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 --------------------------------------------------------------------- $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 ------------------------------------------------------------------------------------------------------ Guoying
What is in lh.volume.average.fwhm10.mgh? It is named as if it is a file with surface data in it.
On 02/11/2014 11:04 AM, Wang, Guoying wrote:
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
$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
Guoying
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Douglas N Greve -
Wang, Guoying