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 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. > > > > > -------------- next part -------------- > > > > > An HTML attachment was scrubbed... > >>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 05/3 > > > > 92deba7/attachment-0001.html > > > > > -------------- next part -------------- > > > > > A non-text attachment was scrubbed... > > > > > Name: ExCerCor.png > > > > > Type: image/png > > > > > Size: 81100 bytes > > > > > Desc: not available > > >>>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
0
1
05/ > > 3 > > > > 92deba7/attachment-0001.png > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 2 > > > > > Date: Sun, 5 Jan 2014 15:40:24 -0500 (EST) > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] erroneuos segmentation labeling
of
skull
> > > > > outside of brain > > > > > To: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > Cc: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: alpine.LRH.2.03.1401051539450.16518@nmr.mgh.harvard.edu > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > Hi Yuliya > > > > > > > > > > they are included if they are inside of the ?h.pial
surface.
We
don't > > use > > > > > the cortex aseg label as it is in general less accurate
than
the
> > surfaces. > > > > > > > > > > cheers > > > > > Bruce > > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 3 > > > > > Date: Sun, 5 Jan 2014 15:55:13 -0500 (EST) > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] Motion correction for SPACE
FLAIR
> > > > > To: Octavian Lie octavian.lie@gmail.com > > > > > Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: alpine.LRH.2.03.1401051554470.16518@nmr.mgh.harvard.edu > > > > > Content-Type: text/plain; charset="windows-1252" > > > > > > > > > > Hi Octavian > > > > > > > > > > it's not so easy to reduce the bandwidth in the T2-space sequences, > > but > > > > > certainly you can try. Geometry-matched just means that
the
FOV
and > > > > > matrix sizes are the same. > > > > > > > > > > cheers > > > > > Bruce > > > > > On Fri, 3 Jan 2014, Octavian Lie wrote: > > > > > > > > > > > Dear Bruce, > > > > > > > > > > > > Best wishes for 2014! > > > > > > > > > > > > I will heed your advice and cc to the list. Indeed, the
MGH
protocol > > I > > > > > > obtained from Andre has one acquisition (NSA). > > > > > > Related, I cc this post: > > > > > > > > > > > > We have been trying adaptations of the T2spaceFLAIR MGH
protocol
on > > > > > > our Phillips 3T scanners (sequences called VISTA).
Incorporation
of > > > > > > the T2 space FLAIR has been mostly successful at editing
out
the
> > dura > > > > > > from the pial surface. The only concern are minute
differences
> > > > > > occasionally appearing as small indentations (at most
times
<1-2mm) > > > > > > between the woFLAIR.pial and the final pial surfaces,
including
in > > > > > > intrasulcal (duraless) areas; the amount of these small mismatches > > is > > > > > > variable from patient to patients, with some trials with
almost
> > > > > > perfect overlap, and others with visible, if small,
differences.
I > > > > > > wonder if this has been your experience too, and if this
is
due
> > mostly > > > > > > to bb registration limits or to differences in pixel
bandwidth
> > between > > > > > > mprage and space flair sequences (in our case, see
below).
> > > > > > In FSwiki, the recommendation is that T2 space flair
?should
be
> > > > > > bandwidth, geometry and readout matched to the mprage?. > > > > > > > > > > > > 1. Speaking about pixel bandwidth, logistics most likely
would
not > > > > > > allow application of a MEMPR sequence on our Phillips.
According
to > > > > > > Siemens MPRAGE MGH specs, "exceptions indicate that if a multiple > > echo > > > > > > sequence is not available, one should choose a bandwidth
of
195
> > > > > > Hz/pixel for the MPRAGE". In that case/ using the
Siemens
Trio
> > MPRAGE > > > > > > protocol as if the MEMPR is not available, how one would
adjust
the > > > > > > bandwidth in T2spaceFLAIR protocol (currently ~650 in
the
Siemens > > > > > > space flair and MEMPR protocols) to "match" it to the
"simple"
> > MPRAGE > > > > > > protocol (decreasing it to 195 ?). Would it be a
workaround?
