I am trying to overlay my own ROIs onto the pial surface using mri_vol2surf.
this is my command line:
mri_vol2surf --src wrawKH_MAE3_4/Agap1_2_gap-nogap_p05u-05u --src_type analyze --srcreg wrawKH_MAE3_4/register.dat --fwhm 3 --hemi lh --surf pial --surfreg /cajal/public/programs/freesurfer/subjects/wrawKH_MAE3_4/surf/lh.pial --out wrawKH_MAE3_4/surf/lhpialoverlaytest --out_type paint --trgsubject wrawKH_MAE3_4
and this is my output:
INFO: output format is paint
srcvol = wrawKH_MAE3_4/Agap1_2_gap-nogap_p05u-05u
srctype = analyze
srcreg = wrawKH_MAE3_4/register.dat
srcregold = 0
srcwarp unspecified
surf = pial
hemi = lh
trgsubject = wrawKH_MAE3_4
surfreg = /cajal/public/programs/freesurfer/subjects/wrawKH_MAE3_4/surf/lh.pial
interp = nearest
float2int = round
INFO: float2int code = 0
INFO: reading as a two-file NIFTI
INFO: using NIfTI-1 sform
Done loading volume
INFO: smoothing volume at fwhm = 3 mm (std = 1.27398)
Reading surface /cajal/public/programs/freesurfer/subjects/subject-unknown/surf/lh.pial
MRISread(/cajal/public/programs/freesurfer/subjects/subject-unknown/surf/lh.pial): could not open file
No such file or directory
mri_vol2surf: could not read surface /cajal/public/programs/freesurfer/subjects/subject-unknown/surf/lh.pial
No such file or directory
the program seems to read the input images correctly, but can't read the surface images. I don't know what is up with the 'subject-unknown.' I specified the subject and it still doesn't know the path. I am kind of at a loss.
Adam
adam
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