credit. @Yair: Sorry. I did not meant the term 'hacking' in any offending way and I'm definitely convinced from all I've seen and heared in the last years, that your work is legal and helpful for Matlab users and in consequence for TMW. I'm used to distinguish the illegal 'cracking' from the legal 'hacking', which means digging in the codes for the not barely obvious features. If any of your investigations and publications of the golden beans you've found is not legal -what is not the case!-, I'd strongly recommend that you get payed by TMW to catch up a legalization retrospectively.
Please always check NIfTItools.pdf for detail descriptions and latest updates.If you are confused by the Left / Right of an ANALYZE image, please read UseANALYZE.pdf.You may also want to go through FAQ.pdf for practical solutions and real examples.Basic Programs:1. Loaduntouchheaderonly.m: Load only the header section of NIfTI or ANALYZE file. The input file will be automatically detected.
NIfTI structure will be returned for NIfTI file, and ANALYZE structure will be returned for ANALYZE file.2. Loadnii.m: Load N-Dimensional NIfTI file (where N can be from 3 to 7) or ANALYZE file (where N can be from 3 to 4), and apply header info (e.g. Affine geometric transform, voxel intensity scaling, etc.) to the data. If your file has more than 3-Dimension (e.g.
Time series etc.), you can also specify a range to extract only 1 or several volumes.3. Savenii.m: Save N-Dimensional NIfTI structure (where N can be from 3 to 7) that is loaded by 'loadnii.m' or made by 'makenii.m' into a NIfTI file.4. Makenii.m: Make N-Dimensional NIfTI structure (where N can be from 3 to 7) based on the N-Dimensional matrix and other optional parameters (e.g. Voxelsize, origin, etc.).
Using 'savenii' command, the NIfTI structure that is made by 'makenii' can be saved into a NIfTI file.5. Makeana.m: Make 3D ANALYZE structure based on the 3D matrix and other optional parameters (e.g. Voxelsize, origin, etc.). Using 'saveuntouchnii' command, the ANALYZE structure that is made by 'makeana' can be saved into an ANALYZE file in order to be compatible with some ANALYZE only programs.6.
Reslicenii.m: Re-sample 3D (or 4D) NIfTI file, or ANALYZE file with affine matrix M in.mat file, and save the re-sampled data into a new NIfTI file. The program will base on the affine matrix, which is especially useful for oblique images with non-orthogonal rotation or shearing that cannot be loaded with 'loadnii.m'.
You can also specify voxelsize, etc. It will not cause negative effect, as long as you remember not to do slice time correction after using 'reslicenii.m'.7.
Padnii.m: Pad the volume(s) in NIfTI structure from any of the six sides, while keeping the originator, voxel size, data type, and description unchanged. The program is especially useful after you use reslicenii, since the new volume will most likely have different dimensions.8. Clipnii.m: Clip the volume(s) in NIfTI structure from any of the six sides, while keeping the originator, voxel size, data type, and description unchanged. The program is especially useful after you use reslicenii, since the new volume will most likely have different dimensions.9. Viewnii.m: View & Edit 3D (or 4D) NIfTI or ANALYZE structure that is loaded by 'loadnii.m' or made by 'makenii.m'. Activation map, ROI, etc. Can be overlaid on top of a background image (see above picture).
Plotted view can be embedded into your existing figure window. If you use it as an individual program, it can also edit the orientation and voxel value of the image, view volume histogram, and save the modified image.10. Loaduntouchnii.m: Load N-Dimensional NIfTI file (where N can be from 3 to 7) or ANALYZE file (where N can be from 3 to 4), but do not apply any changes that are indicated in the header. WARNING: Do not use 'viewnii.m' to view the structure that is loaded by 'loaduntouchnii.m'.11. Saveuntouchnii.m: Save N-Dimensional NIfTI structure (where N can be from 3 to 7) or ANALYZE structure (where N can be from 3 to 4) that is loaded by 'loaduntouchnii.m' or made by 'makeana.m' into a new NIfTI or ANALYZE file. If you do not modify the loaded dataset, the header and data in the new saved file should be the same as those in the original file.Other Programs:1. Collapseniiscan.m: Integrate multiple single-scan NIfTI or ANALYZE files into a multiple-scan NIfTI file.2.
Expandniiscan.m: Break a multiple-scan NIfTI file into multiple single-scan NIfTI files.3. Saveuntouchslice.m: Save back to the original image with a portion of slices that was loaded by loaduntouchnii. You can process those slices matrix in any way, as long as their dimension is not altered.4. Getniiframe.m: Return the number of time frames of a NIfTI file.5. Fliplr.m: Flip NIfTI or ANALYZE file Left-Right along the plane across the originator, and save the L-R flipped data into a NIfTI file. WARNING: Please use this program with caution, although you can always flip it back.6. Loadniiext.m: Load header extension from a NIfTI file.7.
Matintohdr.m: Integrate affine matrix in old SPM.mat file into its.hdr header file. Thus, the ANALYZE file is converted into a NIfTI file with the updated.hdr header file.
