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Just to add to the archives of this thread, I was able to load the rfMRI_REST1_RL.nii of 100307 using SPM's functions of 'spm_select', 'spm_vol', and 'spm_read_vols', but only using SPM12. It did not work with SPM8. (Both were tested using Matlab 2012b).
As an aside, it may be challenging to work with many REST files in that fashion in matlab, because once loaded as double precision, each 4D volumetric time series is over 8 GB.
cheers,
-MH
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Michael Harms, Ph.D.
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Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: [email protected]
From: <Glasser>, Matt Glasser <[email protected]>
Date: Sunday, March 2, 2014 11:49 AM To: L Deng <[email protected]>, "[email protected]" <[email protected]> Subject: Re: [HCP-Users] a problem in opening multi-volume .nii file The files are fine in FSL and Connectome Workbench, so I'm not sure what the problem is. If you need to read the NIFTIs into matlab you could use FSL's read_avw.m for this.
Peace,
Matt.
From: L Deng <[email protected]>
Reply-To: L Deng <[email protected]> Date: Saturday, March 1, 2014 7:28 AM To: "[email protected]" <[email protected]> Subject: [HCP-Users] a problem in opening multi-volume .nii file
Hello. I have problem in opening the multi-volume nii file. I downloaded the pre-processed resting state fMRI data (10 unrelated subjects), checked the integrity of the files, and unzipped them according the instruction in the Q3_Release_Reference _Manual.
However, the problem is, when I tried to load the rfMRI_REST1_LR(or RL).nii into MATLAB workspace using the function 'spm_read_vols' in SPM8, it always failed. And I found that MATLAB can actually access the first 10 volumes of the .nii file, but failed to
read the rest of it. This problem appeared in ALL of the 10 unrelated subjects' rfMRI_REST1_preproc data.
I believe that this problem is caused by the .nii file itself for the additional reasons below:
1) I tried to convert the 4D nii into 1200 3D niis by using the 'dcm2nii' tool in the MRICRON package, and it can only convert the first 10 volumes,
2) I viewed the LAST 10 volumes of the nii file using MRICRON, and very interestingly, the brain was misplaced in the last 10 volumes,
3) this problem appeared in different platforms(windows, linux, 32-bit, and 64-bit).
All files are unlikely to be corrupted during the downloading process, because I have checked the hash of the files. So, I am quite puzzled with this problem. Please offer some advise.
Thank you for your time!
Lifu
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- [HCP-Users] a problem in opening multi-volume .nii file L Deng
- Re: [HCP-Users] a problem in opening multi-volume .n... Glasser, Matthew
- Re: [HCP-Users] a problem in opening multi-volum... Harms, Michael
- Re: [HCP-Users] a problem in opening multi-v... Bryan Paton
