Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and pial)

On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote:

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Dear Freesurfer,

I have a batch of myelin water image (MWI) from patients and controls, and trying to have inflated cortex registered on standard surface for GLM (Qdec).

With the commandlines below i get my inflated surface of MWI map of my patients and controls.

1-using bbregister to put MWI into FS space and to calculate register.dat:
bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat --o mwf_FS --t1

2-using mri_vol2surf to extract inflated surface of MWI:
mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type paint --inflated (or --surf sphere)

However the tksurfer could not open the inflated surface and the error message is:
ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices!
Probably trying to use a scalar data file as a surface!

I used the commandline below for #2:
mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o mwf-lh.w --out_type paint
and i got the error:

ERROR: MRISread: file '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!

As tksurfer could not open my surfaces with errors above, i think perhaps the vol2surf procedure is not done properly. Where is the problem? i need to get the inflated cortex and then putting ob sphere (using mris_sphere) and the registering to standard surface using mris_register for GLM in Qdec, right?


It is two weeks i am struggling with these commands, any helps highly appreciated.


Best,
Reza