If anyone sees a need to read NIfTI-2 files, or reading.nii.gz/.hdr.gz/.img.gz files in -nojvm mode under MATLAB, or reading these files under GNU Octave, please try my new toolbox 'JNIfTI'It uses memmapfile in MATLAB for fast disk-reading. It also support conversion from the rigid NIfTI-1/2 binary format to the more flexible text/binary JSON based new JNIfTI format, defined in the JNIfTI specification, making the data file smaller in size, faster to load/save, human-readable and extensible.The JNIfTI toolbox can use Java based gzip compression, same as in this toolbox, but can also use the ZMat toolbox for fast compression/decompression.
Unfortunately I have found this to be very buggy. A simple example of this is to load an image and then save a copy of it using the loadnii and savenii functions. On my machine this results in the copy having a slightly different vox2ras matrix (and it is definitely not a rounding error). As such this toolbox has given me a lot of trouble over the last few months, it is extremely difficult troubleshooting your code when you can't even be sure that utility functions such as these are doing their job. I mean this criticism only to be constructive and to serve as a warning to others and I nevertheless thank the author for their efforts. Hi Jimmy,I'm trying to use your toolbox to change the datatype of my images from int16 to float32. I've seen in an earlier comment that this might be possible, but I have some trouble with the conversion.
This is what I have done so far:datatype = 16;% change datatype to float32nii2 = makenii(myoldniifile.nii, , datatype);savenii(nii2, 'mynewniifile.nii');the error message i get is: Datatype is not supported by makenii.Is it possible to convert nii files this way or am I doing something wrong here?Thank you in advance for any help.Best wishes! Thank you for these tools.
They have proved to be extraordinarily useful. However, recently I have found that the loadnii module has stopped working. I redownloaded the toolset and still have the same issue.When I type loadnii('path/to/file')The error I receive is:Undefined function 'bitset' for input arguments of type 'char'.Error in xformniichangehdr (line 465)hdr.dime.xyztunits = char(bitset(hdr.dime.xyztunits,2,1));Error in xformnii (line 154)hdr,orient=changehdr(hdr,tolerance,preferredForm);Error in loadnii (line 185)nii = xformnii(nii, tolerance, preferredForm);Any debugging ideas? A small issue where I think the reliability of the 'tolerance' option can be improved. When checking the affine matrix in xform.m it would be helpful to remove the resolution scaling form the matrix first, as if you have highly anisotropic voxels (common in MRI, say 0.7x0.7x5.0) it makes it very difficult to do a rational 'tolerance' calculation to determine the matrix orientation. In this example all the elements in the third column are.5, so even for nearly straight matrices the secondary element in col 3 (n.5) will be larger than the primary elements in col 1 and 2 (n.0.7). Here is my suggested change (from my git patch file):- a/niftitools/xformnii.m b/niftitools/xformnii.m@@ -324,13 +324,15 @@ function hdr, orient = changehdr(hdr, tolerance, preferredForm)hdr.hist.srowy(4)hdr.hist.srowz(4);- if det(R) 0 isequal(R(find(R)), sum(R)')+ if det(R) 0 isequal(R(find(R)), sum(R)')hdr.hist.oldaffine = R;0 0 0 T;1 ;- Rsort = sort(abs(R(:)));- R( find( abs(R).
Hi Jimmy (and all the users of this toolkit),Thanks a lot for this great toolkit and all the discussion!I have a question regarding extracting data from a ROI:I have T1 maps in 4-dimensional (X,Y, slices, time) (in.nii format) and volume of interest files (in.nii format). I want to extract time activity curve from T1 maps for this particular VOI and want to plot it in MATLAB.Description of viewnii shows that we can do this using this toolbox but I couldn't figure out how?I would really appreciate if anyone could please help me in sorting this out!Thanks,Sahil. I am brand new to this toolbox (and MatLab) and I am trying to load a.nii file. I entered into the command window the following: topface = loadnii('/Users/MRIuser/fMRI/Homunculus2/P121/Experiment.feat/stats/zstat1.nii')Then, the command line immediately converted into: uiopen('/Users/MRIuser/fMRI/Homunculus2/P121/Experiment.feat/stats/zstat1.nii',1)Also, a tab opened in my editor window labeled zstat1.nii with many random characters. But, there was no created variable called 'topface.'
Any suggestions? Hi,Thanks for the toolbox. I have following issue:I have a 3D matrix in MATLAB which I need to convert to NIfTI or ANALYZE format so as to view it in SPM8.
For this I am using 'Tools for NIfTI and ANALYZE image'. My problem is once I convert this 3D matrix to ANALYZE format using makeana command, I get the brain volume that is rotated/flipped w.r.t the original volume.How can I resolve this?NOTE: co-registering this to original brain volume did not help, the result was still flipped.Thanks,Janki. You can use 'loaduntouchnii / saveuntouchnii' pair. Here's an example:nii = loaduntouchnii('avg152T1LRnifti.nii');nii.hdr.hist.descrip = 'Mengye';saveuntouchnii(nii, 'newavg152T1LRnifti.nii');Unless you touch nii.img by yourself, e.g.
Nii.img(1)=0, it will not be changed, although it is also loaded and saved. Only the header (nii.hdr) is edited in the way you make the change.In addition, if the input file is in Analyze 7.5 format, the output will be kept in Analyze 7.5 format. If the input is in NIfTI format, the output will be kept in NIfTI format.That is why I have 'loaduntouch' as well as 'load' feature. However, in most case, you want to use 'load' feature, since you don't want to interpret affine matrix in the header, and make all sorts of flipping and rotation by yourself, do you? Data for 'plot' only contain the coordinates information, while data for 'makenii' need intensity value which is assumed to be distributed on a grid with its coordinates from 1 to the dimention of the grid. In addition, unlike plot, coordinates for images contain only the integer.
