I think there might still be something wrong with the mri/orig.mgz, try this command to see if it is ok
mri_convert mri/orig.mgz deleteme.mgz
doug
On 01/07/2014 09:01 AM, Bruce Fischl wrote:
hmmm, I'm not sure what is going on then. Make sure that your path in the mri_surf2vol command line is correct for the orig.mgz I guess. Other than that, maybe Doug can comment? On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
I am sorry i gave the wrong command: following is the result:
UN:~/CHR01> mri_info mri/orig.mgz Volume information for mri/orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 1670.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -0.3715 : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 18.5846 : x_s = -0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 6.4364 talairach xfm : mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 -0.0000 0.0000 127.6285 0.0000 -0.0000 1.0000 -109.4154 -0.0000 -1.0000 -0.0000 134.4364 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 127.6285 0.0000 0.0000 -1.0000 134.4364 0.0000 1.0000 0.0000 109.4154 0.0000 0.0000 0.0000 1.0000
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:43:27 -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
something is wrong with that file. Can you check permissions on it and size?
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
This is the output :
UN:~/CHR01/mri> mri_info mri/orig.mgz mghRead(mri/orig.mgz, -1): could not open file
What did I missed while processing?
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:38:36 -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
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
> > > > > > > > > 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. > > > > > > > > >