(Please > > > > > > comment on the Siemens case, obviously, I do not expect
any
light on > > > > > > Phillips without further testing). > > > > > > 2. Could you clarify what geometry matched means? > > > > > > Please advise, > > > > > > > > > > > > Thank you, > > > > > > > > > > > > Octavian > > > > > > > > > > > > On Fri, Jan 3, 2014 at 9:12 PM, Bruce Fischl > > > > fischl@nmr.mgh.harvard.edu wrote: > > > > > >> Hi Octavian > > > > > >> > > > > > >> can you cc the list so that others can answer? What is
NSA?
We
> > don't > > > > have a > > > > > >> ton of experience with it, but 1 has seemed ok (not
sure if
we've > > ever > > > > tried > > > > > >> two) > > > > > >> Bruce > > > > > >> > > > > > >> > > > > > >> > > > > > >> On Thu, 2 Jan 2014, Octavian Lie wrote: > > > > > >> > > > > > >>> Dear Bruce, > > > > > >>> > > > > > >>> Thank you. We used one vs 2 NSA T2 space FLAIR
sequences,
without > > a > > > > > >>> consistent difference in results, with the 2-NSA run
obviously
> > > > doubling > > > > > >>> the > > > > > >>> scan time. Is there a preferred number of NSA you
recommend,
or we > > > > should > > > > > >>> be > > > > > >>> fine with one? Both are at resolution 1X1X1 mm. > > > > > >>> Thank you, > > > > > >>> > > > > > >>> Octavian > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> On Thu, Jan 2, 2014 at 11:56 AM, Bruce Fischl > > > > fischl@nmr.mgh.harvard.edu > > > > > >>> wrote: > > > > > >>> Hi Octaviaan > > > > > >>> no, not really. You should motion correct and average
them
using > > > > > >>> something like mri_motion_correct* > > > > > >>> > > > > > >>> We do typically bandwidth/readout match them to the
memprages
so > > > > > >>> that there is no differential distortion > > > > > >>> > > > > > >>> cheers > > > > > >>> Bruce > > > > > >>> > > > > > >>> > > > > > >>> On Wed, 1 Jan 2014, Octavian Lie wrote: > > > > > >>> > > > > > >>> Dear All, > > > > > >>> > > > > > >>> We recently implemented pial correction using T2 > > > > > >>> space FLAIR with freesurfer > > > > > >>> v 5.3, mostly successfully. We use 2-3 MPRAGE > > > > > >>> (sagittal + axial and/or > > > > > >>> coronal) volumes as 001.mgz, 002/003.mgz for the > > > > > >>> motion correction step in > > > > > >>> recon-all pipeline. > > > > > >>> The typical times for acquiring space FLAIR in our > > > > > >>> settings vary from 2.5 to > > > > > >>> 6 min, depending on the resolution/NSA no. I was > > > > > >>> wondering how freesurfer > > > > > >>> deals with motion artifacts in the space FLAIR > > > > > >>> sequence (especially with > > > > > >>> longer acquisition times), and if there is a > > > > > >>> strategy to minimize motion > > > > > >>> distortion with these (such as getting second runs > > > > > >>> for averaging, etc). > > > > > >>> Please advise, > > > > > >>> > > > > > >>> Octavian. > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> 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. > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 4 > > > > > Date: Sun, 5 Jan 2014 19:25:53 -0500 > > > > > From: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > Subject: Re: [Freesurfer] erroneuos segmentation labeling
of
skull
> > > > > outside of brain > > > > > To: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > Cc: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: > > > > > CAGE5uFcchoLxBvaf5Lze9z9_QPU4NGa83WFwZ90auZX3-idsFg@mail.gmail.com > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > Hello Bruce, > > > > > > > > > > thank you very much for your fast response and clarifying
that
> > potential > > > > > voxels outside the pial surface do not impact cortical
measures.
> > > > > > > > > > Best, > > > > > Yuliya > > > > > > > > > > > > > > > > > > > > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl > > > > fischl@nmr.mgh.harvard.eduwrote: > > > > > > > > > > > Hi Yuliya > > > > > > > > > > > > they are included if they are inside of the ?h.pial
surface.