Therefore, you cannot directly extract the data from a plot and make it to an image.Export your plot data to an image would be an easy alternative. I think you already did good. All you have to do is to hide the background image and the axes before you export the plot to an image. Here's how to do so:1. Before export, use mouse click your plot (make it active);2. Hide the axes by running:set(gca,'visible','off');3. Hide the background image by running:h = get(gca,'child');for i=1:length(h)if strcmpi(get(h(i),'type'),'image')set(h(i),'visible','off');endend4.
Export the plot to an image. Now it does not have the background and axes.
Thank you very much for this useful product. I do have a question, if anyone could help me out.I loaded a.nii file, did some processing and have a new plot that I would like to extract data from and ultimately save as.nii. It is a simple plot that was a result of finding the boundaries of an object. I extracted the data from the plot and entered it into a cell, but the 'makenii' function does not support this datatype. I tried converting the cell to a.mat, but that did not produce a satisfactory result either. I also tried saving the plot as an image and then using 'makenii,' which worked, but the result included the border and axes of the image. I want only the data, without the background or axes.
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Does anyone have any suggestions? 'collapseniiscan' is used to integrate multiple single-volume NIfTI or ANALYZE files into one multiple-volume NIfTI file. In your case, if you want to concatenate two 4D NIfTI images into one 4D NIfTI images, you should apply 'expandniiscan' to your both 4D images. All volumes must be in the same folder, and make sure the file name is correctly renamed (i.e. From 001999 instead of 1999). Then, apply 'collapseniiscan' to all those expanded volumes in the specific folder, and you will get a concatenated 4D NIfTI image file.
Hello,This package works very well for my research. Thanks first. But now I have a problem with vector image. I want to change the pixel value of a xyz vector image by taking its absolute values. I first used: nii = loadnii(1xyz.img), if I use viewnii(nii), I found everything correctly.
Moving the crosshair to 139,63,91, I can read the value is (-0.1784,0.8963,0.3663), which is correct. But if I used: a = nii.img; a(139,63,91,1:3), it will display values as 0.35555,0.9434,0.6535. It seems that the value of a is always positive. I tried to use nii = loaduntouchnii(1xyz.img); a = nii.img; It has the same positive value.Do you have any suggestion about this inconsistency between the value of nii.img and that displayed by viewnii(nii)?Thanks a lot.
Hello,This package works very well for my research. Thanks first. But now I have a problem with vector image. I want to change the pixel value of a xyz vector image by taking its absolute values. I first used: nii = loadnii(1xyz.img), if I use viewnii(nii), I found everything correctly. Moving the crosshair to 139,63,91, I can read the value is (-0.1784,0.8963,0.3663), which is correct.
But if I used: a = nii.img; a(139,63,91,1:3), it will display values as 0.35555,0.9434,0.6535. It seems that the value of a is always positive. I tried to use nii = loaduntouchnii(1xyz.img); a = nii.img; It has the same positive value.Do you have any suggestion about this inconsistency between the value of nii.img and that displayed by viewnii(nii)?Thanks a lot. You need a reference image by the way, so you can see what will happen before and after you apply the transformation matrix.
Here's the example:1. Download 'avg152T1RLnifti.nii' from NIfTI site. I use it as reference image.2. View how the reference image looks like: nii=loadnii('avg152T1RLnifti.nii');viewnii(nii);3.
Assume that I have a Transformation Matrix, which will let the reference image turn 30 degree counter-clockwise on XY plane, here will be the matrix: T=cos(pi/6) -sin(pi/6) 0; sin(pi/6) cos(pi/6) 0; 0 0 1;4. Get oldxyz from reference image: rl=loaduntouchnii('avg152T1RLnifti.nii');oldxyz=rl.hdr.hist.srowx(1:3);rl.hdr.hist.srowy(1:3);rl.hdr.hist.srowz(1:3);5. Apply your transformation matrix, and save newxyz into a new image: newxyz=T.oldxyz; rl.hdr.hist.srowx(1:3)=newxyz(1,:); rl.hdr.hist.srowy(1:3)=newxyz(2,:); rl.hdr.hist.srowz(1:3)=newxyz(3,:); saveuntouchnii(rl, 'rl30.nii'); Now you already have the 'rl30.nii', which is a transformed NIfTI image can be used anywhere.6. In order to view this image using my toolbox, you need to reslice it: reslicenii('rl30.nii', 'rl30b.nii'); Now, you can load and view the rotated image: rl30b=loadnii('rl30b.nii'); viewnii(rl30b);Hopefully this answers your questions. To reply your first comment: The problem is that you mixed 'makenii' with 'untouch' version. If you use 'makenii' to get NIfTI structure, it has to be saved using 'savenii'.To reply your second comment: If you know NIfTI structure well, sure you can modify it and then use 'savenii' to save it. You can even save 'non-orthogonal' NIfTI structure to the file with 'savenii'.The reason that I interpret the header with 'loadnii' and limit it to 'orthogonal' transformation is all about convenience, at least for my work.BTW, if you take the original NIfTI file, and bring it to other software to display (e.g.
