Hi Doug, Thanks. I was wondering if you think this would do the job: 1) use fmcpr.nii.gz 2) split it to 3d volumes 3) do mri_vol2vol for all the volumes separely 4) concatenate the resampled volumes together to get a 4d volume. If you don't think this is a good approach, I appreciate it if you could walk me through the steps.
Thanks in advance for your help Best regards, Ehsan On Tue, Mar 22, 2016 at 3:53 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > The problem is not the command, it is the size of the data it generates. > You can try reducing the size of the anatomical to a bounding box around > the brain. This is a bit tricky as you also have to compute a new > registration. I can help step you through the process if you want to go > in that direction. > > On 03/22/2016 11:50 AM, Ehsan Tadayon wrote: > > Hi Doug, > > > > Thanks for your response. What I'm trying to do is to get each voxel's > > times course in structural space and I was under the impression that > > mri_vol2vol --mov func.nii would be the right way to go. Would you > > please let me know what the best way would be to do this? > > > > best, > > Ehsan,. > > > > > > On Wed, Mar 16, 2016 at 11:27 PM, Douglas Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > that's going to create a pretty big volume as it will map your > > functional time course to a 256^3 float volume. If you have 100 > > time points, then that will be about 7G. > > > > On 3/16/16 3:27 PM, Ehsan Tadayon wrote: > >> Hi Bruce, > >> > >> Thanks for your response. I'm using : > >> > >> freesurfer version: > >> freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on OS X Yosemite > >> 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command that I'm using: > >> > >> mri_vol2vol --mov func.nii.gz --fstarg --reg register.dat --o > >> func.anat.nii.gz > >> > >> Thanks in advance for your help. > >> > >> best regards, > >> Ehsan. > >> > >> > >> > >> > >> On Tue, Mar 15, 2016 at 11:49 PM, Bruce Fischl > >> <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> > >> wrote: > >> > >> Hi Ehsan > >> > >> We need the full command line and screen output and also what > >> your hardware and software environments are to help you. > >> Certainly sounds like you ran out of memory though > >> > >> Cheers > >> Bruce > >> > >> > On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon > >> <ehsan.tadayo...@gmail.com > >> <mailto:ehsan.tadayo...@gmail.com>> wrote: > >> > > >> > Ehsan > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto: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. > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > 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. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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