Dear freesurfer experts,

          I am trying to compute the differences in subcortical volumes between two groups. I have read previous mail, https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17597.html , and  in this mail, your answer was ‘you can do a subcortical volume analysis by working with the aseg.stats file directly  or compute with mri_glmfit’. So, I tried to use ‘mri_glmfit’ to calculate it . but without specifying  the argument ‘—surf’ (because it is mentioned in your webpage that ‘if –surf is not specified, then mri_glmfit will assume that the data are volume-based and use the geometry as specified in the header to make spatial calculations’).  However, when I ran the command, it gave me the error message which said :’ you must use—surface subject hemi’ with surface data’. Do I  misunderstanding some point?

          On the other hand,  if there is statistical differences in subcortical volumes. How to display them in freesurfer?  Sorry, I am a beginner.  I know someone asked this question before, but I am still not fully understand it .

Thank you for your  help and reply  in advance !

Please find the command and error message attached

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$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $

cwd /gdata1/freesurfer_data/subjects/gy_stat/time1_average_cross/aseg_test

cmdline mri_glmfit --y lh.volume.average.fwhm10.mgh --fsgd y_fsgd.txt doss --C lh-volume-age-gender-ICV-cor.mtx --glmdir lh.seg_volume_sexageicv.glmdir

sysname  Linux

FixVertexAreaFlag = 1

UseMaskWithSmoothing     1

OneSampleGroupMean 0

y    /gdata1/freesurfer_data/subjects/gy_stat/time1_average_cross/aseg_test/lh.volume.average.fwhm10.mgh

logyflag 0

usedti  0

FSGD y_fsgd.txt

glmdir lh.seg_volume_sexageicv.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Loading y from/………/  lh.volume.average.fwhm10.mgh

ERROR: you must use ‘—surface subject hemi’with surface data

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Guoying