SPM), they will also reslice it for you.Thank you very much for your rating! Without more detail, I cannot duplicate your problem. Please send me your data that indicates it. On the other hand, I wish you could take a look at my web page to better understand this tool. In order to display, you must use 'loadnii' instead of 'loaduntouchnii'.
Your data is interpreted properly (touched). There could be many cases, e.g. Scale factor is specified in the header file, your data has different orientation, etc. However, in no situation it treats double datatype differently.
I assume that you have a series of 3D NIfTI (or Analyze) files with the same header information (i.e. Same dimension, voxel size, originator. Etc.), and you want to integrate it into a single 4D file with time series in the file.If this is the case, you can use my 'collapseniiscan.m' to do so. Type help collapseniiscan to get more information.For file extension, this function will follow whatever you have. You will still get a single.hdr/.img file afterwards.Since all NIfTI compatible software should be able to load a 4D NIfTI (or Analyze) file, we do not support any conversion from.hdr/img to.nii file. You are not supposed to use 'loadniihdr.m' & 'loadniiimg.m'.
Both are internal functions, and are not supported when you call them directly.If you want to take look at the header information, please use 'loaduntouchheaderonly.m'.If you would like to change the voxel value, please use 'loadnii.m' to load the NIfTI file, and then use 'viewnii.m' to edit voxel value at crosshair (under 'Edit' tab), and then click 'Save displayed image' under 'File' tab.The reason of inconsistency in your case is caused by the scaling factor in the header that was not properly interpreted by yourself. HiI am using Tools for NIfTI and ANALYZE image.
It is really helpful and my sincere thanks to share your work for the research community.I am using the images in.hdr and.img format. I am trying to change the pixel value 1 into 5 and then save it as.img. I viewed the saved images using the function viewnii. I could find the pixel value as 5, which i did.
But if i open these images in viewer like MRIcroN and FSLVIEW it shows a pixel value as 0.01961. I could not find the reason. Can you please help me in finding the solution to the above problem. I can see that GMax of the output image is 5. But for the input image it is 0.I have put the lines of code which were used by me.I would like to send my input file, so it would be better to know my issue.
Please let me know a way to send my input file.nii1.hdr,nii1.filetype,nii1.fileprefix,nii1.machine = loadniihdr('1sub110A-1285med');nii1.img,nii1.hdr = loadniiimg(nii1.hdr,nii1.filetype,nii1.fileprefix,nii1.machine);z=find(nii1.img);%number of index-4610img1=zeros(size(nii1.img));img1=uint8(img1);img1(z)=5.00000;nii1.img=img1;savenii(nii1,'out1.img');Thanks in advance for your help. First, when you use 'savenii.m', the file that you saved will always be in NIfTI instead of Analyze format.Second, use 'loaduntouchnii' to load both original Analyze file and saved NIfTI file, and check what is the dimension size and data type of '.img' field.Finally, I have tested to use 'loadnii.m' to load many Analyze and NIfTI files and then use 'savenii.m' to save into NIfTI files.
I did not find data size 'increase remarkably'. If it is possible, please upload your original Analyze data to somewhere that I can access, and email me the link (DO NOT USE EMAIL ATTACHMENT), so I can try to duplicate your problem.By the way, I will not be available until Aug 2. First, both 'loadnii' & 'loaduntouchnii' support SPM NIfTI images. As a matter of fact, there is only one NIfTI standard, all NIfTI compatible software should comply with that standard.Second, in order to duplicate the error, please upload that image onto anywhere that I can have read access.
PLEASE DO NOT SEND BY EMAIL ATTACHMENT.As you have noticed, NIfTI images can be in any spatial orientation, while 'loadnii' can only have 48 orthogonal orientations. In that case, the program will prompt you to use 'reslicenii' to interpolate the image. Since you did not get the appropriate prompt, I am interested to take a look at the image that you are loading.Please check my NIfTI web page for more details. Hi Jimmy,I have some problem. My goal is to change the negative value and the NAN value in an image into 0 and then save it as.nii. I used the loadnii program and then changed the value into 0, and then used the savenii. Everything seemed to be fine.
But I finally found that the FOV of the image changed a little from: Field of VIew-Width: 204; Field of View-Height: 256; Slice Thickness:1 to Field of View-WIdth:203.992; Field of View-Height:255.909;Slice Thickness: 0.99968. But the image dimensions remained the same. Do you understand what I mean? I mean the voxel size changed.
Could you please have a look at this problem? It is very strange.Thanks a lot.Xiaoying. Hi Jimmy,I have some problem.
My goal is to change the negative value and the NAN value in an image into 0 and then save it as.nii. I used the loadnii program and then changed the value into 0, and then used the savenii. Everything seemed to be fine. But I finally found that the FOV of the image changed a little from: Field of VIew-Width: 204; Field of View-Height: 256; Slice Thickness:1 to Field of View-WIdth:203.992; Field of View-Height:255.909;Slice Thickness: 0.99968. But the image dimensions remained the same. Do you understand what I mean?
I mean the voxel size changed. Could you please have a look at this problem? It is very strange.Thanks a lot.Xiaoying. Hi Juan:You can check 'Question about overlay' category under:There are several questions and answers in this topic.You said that you have the x,y and z directions of each voxel.
