External Email - Use Caution Hi Doug,
I ran mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C groupdiff.mtx \--glmdir aseg.glmdir this created a folder aseg.glmdir which contains another folder groupdiff, where sig.ghm is, I then tried to visualise results using freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5 -viewport 3d Many thanks in advance! Francisca On Tue, Jun 1, 2021 at 1:40 AM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > How did you create the sig.mgh that you are trying to overlay? > > On 5/28/2021 11:16 AM, Francisca Ferreira wrote: > > External Email - Use Caution > Dear Experts, > > I have extracted subcortical vols corrected for intracranial vols using > asegstats2table and I ran mri_glmfit using the following command > > mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C > groupdiff.mtx \--glmdir aseg.glmdir > > this seems to have worked. > I am now trying to visualise my results adapting the recommended wiki > command > > freeview -f > /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5 > -viewport 3d > > Freeview crashes and I'm getting the following error > > Number of vertices in overlay data (64 or 64) does not match with surface > (163842). > Number of vertices in overlay data (64 or 64) does not match with surface > (163842). > > Is there something wrong with the commands priot to this step? > > > > > > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1dYHFn7zS6B646bWS9lFLOInJlhX5O-D2krlFdkSw8d8E87WUGXoPX-5ZIjvu5BZgJGqV4WcKBC8HZ5ngAJCv5uwvhDEhDjesPMvsPecL4LixYYDUXswY3Mk_4ZVP8VjlzSUERHT6fBiwa2YCF359vMYgXHvhrUMDOkb7f0keLG7BP6EGKV2lh7rk_OgigOKCd8jF0dvfM2btGPhw8_jWl7oNkLp9eHIYq--EonKLebQull7L8D_DuHSTmL-RI6I09hqvXMCPvzhYxdzPCGHdHg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://secure-web.cisco.com/1dz6MBaZ4CWlcN057t5KUwTLiDxU7Gt4GlmynrD0X76B3ja_x_8lvda9ONecmoOo9l-H8ED-qe4-YpazYh8RrGkprEjor9AwgaXrL5xKS6cX1580zuuYucQcGCRgIUnmJZZCuE1OJ0vecTWAuWdLmJ71AUd9271Y1x8BiROUHvP9gkqmZwOzPn8zZW-MGIlZAfjFTVb556fGMu8qNrPBVJmVjp-R6s-6akYYuUXn_Dou4pstNV9bM4MmirQXcc8eLgVEzjZieBZ_zj68cG4bcaA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. >
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