We
> > don't > > > > use > > > > > > the cortex aseg label as it is in general less accurate
than
the
> > > > surfaces. > > > > > > > > > > > > cheers > > > > > > Bruce > > > > > > > > > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > > > > > > > > > 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. > > > > > >> > > > > > >> > > > > > >> > > > > > > > > > > > > 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. > > > > > > > > > > > -------------- next part -------------- > > > > > An HTML attachment was scrubbed... > >>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 05/e > > > > c136ff2/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 5 > > > > > Date: Sun, 5 Jan 2014 20:29:06 -0500 (EST) > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] erroneuos segmentation labeling
of
skull
> > > > > outside of brain > > > > > To: Yuliya Yoncheva yuliya.yoncheva@gmail.com > > > > > Cc: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: alpine.LRH.2.03.1401052028520.16518@nmr.mgh.harvard.edu > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > exactly, or measures derived them them like whole-brain
volume
> > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > On Sun, 5 Jan 2014, Yuliya > > > > > Yoncheva wrote: > > > > > > > > > > > Hello Bruce, > > > > > > thank you very much for your fast response and
clarifying
that
> > potential > > > > > > voxels outside the pial surface do not impact cortical
measures.
> > > > > > > > > > > > Best,? > > > > > > Yuliya > > > > > > > > > > > > > > > > > > > > > > > > On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl > > > > fischl@nmr.mgh.harvard.edu > > > > > > wrote: > > > > > > Hi Yuliya > > > > > > > > > > > > they are included if they are inside of the ?h.pial
surface.
We
> > > > > > don't use the cortex aseg label as it is in general less > > > > > > accurate than the surfaces. > > > > > > > > > > > > cheers > > > > > > Bruce > > > > > > On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 6 > > > > > Date: Sun, 5 Jan 2014 20:50:51 -0500 (EST) > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] recon-all exited w/errors > > > > > To: "Boric, Katica A." KBORIC@mgh.harvard.edu > > > > > Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: alpine.LRH.2.03.1401052049480.16518@nmr.mgh.harvard.edu > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > Hi Katica > > > > > > > > > > what format was the input image to recon-all? Can you
verify
that
> > tkmedit > > > > > has the directions correct (that is what it labels as
anterior
is
> > actually > > > > > anatomically anterior, etc...). If so, then the talairach
just
failed > > and > > > > > you will need to either try an alternative (like the MNI
or
SPM
> > > > talairachs) > > > > > or generate it manually. > > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > > > > > > > > > > > On Thu, 2 Jan 2014, Boric, Katica A. > > > > > wrote: > > > > > > > > > > > Happy New Year freesuerfers! > > > > > > I run into this error while doing?recon-all : > > > > > > > > > > > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > > > > > > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > > > > > Manual Talairach alignment may be necessary, or > > > > > > include the -notal-check flag to skip this test, > > > > > > making sure the -notal-check flag follows -all > > > > > > or -autorecon1 in the command string. > > > > > > > > > > > > I would really appreciate if someone could give me some
advice
on > > how to > > > > fix > > > > > > this error. > > > > > > > > > > > > Thank you very much! > > > > > > > > > > > > Katica Boric, > > > > > > > > > > > > > > > > > > ps:?Here is the error log: > > > > > > > > > > > > #@# Talairach Failure Detection Thu Jan ?2 14:20:32 EST
2014
> > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > > > > > ?talairach_afd -T 0.005 -xfm transforms/talairach.xfm? > > > > > > > > > > > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > > > > > > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > > > > > INFO: Attempting MINC mritotal to perform Talairach
align
> > > > > > #-------------------------------------------- > > > > > > #@# Talairach Thu Jan ?2 14:20:33 EST 2014 > > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > > > > > ?mri_nu_correct.mni --n 1 --proto-iters 1000 --distance
50
> > --no-rescale > > > > --i > > > > > > orig.mgz --o orig_nu.mgz? > > > > > > > > > > > > > > > > > > ?talairach --i orig_nu.mgz --xfm
transforms/talairach.auto.xfm?
> > > > > > > > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > /usr/local/freesurfer/bin/talairach > > > > > > --i orig_nu.mgz --xfm transforms/talairach.auto.xfm > > > > > > $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ > > > > > > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP
Tue
Jan
8 > > > > 20:57:42 > > > > > > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > > > Thu Jan ?2 14:21:30 EST 2014 > > > > > > tmpdir is transforms/tmp.talairach.34005 > > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > mri_convert orig_nu.mgz
transforms/tmp.talairach.34005/src.mnc
> > > > > > mri_convert orig_nu.mgz
transforms/tmp.talairach.34005/src.mnc?
> > > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter
Exp $
> > > > > > reading from orig_nu.mgz... > > > > > > TR=8.23, TE=3.22, TI=450.00, flip angle=12.00 > > > > > > i_ras = (-1, -9.03383e-08, 0) > > > > > > j_ras = (-1.3411e-07, 2.66591e-08, -1) > > > > > > k_ras = (1.59256e-07, 1, -5.93718e-09) > > > > > > writing to transforms/tmp.talairach.34005/src.mnc... > > > > > > -------------------------------------------- > > > > > > mritotal -verbose -debug -clobber -modeldir > > > > > > /usr/local/freesurfer/mni/bin/../share/mni_autoreg
-protocol
icbm > > > > > > transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm > > > > > > Legacy library shellwords.pl will be removed from the
Perl
core
> > > > distribution > > > > > > in the next major release. Please install it from the
CPAN
> > distribution > > > > > > Perl4::CoreLibs. It is being used at > > > > /usr/local/freesurfer/mni/bin/mritotal, > > > > > > line 460. > > > > > > ? > > > > > > ? > > > > > > Thu Jan ?2 14:21:43 EST 2014 > > > > > > talairach done > > > > > > > > > > > > ?cp transforms/talairach.auto.xfm
transforms/talairach.xfm?
> > > > > > > > > > > > #-------------------------------------------- > > > > > > #@# Talairach Failure Detection Thu Jan ?2 14:21:44 EST
2014
> > > > > > /home/XX/XXX/subjects/XXX_SurferOutput/mri > > > > > > > > > > > > ?talairach_afd -T 0.005 -xfm transforms/talairach.xfm? > > > > > > > > > > > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > > > > > > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > > > > > > Manual Talairach alignment may be necessary, or > > > > > > include the -notal-check flag to skip this test, > > > > > > making sure the -notal-check flag follows -all > > > > > > or -autorecon1 in the command string. > > > > > > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > > > > > Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP
Tue
Jan
8 > > > > 20:57:42 > > > > > > UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > > > > > > > > > recon-all -s xxx_SurferOutput exited with ERRORS at Thu
Jan
?2
> > 14:21:45 > > > > EST > > > > > > 2014 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 7 > > > > > Date: Sun, 5 Jan 2014 23:35:55 -0800 > > > > > From: Frank Hsieh two.frank@gmail.com > > > > > Subject: [Freesurfer] ROI masks created in FreeSurfer used
in
FSL?? > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: > > > > > CABBeRCEt37ZwE1-jHuZGC3Vw-D_v2+svOAnQUcSP6kW37qT4oQ@mail.gmail.com > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > Dear FreeSurfer Users, > > > > > > > > > > I ran recon -all on my structural image and created ROI
masks
(using > > > > > mri_label2vol) based on FreeSurfer's cortical
parcellation.
I'd
like > > to > > > > use > > > > > these masks for further analysis with FSL. However, it
seems
that
the > > ROI > > > > > masks generated with mri_label2vol have different header information > > than > > > > > that of the original structural image. As a result, I was
unable
to > > carry > > > > > out further analysis with FSL (e.g., converting these ROI
masks
into > > > > > functional space with hires2example_func.mat). I was
wondering
if
> > there is > > > > > a way to solve this issue. > > > > > > > > > > Many thanks in advance. > > > > > Frank > > > > > -------------- next part -------------- > > > > > An HTML attachment was scrubbed... > >>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 05/a > > > > 552481b/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 8 > > > > > Date: Mon, 6 Jan 2014 17:11:54 +0900 > > > > > From: Muhammad Naveed Iqbal Qureshi
> > > > > Subject: [Freesurfer] converting .thickness files of T1
MRI
from
> > > > > FreeSurfer into AFNI > > > > > To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: BLU174-W27296B6C59F4D34F89293AC4B70@phx.gbl > > > > > Content-Type: text/plain; charset="ks_c_5601-1987" > > > > > > > > > > Hi, > > > > > I want to know that how can I convert FreeSurfer
.thickness
files
to > > AFNI > > > > readable format > > > > > I tried the following Command but it gives error > > > > > > > > > > > > > > > mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
Exp
$
> > > > > reading from > > /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... > > > > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > > > > i_ras = (-1, 0, 0) > > > > > j_ras = (0, 0, -1) > > > > > k_ras = (0, 1, 0) > > > > > writing to > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik...
