Ah, I see! thank you-- Regards
--VM On Thu, Dec 22, 2016 at 11:42 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > It may change with the data set. Eg, in fMRI, the top of the head my be > cut off in one subject and so the top of the head will be out of the > mask. Also, there my be some differences in the definition of the medial > wall across subjects. This does not change with contrast. > > > On 12/22/2016 02:40 PM, neuroimage analyst wrote: > > Thanks, Doug for that quick response! > > > > Does mask.mgh varies between different set of subjects and (or) > > different set of contrasts for a given hemisphere? Since fsavearge > > doesnt change, the mask that is used for statistical comparisons > > should change neither unless I change --trgsubject to some other. Am i > > right? > > > > thanks > > > > regards > > > > VM > > > > On Thu, Dec 22, 2016 at 11:32 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > > > On 12/22/2016 01:33 PM, neuroimage analyst wrote: > > > Hi, > > > > > > I am just curious whether the mask.mgh file returned in glmdir > > folder > > > created from lh.cortex.label? > > In part. It will also include any voxels that have 0 values in any of > > the inputs (--y) > > > > > > If so, how can I create my own surface mask from the label file? > > > (mri_label2vol and mri_vol2surf ?) > > mri_label2label with the --mask option > > > > > > > > > Second: How can I compare the subcortical volumes between the 2 > > groups > > > using glm tools in freesurfer? Specifically, how do I call > > > mris_preproc and mri_glmfit? > > Run asegstats2table to create a table, then run mri_glmfit as > > before but > > with --table instead of --y > > > > > > I appreciate your response. > > > > > > Thank you > > > > > > Regards > > > > > > --VM > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > 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 Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline > > <http://www.partners.org/complianceline> . 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. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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