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. > >