[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

.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_

[Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

Dear Freesurfer experts, Could someone please let me know what is the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks of mri_covert? >From the internet and by typing mri_convert on the command line I only managed to find the following information: -iis, --in_i_size -ijs, --in_j_s

Re: [Freesurfer] mri_convert: the meaning of the arguments -iid, -ijd, -ikd, -iis, -ijs, and -iks?

Many thanks for the answer! Best, Maria 2017-04-25 21:05 GMT+03:00 Douglas Greve : > -i{ijk}s will change the voxel size of the columns, rows, and slices, > respectively > > -i{ijk}d will change the direction cosines of the cols, rows, slices > > > > On 4/25/17 11:47

[Freesurfer] Extract time courses corresponding to a brain structure from an stc file

Dear Freesurfer experts, I would like to extract time courses of certain brain structures from the stc file in Matlab. Could someone please let me know how I can determine the lables of 10242 verices of my stc file? Or is there some matlab function that gives the time course of a barin structure.

[Freesurfer] register.dat file between fMRI runs?

Dear Freesurfer experts, I have used fslregister to register fMRI data to anatomical data. However, now I would like to register all fMRI runs to the fMRI run that I have registered to the anatomical data. Could someone please let me know how to get a register.dat file between fMRI runs? Many th

[Freesurfer] How to register fMRI data without upsampling voxel size?

External Email - Use Caution Dear Freesurfer experts, Could you please let me know how to normalize fMRI data without upsampling the original voxel size from 5 x 5 x 7 mm to 2 x 2 x 2 mm? I have tried this as follows: 1. Register functional (data.nii) to anatomical matrix

[Freesurfer] Is the slice delay of each slice needed for slice time correction with preprocess-sess?

External Email - Use Caution Dear all, Have I understood correctly that the slice delay of each slice is not needed when performing slice time correction with preprocess-sess? I am processing an open OASIS fMRI dataset. The dataset has fMRI data in nifti format and JSON files tha