The x,y and z directions must be converted into the index regarding to the first voxel. Probably, you already have the brain region that represents the eigen image. Let's assume that you have it in a binary image called 'brainmask.nii', while the anatomical image is called 'ana.nii'. Here's what you can try:1. Use 'ana = loadnii(ana.nii)' to load the anatomical image, and make sure that variable 'ana.img' is either in 'single' or 'double'.
If not, use step 2 to convert it.2. To convert variable 'ana.img' to 'single', you need to use 'makenii' command: 'ana = makenii(single(ana.img), ana.hdr.dime.pixdim(2:4), ana.hdr.hist.originator(1:3))'.3. Use 'mask = loadnii(brainmask.nii)' to load the brainmask image, and assign value and index to 'opt' struct: 'opt.setvalue.idx = find(mask.img); opt.setvalue.val = eigenvector;'.
You can see more detail to use 'setvalue' by command: 'help viewnii'.4. Add other values to 'opt' struct: 'opt.command = 'init'; opt.useinterp = 0;'.5. Plot eigen image with underlaid background by command: 'viewnii(ana, opt);'.6. Don't click 'interp on/off' menu.
It doesn't work properly. If you would like to see the interpolated one, use: 'opt.useinterp = 1; viewnii(ana, opt);' instead.If you still have question, please feel free to ask me.Jimmy. Hi Jimmy.Thank you very much for this extremely useful toolbox.My question is about how to overlay in the image. I need to overlay the principal eigenvector of each voxel on the image; I have the x,y and z directions of each voxel in a matlab array already but I want to know how can I display over the same image or if its possible to modify your code to keep just the principal image and get rid of all the options that you gave like color and position of crosshair, etc.
Because I mainly need to show the image and display the eigenvectors over it.Thanks,Juan. I am using AnalyzeDirect Software for lung cancer detection and retrieval. I have segmented the lungs from chest CT scan of more than 300 slices (DICOM). I have saved the result in.avw format as well as in Analyze7.5 format. Now when i tried to open these files in MATLAB i got these problems1) the code only suppports 'hdr/.img' format i.e Analyze7.5 format. I was not able to load.avw file2) as no. Of slices are more than 300 it gives 'Out of Memory' error when i opened '.hdr/.img' data.how to resolve these two problems.
Hi Anne-Lene:Don't worry. The following tips will give you some more help.If you did not see difference after using 'expendniiscan', it means that you only have 1 scan (1 volume) in your file. Since you said '.look at the nifti images separatley.' , I thought you have several images (volumes or scans) in 1 file, and would like to treat them separately.The first step you need to do is to load your image into MATLAB by 'loadnii' command (Please look at 'help loadnii' before using it).Let's say you have an image 'file1.nii' (or 'file1.img/hdr'). By command:nii = loadnii('file1.nii');ornii = loadnii('file1.img');You can get a 3D matrix in 'nii.img', and its header information in 'nii.hdr'.You mentioned that you would like to change the image into another datatype. Hi Anne-Lene:No questions are stupid.Yes. You can use my tool to look at NIfTI images separately and also convert them to another datatype.Since NIfTI supports both img/hdr and nii extensions, so my tool supports any of them.Most help can be obtained by using help command.
Help makenii.There are several other resources that you can get help:Command 'expandniiscan' is used to break a multiple-scan NIfTI file into multiple single-scan NIfTI files, so you can look at them separately.If you want to convert img data type, you can use 'savenii' after use 'makenii' command. If you are familiar with NIfTI structure, you can modify 'hdr.dime' directly, and then use 'savenii' to save.If you have further question, please make it more specific, so I can help you.Jimmy. Hi!I am a beginner in using nifti so this may seem like a stupid question, but i hope you can help me.I have used fsl prelude to unwrap my mri images, and they are now in the nifti format. I now need to compare these to images with images that I have unwrapped with a matlab algoritm that i made myself.Can i use your tools to look at the nifti images separatley and perhaps convert them to another datatype that i can use in matlab?I tought maybe your tip in the help savenii could help me, but i don't see how to use it, do i need img/hdr files instead of nii?I will be very greatful for some guidance.Anne-Lene. Hi Michael:First, I am wondering how you could simply rename an.img file to a.nii file. NIfTI supports both extensions, but for.img extension, you need to save the header separately in.hdr file. So there is no way for people to just '.
Rename the.img file to.nii file.' Like you said.Second, I looked into Francesca's data, and the size of the image data does not match the size that is indicated in the header. For such a file, I cannot image any software can process it.I am glad to take a look at your samples. Would you please upload them onto your server, and post the link here?Thanks,Jimmy. Hi Wei:Thanks for the rate.When you use 'loaduntouchnii.m', it just load the img and hdr, but does not apply any changes (e.g.
Sclslope, affine matrix, etc) indicated in the header. Therefore, I always suggest people to use 'loadnii.m' in most cases. Please check the description of 'loaduntouchnii.m' & 'loadnii.m' on.You are right, the unexpected value was caused by the 'sclslope' parameter, which is properly applied when you use 'loadnii.m'. However, I am not sure whether you have noticed that this is a radiological image, i.e. Right on LHS and Left on RHS.
