Re: [Freesurfer] dimension mismatch between source and mask

You should only need those first two commands (+ the mri_mask). Use --interp nearest with the ribbon On 04/10/2017 12:27 PM, Maria Hakonen wrote: > > 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 -

Re: [Freesurfer] dimension mismatch between source and mask

Probably you'll want to use mri_vol2vol so that you can incorporate your registration between the fMRI and the anatomical On 04/10/2017 10:28 AM, Bruce Fischl wrote: > 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.

Re: [Freesurfer] dimension mismatch between source and mask

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 m

Re: [Freesurfer] dimension mismatch between source and mask

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 follo

[Freesurfer] dimension mismatch between source and mask

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 _

Re: [Freesurfer] Dimension mismatch between source and mask

Hi Isabelle when you say you reanalyzed it from scratch, did you actually delete the subject dir and start over or just rerun autorecon1? If the latter, that won't reanalyze from scratch but will keep existing edits and such. Did you do anything out of the ordinary the first time you ran it? T

[Freesurfer] Dimension mismatch between source and mask

Dear FreeSurfer experts, After running the following command: recon-all -autorecon2 -autorecon3 -subjid S08_FS I get the following error: /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n threshold mask volume at 5 E