can you run
mri_info mri/orig.mgz On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
yes as you can see below: UN:~/CHR01/mri> ls aparc.a2009s+aseg.mgz orig aparc+aseg.mgz orig.mgz aseg.auto.mgz orig_nu.log aseg.auto_noCCseg.label_intensities.txt orig_nu.mgz aseg.auto_noCCseg.mgz rawavg.mgz aseg.mgz rh.ribbon.mgz brain.finalsurfs.mgz ribbon.mgz brainmask.auto.mgz segment.dat brainmask.mgz T1.mgz brain.mgz talairach.label_intensities.txt ctrl_pts.mgz talairach.log filled.mgz talairach_with_skull_2.log lh.ribbon.mgz talairach_with_skull.log mri_nu_correct.mni.log transforms mri_nu_correct.mni.log.bak wm.asegedit.mgz norm.mgz wm.mgz nu.mgz wmparc.mgz nu_noneck.mgz wm.seg.mgz UN:~/CHR01/mri>
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:34:20 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
does mri/orig.mgz exist? On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Now another error UN:~> mri_surf2vol --surfval surf/rh.thickness paint --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 Using identity matrix for registration mghRead(mri/orig.mgz, -1): could not open file mri_surf2vol ERROR: reading mri/orig.mgz header
Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel : +82-62-715-3266 Email : mniqureshi@gist.ac.kr URL : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to
Date: Tue, 7 Jan 2014 08:26:56 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
sorry, I wasn't clear. Try:
mri_surf2vol --surfval surf/rh.thickness paint --hemi rh --fillribbon
\
--template mri/orig.mgz --volregidentity {$subj} --outvol
{$subj}_rh.ribbon.nii
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Still the same error UN:~> mri_surf2vol --surfval surf/rh.thickness.paint --hemi rh
--fillribbon
--template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness.paint
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:20:43 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
try adding "paint" after "surf/rh.thickness". The -surfval switch
takes an
optional format parameter after the file name I think
cheers Bruce
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
> Hi Bruce, > I have tried to convert by using the following commands but
still
some
error
> occur. > > UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ > UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh
--fillribbon
> --template mri/orig.mgz --volregidentity {$subj} --outvol > {$subj}_rh.ribbon.nii > gdiagno = -1 > ERROR: cannot recognize the type of surf/rh.thickness > > Can you help me. > Thank you. > > Best Regards, > Muhammad Naveed Iqbal Qureshi > > > > Date: Tue, 7 Jan 2014 08:13:45 -0500 > > From: fischl@nmr.mgh.harvard.edu > > To: mniqureshi@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6 > > > > Hi Muhammad > > > > have you looked at the help? It's pretty extensive. If you
have
trouble
> > post again and Doug should be able to guide you > > > > cheers > > Bruce > > On Tue, 7 Jan 2014, Muhammad > > Naveed Iqbal Qureshi wrote: > > > > > Thank you Bruce, > > > > > > Please guide me how can I use mri_surf2vol command on
lh/rh.thickness
> files > > > to get the output as lh/rh.ribbon.nii for AFNI SUMA. > > > Thank you > > > > > > Best Regards, > > > Muhammad Naveed Iqbal Qureshi > > > > > > > From: freesurfer-request@nmr.mgh.harvard.edu > > > > Subject: Freesurfer Digest, Vol 119, Issue 6 > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > Date: Mon, 6 Jan 2014 10:51:33 -0500 > > > > > > > > Send Freesurfer mailing list submissions to > > > > freesurfer@nmr.mgh.harvard.edu > > > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > or, via email, send a message with subject or body 'help'
to
> > > > freesurfer-request@nmr.mgh.harvard.edu > > > > > > > > You can reach the person managing the list at > > > > freesurfer-owner@nmr.mgh.harvard.edu > > > > > > > > When replying, please edit your Subject line so it is more
specific
> > > > than "Re: Contents of Freesurfer digest..." > > > > > > > > > > > > Today's Topics: > > > > > > > > 1. erroneuos segmentation labeling of skull outside of
brain
> > > > (Yuliya Yoncheva) > > > > 2. Re: erroneuos segmentation labeling of skull outside of
brain
> > > > (Bruce Fischl) > > > > 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) > > > > 4. Re: erroneuos segmentation labeling of skull outside of
brain
> > > > (Yuliya Yoncheva) > > > > 5. Re: erroneuos segmentation labeling of skull outside of
brain
> > > > (Bruce Fischl) > > > > 6. Re: recon-all exited w/errors (Bruce Fischl) > > > > 7. ROI masks created in FreeSurfer used in FSL?? (Frank
Hsieh)
> > > > 8. converting .thickness files of T1 MRI from FreeSurfer
into
> > > > AFNI (Muhammad Naveed Iqbal Qureshi) > > > > 9. brain orientation in qdec (L. Schweren) > > > > 10. Re: converting .thickness files of T1 MRI from
FreeSurfer
> > > > into AFNI (Bruce Fischl) > > > > 11. recon-all error (Emad Ahmadi) > > > > 12. Fwd: Anatomical segmentation - question (Rotem Saar) > > > > > > > > > > > >
> > > > > > > > Message: 1 > > > > Date: Sun, 5 Jan 2014 15:14:39 -0500 > > > > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > Subject: [Freesurfer] erroneuos segmentation labeling of
skull
outside
> > > > of brain > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > Message-ID: > > > >
CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com
> > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > Dear FreeSurfer community, > > > > > > > > I am visually inspecting the quality of my recon -all
output
for a
> large > > > > dataset and have a rookie question. > > > > > > > > In some instances, when skull stripping ended up leaving
some
of
the
> > > skull, > > > > these voxels are associated with a "sgmtn label" (cerebral
cortex). In
> > > > other instances, although there are a small number of
skull
voxels
> that > > > > were not removed automatically, these voxels do not have
an
associated
> > > > "sgmnt label" available in TkMedit Tools. > > > > > > > > Is it the case that only the voxels for which there is a
segmentation
> > > label > > > > are actually added to the total grey volume estimate? > > > > > > > > Thus, voxels, which have not been automatically labelled
would
not
> impact > > > > volume computations? > > > > > > > > Thank you kindly for your help. > > > >