Hi Ben, There should be a procsurffast flag called -volproj_lowmem which avoids this mri_vol2vol memory issue. -Louis
On Wed, 21 May 2014, Douglas N Greve wrote: > > mri_vol2vol when used in this way does not manage memory very well. It > resamples the time series into a 256^3 volume of floats. Even for a > small number of time points, this becomes unmanagebly huge > > > > > On 05/21/2014 06:06 PM, Ben Mooneyham wrote: >> Hello all, >> >> I am doing pre-processing for resting-state fMRI volumes, but I have >> encountered an error and am unsure of how to correct it: >> >> I have previously determined the nonlinear warping transformations >> from my subjects' anatomical (T1) space to the 2mm MNI template using >> ANTs. At the end of my pre-processing pipeline, I am trying to >> transform my subjects' functional volumes (206 TRs of 2sec) into this >> MNI space by 1) transforming the functional volumes into subject T1 >> space using mri_vol2vol, and 2) applying the nonlinear warp (from >> ANTs) to the volumes in subject-T1 space to ultimately have my >> subjects' functional data in MNI space. >> >> However, I am getting an error while running mri_vol2vol, where it >> "cannot allocate region." I gather from looking around online that >> this is a memory issue, but I am not sure how to fix it. Thoughts? It >> is crucial that I be able to translate my functional data into common >> MNI space before performing second-level analyses... >> >> I do not encounter this issue when performing this transformation on >> functional connectivity maps (where I take an ROI defined in MNI >> space, transform it into T1, and then subject-EPI space, calculate the >> FC with the rest of the brain, and then invert the process by >> transforming back into T1, and finally MNI space). How can I get this >> to work with a larger file? >> >> Thank you in advance for your help, >> >> Ben Mooneyham >> >> -- >> Graduate Student >> UCSB - Department of Psychological & Brain Sciences >> Building 429 Room 102 >> (210) 912-6076 >> bwmooney...@gmail.com <mailto:bwmooney...@gmail.com> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
