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 --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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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


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