Hi Bruce,
Thank you for the reply! I have now tried: mri_vol2vol --mov mri_data.mgh --reg register.dat --o mri_data-tal.mgh --tal --talres 2 mri_vol2vol --mov ribbon.mgz --reg register.dat --o ribbon-tal.mgh --tal --talres 2 mri_convert -rl mri_data-tal.mgh ribbon-tal.mgz mask.mgz mri_mask mri_data-tal.mgh mask.mgz masked_fmri.mgz mri_convert masked_fmri.mgz masked_fmri.nii I got: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from masked_fmri.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to masked_fmri.nii... However, when I opened the masked_fmri.nii in fslview, the masked_fmri seems to be empty (intensity is zero and no brain is shown). I would need to get a matrix containing voxels in the grey matter at all time points. Could you please let me know what I am doing wrong above? Or is there some better way to do this? I am new with Freesurfer, so sorry if my questions are trivial. Best, Maria 2017-04-10 17:28 GMT+03:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Maria > > are they in register? If so you can do: > > mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz > mri_mask fmri_data.mgh mask.mgz masked_fmri.mgz > > cheers > Bruce > > > > On Mon, 10 Apr 2017, Maria Hakonen wrote: > > Dear Freesurfer experts, >> I have tried to mask fMRI data with grey matter mask as follows: >> mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz >> >> However, I am getting an error " dimension mismatch between source and >> mask". >> >> Could someone please let me know how to solve this problem? >> >> Best, >> Maria >> >> > _______________________________________________ > 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. > >
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