Here, L/RHS means Left/RightHandSide.When you use 'loadnii.m', it will do all the proper flipping and rotation according to the affine matrix in the header, and the img will always be in RAS orientation (i.e. X: L-R, y: P-A, z: I-S). In your particular case, instead of use 32 32 23, you should use 33 32 23, since x axis is flipped, i.e. Newx = maxx(64) - oldx(32) + 1 = 33.Other software may choose to do so with proper labeling around Axial / Sagittal / Coronal view, e.g. FSL does so.Please feel free to let me know if you have further question.Jimmy. Hi Jimmy,When reading a nifti file I found the voxel gray values are different with other tools.
What I did is:- 'untouch load' the file: fmrimean = loaduntouchnii(./meanfM00223004');- print voxel value of mrimean.img(32,32,23). The value is 9506.- But when I open the same file with fslview, I found the same voxel has different value. And other voxels are also different. The fslview snapshot is attached.
Because in fslview the voxel coordinates begins from 0 to dim-1, the same voxel in fslview has coordinate 31 31 22.- Use the application 'Imageviewer' from itk, and found the voxel value is same with fslview. Also attached snapshot. Same to fslview the coordinate are 31 31 22 for the same voxel.- check the header of the nifti file by fsl tool 'fslhd':datatype 4nbyper 2bitpix 16That means it's int16.-Check the fmrimean structure in matlab, and found the data type is 4:datatype: 4bitpix: 16But why did your nifti tool give different gray value with other packages?
I put all the snapshot and the nifti files at for your reference.By the way this is excellent tool. Hi Francesca:First, thank you very much for the rating, and I really appreciate it.It seems that 'lCC19850624TRTN2x2x2b1000afa.nii' is corrupted. Have you tried to open it successfully under MRIcro? If so, please upload this file and let me take a look at it?In addition, from the error message that you posted, it seems that you are using a very old version of my tools. I noticed this by the line number showing the error. However, I still believe that the error is caused by the corrupted image.Please let me know,Jimmy. Dear Jimmy,i'm just a beginner with all this 'nifti imaging world' but I've already done enough for understanding that you've done a very great and smart job!thanks!Well, i have a problem with loading a.nii file.
(obtained by exporting a.ROI file with MRIcro). I'll post the error that i get:%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ROI=loadnii('lCC19850624TRTN2x2x2b1000afa.nii');??? Error using reshapeTo RESHAPE the number of elements must not change.Error in loadniiimgreadimage at 266img = squeeze(reshape(img, hdr.dime.dim(2:4) length(imgidx)));Error in loadniiimg at 62img,hdr = readimage(hdr,filetype,fileprefix,machine,imgidx,oldRGB);Error in loadnii at 66nii.img,nii.hdr =.%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Could you help me?Thanks a lot and all the best!francesca. Hi Wen-Tung:The problem is probably in a module that is used by ImageJ. I tried MRIcron, and got the same result as you described. When hdr.dime.datatype=32 & hdr.dime.bitpix=64, it does not support.
When hdr.dime.datatype=64 & hdr.dime.bitpix=128, it works.In order to make sure what datatype ANALYZE format is supposed to support, I double checked the Analyze document:It says that Analyze format should only support 32/64, rather than 64/128.I also tried other popular software like AFNI. It turns out that 32/64 is supported by AFNI. When I tried 64/128, it complains 'Unsupported ANALYZE datatype =64', which is correct.Therefore, if you have to use datatype=32 complex, you have to find correct software to use. AFNI is one of them that I have just tested.All the best!Jimmy.
Thank you for the note, Jimmy.First, sorry that I didn't write it clearer in my previous posting. ImageJ is a freeware from NIH that have numerous users in medical imaging community. ImageJ has a plugin that can open/save image in Analyze format. I was trying to save an MRI image, after some processing using Matlab scripts, in Analyze format and view it using ImageJ.I tried your very nice example, it works well. Yet, it is still not clear to me why ImageJ cannot read the output file. Using datatype=64, ImageJ can read the file, but this is not the correct datatype and there are sinusoidal modulations across the image.Thank you.Wen-Tung. Hi Wen-Tung:First, thank you for the rating.Your script is correct, but I didn't get any error message.
Trying to read the test.img using ImageJ.' Is it a typo?Here's an example that I tested, and you can duplicate the process:%%%%%%%%%%%%%%%%%%%%%%%%%%%%%img1=rand(3,3)img2=rand(3,3)myMat=complex(img1,img2)datatype=32;ana = makeana(myMat,datatype);saveuntouchnii(ana,'C:Datatest');ana=loaduntouchnii('C:Datatest')nii=loadnii('C:Datatest')%%%%%%%%%%%%%%%%%%%%%%%%%%%%%Did you get error message when testing the above script?Jimmy. Hi Prateep:when you load an image file, e.g.:nii = loadnii('yourimg.nii')nii.hdr.dime.pixdim(2:4) will be the width, height, and depth of a voxel.If you view it with viewnii(nii), click menu 'View' and then click 'Image Information', the 'voxel size' is the width, height, and depth of a voxel.Since both Analyze & NIfTI image should have the same voxel size for all voxels in an image, the maximum and minimum size should be the same.The distance in voxel from origin can be obtained by subtract value at 'XYZ at origin' with value at 'XYZ at crosshair'. For distance in millimeter from origin, since value at 'XYZ at origin' is 0 0 0, you can just read value at 'XYZ at crosshair'.Please feel free to ask more questions,Jimmy. Hi Jimmy,I got some problems using the headers with your nice tool.When I load a 4-D nifti file header with loadniihdr and compare it with the header from the.hdr field using loadnii, I get different pixdim values:loadniihdr:niftihdr = loadniihdr('niftifile');niftiimage = loadnii('niftifile');niftihdr.dime.pixdim is 1 4.5313 4.5313 4.5000 200 1 1 1niftiimage.hdr.dime.pixdim is 1 4.5212 4.5312 4.4900 200 1 1 1The difference of the pixdim arrays is 0 0.01 0 0.01 0 0 0 0Did I found a bug or is there a bug in my head?Pieter. Hi Maddy:Yes, it is easy to do so with my tools. Here’s the steps:1.