> > > > > AFNI BRIK write unsupported > > > > > ERROR: failure writing > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > > > > UN:/media> > > > > > > > > > > Please let me help me to solve this problem > > > > > Thank you :) > > > > > > > > > > > > > > > > > > > > Best Regards, > > > > > > > > > > Muhammad > > > > > Naveed Iqbal Qureshi > > > > > > > > > > > > > > > -------------- next part -------------- > > > > > An HTML attachment was scrubbed... > >>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 06/1 > > > > d3fe803/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 9 > > > > > Date: Mon, 6 Jan 2014 10:45:52 +0100 > > > > > From: "L. Schweren" l.j.s.schweren@umcg.nl > > > > > Subject: [Freesurfer] brain orientation in qdec > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: 005601cf0ac4$16bda9b0$4438fd10$@umcg.nl > > > > > Content-Type: text/plain; charset="us-ascii" > > > > > > > > > > Dear experts, > > > > > > > > > > > > > > > > > > > > I ran recon-all with qcache. When loading the right
hemisphere
of
> > > > fsaverage > > > > > (or any other surface reconstruction) into tksurfer (for
example
> > command: > > > > > tksurfer fsaverage rh white), the left hemisphere surface
is
> > displayed, > > > > and > > > > > it is upside down. When I import annotations they load in
the
same
> > > > > orientation as the surface. However, the coordinates and
the
labels, > > > > > displayed in the Tksurfer Tools window, are not. For
example,
when
I > > move > > > > > the cursor to the temporal lobe, the label says it's
postcentral.
I do > > not > > > > > mind manually turning the surfaces in tksurfer, but I do
need
to
be > > sure I > > > > > am looking at the correct hemispheres, coordinates and
labels.
> > > > > > > > > > I hope you can help me solve this. Thank you in advance. > > > > > > > > > > > > > > > > > > > > Best wishes, > > > > > > > > > > Lizanne > > > > > > > > > > > > > > > > > > > > -------------- next part -------------- > > > > > An HTML attachment was scrubbed... > >>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 06/5 > > > > 583e136/attachment-0001.html > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 10 > > > > > Date: Mon, 6 Jan 2014 08:41:58 -0500 (EST) > > > > > From: Bruce Fischl fischl@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] converting .thickness files of
T1
MRI
from > > > > > FreeSurfer into AFNI > > > > > To: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com > > > > > Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: alpine.LRH.2.03.1401060840550.16518@nmr.mgh.harvard.edu > > > > > Content-Type: text/plain; charset="iso-8859-15" > > > > > > > > > > Hi Muhammad > > > > > > > > > > try: > > > > > > > > > > set sdir=/home/naveed/freesurfer/subjects/CHR01/surf > > > > > mris_convert -c $sdir/rh.thickness $sdir/rh.orig > > $sdir/rh.thickness.brik > > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > On Mon, 6 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote: > > > > > > > > > > > Hi, > > > > > > I want to know that how can I convert FreeSurfer
.thickness
files to > > > > AFNI > > > > > > readable format > > > > > > I tried the following Command but it gives error > > > > > > > > > > > > > > > > > > mri_convert /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness > > > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter
Exp $
> > > > > > reading from > > /home/naveed/freesurfer/subjects/CHR01/surf/rh.thickness... > > > > > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > > > > > i_ras = (-1, 0, 0) > > > > > > j_ras = (0, 0, -1) > > > > > > k_ras = (0, 1, 0) > > > > > > writing to > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik...
