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
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:
- How can I run analysis in subcortical volumes?
- Is it possible to run mri_glmfit on the whole brain not lh and rh
separately ?
Best regards, 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 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 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:
- How can I run analysis in subcortical volumes?
- 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 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/
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 . 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.
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> 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> 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/> 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.
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 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> 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> 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/> 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 greve@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
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>> > 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 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> 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
I see , so volumes are also surface based.
On Tue, 20 Feb 2018 at 23:16, Douglas N Greve greve@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 <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 --maskfsaverage/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 betweeny
> 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> 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 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> 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 greve@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
freesurfer@nmr.mgh.harvard.edu
-
amirhossein manzouri -
Douglas N Greve