Load nii file;2. Find an unused intensity level. If not available, add another level;3. Find the index of the circle and circles in successive slices;4. Mark them with the value that you choose in Step 2;5. Create a colormap file;6.
View brain with circles;If you are still having problem to create circles, please upload the 2 nii file to your ftp server. The first nii file should be the original volume, the second one should be the one with initial circle. Please also tell me exactly what slices do you want the circle to be drawn, and what color do you want the circle to be drawn. I will then reply you with the modified nii containing the circles.Jimmy. Hi Jimmy,Wonderful piece of work and a very useful one at that! I would be pleased to know if I can use it for my specific case.A rod-like observation chamber that we have inserted in the skull shows up as a circle in some of the initial slices of MRI.
What I want to do is to project the exact outline of the circle onto a few other deeper slices, so that it can be found, where exactly the projection of the chamber lies in the successive slices. Thereby, the region that would be encircled if the rod-like chamber were to be inserted further inside can also be found. Simply put, it is like overlaying a circle of specified diameter and position onto each successive slice.I tried doing it with the viewnii function with the circle saved in.jpeg/.fig formats, giving the figure handle and the nii, using the description in the help section of the view function. But I had trouble with the figure properties, especially the function ‘set’. I get errors in almost every figure property, starting from ‘menu bar’ at line number 291 in the program.
I am a beginner in matlab. I was actually surprised I could use other functions, which is why I say that your file is so user-friendly.
I would be happy to know how I can go about doing itTo sum up, all I want to know is, if there is a way of plotting a circle,( given its radius and position in those co-ordinates), onto successive slices. Hi Jimmy,I'm sorry to repeat my question, but the entries of AC origin are still not clear to me, mainly because I don't know what is meant by 'AC origin'.I now know that voxels are being counted (not the position in mm). Now, is it the origin in question related to the x, y, z offset of the slab of slices in the brain (i.e. The offset when positioning the slices during the scan), or is it the origin within the slab of slices itself?
I presume it is the former.If it is the former, then I'm not sure why it has to be relative to img(1,1,1), as opposed to the overall offset of the slab. I have my offset in mm in the readout, phase encode, and slice directions. Can I just convert these values to numbers of voxels?Finally, is the z coordinate negative upwards, or negative downwards? A more superior slice would have a larger negative z coordinate than a more inferior slice)As a side note, I'm only using makenii and savenii, to then analyze the data in FSL.Hopefully I've made my confusion clearer this time. Thanks for your help,Nicole.
Hi Nicole:First: 'origin' parameter in 'makenii.m' is in voxel, which is relative to the first voxel of 'img' parameter, i.e. Img(1,1,1);Second: It would be much clearer if I use an example to explain this:img=125:249; img=reshape(img,5,5,5);nii=makenii(img,1,1,1,3,3,2);viewnii(nii);Yes, we know AC Origin means 0 0 0 in millimeter. However, you must tell the NIfTI data where is your 0 0 0 millimeter, so other people can also know it when they open your NIfTI data. Therefore, parameter 'origin' can only be expressed in voxel to locate the exact position of your 3D matrix to be the AC Origin.Jimmy.
Hi Jimmy,Your code has been very useful to me; I've been using makenii and savenii. My question is regarding the AC origin for makenii.
First of all, I presume the coordinates should be in mm, like the voxel size. Then, I was wondering if AC origin refers to the position of the central slice. If so, for the 3rd coordinate (referring to axial slices), does negative (e.g.20) indicate an upward translation (i.e. More superior slice)? This is the convention that I'm used to, but I am not sure it applies to makenii as well.Thanks!Nicole.
Stella,Here are the answers:1. It is correct that 'nii002.original.hdr.hist.originator' is 256 0 0 0 0, because 't1icbmnormal1mmpn0rf0' is in Analyze 7.5 format and '001' is in NIfTI format that does not have obvious 'originator' field. Please let me know if you are still not clear.2. 'nii01.hdr.dime.xyztunits' is just an information field.
