I see , so volumes are also surface based. On Tue, 20 Feb 2018 at 23:16, Douglas N Greve <gr...@nmr.mgh.harvard.edu> 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: > > Hi , > > This is the output of long_mris_slopes! > > > > On Tue, 20 Feb 2018 at 23:10, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@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 > > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto: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> > > > <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> > > > <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/> > > > > > > > > > > > > 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. > > > > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@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> > > FileDrop: 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/ > > > > -- > > Best regards, > > Amirhossein Manzouri > > > > > > -- > 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/ > > -- Best regards, Amirhossein Manzouri
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