Back to PLS HelpPosted on 08/01/16 10:58:25
Number of posts: 6
Hello, I am trying to setup a block fMRI analysis and am having trouble loading nifti files into the gui under data files. The window gives an error "unable to open file" when I try to use the nifti file (tried both .nii and .nii.gz), but works fine when the files are converted into analyze format (.img). The user guide says that .nii files can be used in this software, is this just not the case? Thanks in advance!
Replies:
I'm Online
Posted on 08/01/16 11:15:17
Number of posts: 229
Hi..
it can't be a 4-D nifti.. use expand_nii.m to make individual files for each TR.
From the help (apologies for not repeating it for fMRI):
If a PET file is in NIfTI image and contains multiple-scans, it must be expanded to multiple single-scan files with MATLAB program expand_nii_scan.m that is included in PLS Applications.
nancy
Correction - I had an older version of load_nii.m on my matlab path - 4D files should work, but not *.nii.gz
Posted on 08/01/16 13:26:17
Number of posts: 6
Hi Nancy, thank you for the quick reply! I took your advice and ran the expand_nii_scan.m script, however the files are still not loading into the gui. I am getting the message: ERROR: cannot access the image file: denoised_func_data_nonaggr0001.nii.gz. I also tried using the fslsplit command to do the same thing as the script, and the same error message appeared.
On another note, I saw elsewhere on the message board that 4D nifti files are okay to use, just wanted to find out which explanation is correct. https://www.rotman-baycrest.on.ca/index.php?action=view_thread&id=1&module=bbmodule&src=%40random45c35fcb17881
Date:���10-31-06 09:53
Hi Agatha,
PLSgui is able to read 4D NIFTI files, and we are doing this routinely with fMRI data, so I am not sure what is happening. What is the error message you get from the GUI?
Randy
Thank you in advance!
Antoni
Posted on 08/02/16 07:31:41
Number of posts: 394
Hi Antoni,
would mind uploading one of your images to a place were we can download it (e.g. dropbox or googldrive). We can check whether we can load it into PLS. Once you have uploaded it please send me an email with the data location
rmcintosh@research.baycrest.org
thanks
Randy
Posted on 08/11/16 15:26:19
Number of posts: 6
Hi all, thank you for the help! I realized these files weren't working because I did not normalize to standard before inputing them into the gui..
Looks to be working now!
Antoni
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