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

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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 manzouri wrote:
> 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
> UseMaskWithSmoothing     1
> OneSampleGroupMean 1
> y
>
/storage/affective/ume2/confined/Amir/FS/lh.testretest.volume-spc-10.stack.mgh
> logyflag 0
> usedti  0
> mask fsaverage/mri/Lhipp.mgh
> maskinv 0
> glmdir lh.testretest.volume-rate.fwhm10_LHipp
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory lh.testretest.volume-rate.fwhm10_LHipp
> Loading y from
>
/storage/affective/ume2/confined/Amir/FS/lh.testretest.volume-spc-10.stack.mgh
>   ... done reading.
> Saving design matrix to
lh.testretest.volume-rate.fwhm10_LHipp/Xg.dat
> Computing normalized matrix
> Normalized matrix condition is 1
> Matrix condition is 1
> ERROR: dimension mismatch 1 between y and mask
>
> Best regards,
> Amirhossein Manzouri
>
>
>
> On Thu, Feb 15, 2018 at 7:49 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
>
>     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
>         volume_rate_stack but I get "dimensions mismatch 1 between y
>         and mask" error .
>         I wonder:
>         1) How can I run analysis in subcortical volumes?
>         2) Is it possible to run mri_glmfit on the whole brain
not lh
>         and rh separately ?
>
>         Best regards,
>         Amirhossein Manzouri
>
>
>
>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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-- Best regards, Amirhossein Manzouri