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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>     >
>     >
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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
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> --
> Best regards,
> Amirhossein Manzouri
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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