When it is 1, xyz are in 'meters'; when it is 2, xyz are in 'millimeters'; when it is 3, xyz are in 'micrometers'; when it is 0, xyz units are unknown and can only be interpreted by the author. I don't know why this field helped you, and wonder if it is the correct way.3. It is very strange that you got '-2 -2 -2 0 0' for 'nii002.hdr.hist.originator'. I need to look at both 't1icbmnormal1mmpn0rf0.img/hdr' & '001.img/hdr' in order to further answer this question. Would you please upload them to your FTP site and send me the link? Dear everybody:I have found the followingproblems in the using this toolbox.Data: t1icbmnormal1mmpn0rf0.rawb is downloaded from brainweb,then converted to Analyze format(t1icbmnormal1mmpn0rf0.img and t1icbmnormal1mmpn0rf0.hdr )(without.mat).Following procedures are applied:nii001 = loadnii('t1icbmnormal1mmpn0rf0', , 1)savenii(nii001,'001', 1);nii002 = loadnii('001', , 1)It is expected that the header information should be same, but there is following difference:1. In nii001, Originator in nii001.original.hdr.hist is same as in nii.hdr.hist as 0 0 0 0 0.2.In nii002, Originator in nii001.original.hdr.hist is 256 0 0 0 0, while it is -2 -2 -2 0 0 in nii001.hdr.hist.3.
The origin of t1icbmnormal1mmpn0rf0.img shown in MRIcro is 0 0 0, origin of 001.img shown in MRIcro is 2 2 24. Rotorient=,fliporient= in nii001.hdr.hist and nii002.hdr.hist, but not in their origianl header.5. When 001.img is converted to.mgz in FreeSurfer, the error message is as belowmriconvert./orig/001.img./orig/001.mgzreading from./orig/001.img.INFO: reading as a two-file NIFTInifti1Read: unknown space units 0 in./orig/001.hdrHighly appreciate your help if somebody can help to solve the problem.Best regards,Stella,SCE,Nanyang Technoligical UniveristySingapore.
How sclslope affect datatype?Hi Ged:Thanks for the URL you sent me. The way Jonas handling 'sclslope' is to convert image data type to 'double', which makes sense, although it is not specified on NIFTI documentation (see URL below):I modified my 'xform.m'. So it will convert the image data to 'double' in the case that 'sclslope' is used.
I am updating this file to MATLAB Central File Exchange, and NIFTI20060307 will appear there soon.Thanks again for your valuable input,Jimmy-Original Message-Hi Jimmy,Thanks for getting back to me. Unfortunately something else must be wrong in that case, since the image in Matlab has only the values 0 or 1, while the image viewed in FSLview or SPM has a range of values between zero and 1, the image type is uint8.Best,Ged. How to get original information from NIFTI hdr?Hi Ged:Thank you very much for your input.Actually both 'sclslope' and 'sclinter' parameters have been correctlyread and applied to the 'img' variable of the output NIFTI structure (see'xformnii.m' file): nii.img = sclslope. double(nii.img) + hdr.dime.sclinter;The reason to display 'hdr.dime.sclslope' as zero is a feature of mypackage. It signifies that the 'img' variable has already been modified. Youcan also find that 'hdr.hist.qformcode' and 'hdr.hist.sformcode' will beset to zero after proper affine transformation.The original value of 'hdr' can be easily found by: hdr =loadniihdr(filename); You should have correct value (0.003922) there.Jimmy-Original Message-Hi Jimmy,I've found your NiFTI toolbox very useful, but I'm having someproblems with some data stored in uint8.nii with a scaling factor.the data appears to load in as a binary image, and the value ofnii.hdr.dime.sclslope is zero, instead of the correct value(0.003922) which I can see using e.g. Spm5 or avwhd from FSL.Many thanks for any help you can offer,Ged.
22 Jan 20141.27.0.01. Thanks to the feedback and contribution of Chris McNorgan from Western University, the rriorient.m now have optional parameter for orientation vector.2. New program padnii.m is available together with clipnii.m. See example in FAQ.pdf.7 Mar 20131.26.0.0Since voxel size can be less than 0, I will change the default voxelsize in reslicenii.m from rounded minimum voxelsize in original NIfTI header to absolute minimum voxelsize in original NIfTI header. This fixed reslicenii bug.12 Oct 20121.25.0.0Added some new features and fixed some bugs.
For more detail, please visit:21 Sep 20111.24.0.0Thanks to the feedback of Matthew Bickell from University of Cape Town, a bug is fixed when edit voxel in millimeter unit.1 Sep 20111.23.0.0'makenii.m' is now able to automatically detect both single and double complex data type.10 Jun 20111.22.0.0Fixed a bug for yesterday's release9 Jun 20111.21.0.0You can now create RGB NIfTI / ANALYZE file structure using makenii / makeana program.2 May 20111.20.0.0New program 'loaduntouchheaderonly.m' and 'saveuntouchslice.m' is provided. Check for more details.10 Mar 20111.19.0.0New feature is added in 'viewnii' program to let you edit voxel values or set landmarks.
Also thanks to the code from Roman, which speed up 'loaduntouchniiimg' program when the slices are not loaded at once.15 Feb 20111.16.0.01. Fixed an overlay problem in viewnii.m, so the color of min/max is now showing properly.2. Included an overlay example in and.3 Feb 20111.14.0.0Thanks to the feedback of Roman Fleysher from Yeshiva University, I fixed a bug when loading a quaternion form NIfTI data.19 Aug 20101.13.0.0Thanks to Rembrandt from Radboud University Nijmegen (Netherlands), I made 2 small changes to handle the exceptions.13 Apr 20101.12.0.0Fixed a bug in 'collapseniiscan' to collapse Analyze format data.6 Jan 20101.11.0.01. 'loaduntouchnii' now supports loading specific slices of NIfTI or Analyze format.2.