Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit

2018-02-20 Thread amirhossein manzouri
I see , so volumes are also surface based. On Tue, 20 Feb 2018 at 23:16, Douglas N Greve wrote: > so this is thickness data? Hippocampus is a volume-based structure and > so not represented on the surface > > > On 02/20/2018 05:13 PM, amirhossein manzouri wrote: > >

Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit

2018-02-20 Thread Douglas N Greve
so this is thickness data? Hippocampus is a volume-based structure and so not represented on the surface On 02/20/2018 05:13 PM, amirhossein manzouri wrote: > Hi , > This is the output of long_mris_slopes! > > On Tue, 20 Feb 2018 at 23:10, Douglas N Greve >

Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit

2018-02-20 Thread amirhossein manzouri
Hi , This is the output of long_mris_slopes! On Tue, 20 Feb 2018 at 23:10, Douglas N Greve wrote: > where did lh.testretest.volume-spc-10.stack.mgh? If this is an fsfast > output, then use the aseg.mgz in fsaverage/mri.2mm > > > > On 02/16/2018 05:24 AM, amirhossein

Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit

2018-02-20 Thread Douglas N Greve
where did lh.testretest.volume-spc-10.stack.mgh? If this is an fsfast output, then use the aseg.mgz in fsaverage/mri.2mm On 02/16/2018 05:24 AM, amirhossein manzouri wrote: > Hi, > To make the mask: > mri_binarize --i aseg.mgz --match 17 --o Lhipp.mgh > > Run glmfit: > > cmdline mri_glmfit.bin

Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit

2018-02-16 Thread amirhossein manzouri
Hi, To make the mask: mri_binarize --i aseg.mgz --match 17 --o Lhipp.mgh Run glmfit: cmdline mri_glmfit.bin --osgm --glmdir lh.testretest.volume-rate.fwhm10_LHipp --y lh.testretest.volume-spc-10.stack.mgh --mask fsaverage/mri/Lhipp.mgh --surf fsaverage lh sysname Linux FixVertexAreaFlag = 1

Re: [Freesurfer] Using masks from aseg.mgz with mri_glmfit

2018-02-15 Thread Douglas N Greve
Can you send your glmfit command line and terminal output? On 02/15/2018 07:21 AM, amirhossein manzouri wrote: > Hi , > I did longitudinal analysis and now I made masks for Hippocampus and > amygdala masks from fsavergae/mri/aseg.mgz using mri_binarize .I use > the masks with mri_glmfit for

[Freesurfer] Using masks from aseg.mgz with mri_glmfit

2018-02-15 Thread amirhossein manzouri
Hi , I did longitudinal analysis and now I made masks for Hippocampus and amygdala masks from fsavergae/mri/aseg.mgz using mri_binarize .I use the masks with mri_glmfit for volume_rate_stack but I get "dimensions mismatch 1 between y and mask" error . I wonder: 1) How can I run analysis in