The NIFTI MATLAB library is also able to read in the volume based resting state files:
http://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image Thanks. Bryan. On 20 Mar 2014 08:12, "Harms, Michael" <[email protected]> wrote: > > > 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 > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > 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 > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > ________________________________ > > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > ________________________________ > > The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
