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
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Today's Topics:
- 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
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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.