> > > > > > AFNI BRIK write unsupported > > > > > > ERROR: failure writing > > > > > >
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
> > > > > > UN:/media> > > > > > > > > > > > > Please let me help me to solve this problem > > > > > > Thank you :)? > > > > > > > > > > > > Best Regards, > > > > > > Muhammad Naveed Iqbal Qureshi > > > > > > > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 11 > > > > > Date: Mon, 6 Jan 2014 10:40:43 -0500 (EST) > > > > > From: "Emad Ahmadi" emad@nmr.mgh.harvard.edu > > > > > Subject: [Freesurfer] recon-all error > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: 63234.172.19.2.113.1389022843.squirrel@mail.martinos.org > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > > > > Hello & Happy New Year! > > > > > > > > > > I'm running recon-all for one subject on MGH clusters
(ERISone),
and > > it > > > > > exits with error. I would appreciate it if you help me
figure
out
what > > the > > > > > problem is. The log file is attached. > > > > > > > > > > All the best throughout 2014! > > > > > Emad > > > > > > > > > > > > > > > Emad Ahmadi, MD > > > > > ------------------------------------------------ > > > > > Research Fellow > > > > > Department of Radiology > > > > > Massachusetts General Hospital > > > > > Harvard Medical School > > > > > > > > > > 25 New Chardon Street, Suite 400 > > > > > Boston, MA 02114 > > > > > Tel: 617 726 5237 > > > > > Email: emad@nmr.mgh.harvard.edu > > > > > > > > > > -------------- next part -------------- > > > > > A non-text attachment was scrubbed... > > > > > Name: recon-all.log > > > > > Type: application/octet-stream > > > > > Size: 20022 bytes > > > > > Desc: not available > > >>>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
0
1
06/ > > e > > > > 6358cca/attachment-0002.obj > > > > > -------------- next part -------------- > > > > > A non-text attachment was scrubbed... > > > > > Name: recon1job.bash > > > > > Type: application/octet-stream > > > > > Size: 1555 bytes > > > > > Desc: not available > > >>>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
0
1
06/ > > e > > > > 6358cca/attachment-0003.obj > > > > > > > > > > ------------------------------ > > > > > > > > > > Message: 12 > > > > > Date: Mon, 6 Jan 2014 17:51:18 +0200 > > > > > From: Rotem Saar saar.rotem@gmail.com > > > > > Subject: [Freesurfer] Fwd: Anatomical segmentation -
question
> > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > Message-ID: > > > > > CAMjFEmbcEwbXMOyxw-kuep6NSzdnk=rYHSEvwPGSbiXkBZKxtA@mail.gmail.com > > > > > Content-Type: text/plain; charset="windows-1252" > > > > > > > > > > Dear freesurfer experts, > > > > > > > > > > I'm performing anatomical segmentation for Philips dicoms
(3T
> > scanner). I > > > > > got these two images from the same slice while performing
step
number > > 4 in > > > > > the script below ? from some reason, the two images don't
fit.
Should > > I > > > > use > > > > > "scale brain" ? I know this is not recommended thus want
to
consult > > with u > > > > > first ? Can u please comment on why this is happening? Is
there
any > > value > > > > > that corresponds to "how good is the segmentation" ? if
yes,
where
can > > I > > > > > find it ? > > > > > > > > > > My script is written below. > > > > > > > > > > Thanks, > > > > > > > > > > Rotem > > > > > > > > > > Anatomical segmentation: > > > > > > > > > > first step- 23 hours: > > > > > > > > > > *recon-all -autorecon-all -i ~/Desktop/ FOLDER-NAME
/I00001.dcm -s
> > > > > FOLDER-NAME* > > > > > > > > > > second step:(gyrus=green, sulcus=red) > > > > > > > > > > *tksurfer -curv FOLDER-NAME lh/rh inflated* > > > > > > > > > > third step: (talairch registretion) > > > > > > > > > > *tkmedit FOLDER-NAME brainmask.mgz* > > > > > > > > > > File-> transforms-> load transform AUX-> Browse->
talairch.xfm
> > > > > > > > > > forth step: (simetry - allows changing 12df
transformation. if
we
made > > any > > > > > changes we should click "save reg" and run this command
again)
> > > > > > > > > > *tkregister2 --mgz --s FOLDER-NAME --fstal --surf orig* > > > > > > > > > > IF WE CHANGE ANYTHING, CLICK "SAVE REG" AND RUN FROM
STARTING
POING: > > > > > recon-all -all -subjectid FOLDER-NAME > > > > > > > > > > fifth step: (scalp removal: if removed too much, rise up
from
the
> > value > > > > 25: > > > > > > > > > > *recon-all -skullstrip -wsthresh 25 -clean-bm
-no-wsgcaatlas
-s
> > > > > FOLDER-NAME * > > > > > > > > > > to check the result press: *tkmedit FOLDER-NAME
brainmask.mgz
lh.white > > > > -aux > > > > > T1.mgz -aux-surface rh.white *) > > > > > > > > > > for hand correction: *tkmedit FOLDER-NAME brainmask.mgz
-aux
T1.mgz* > > > > > > > > > > tools-> configure volume brush -> MARK: mode=clone,
source=Aux
> > > > > > > > > > tools-> configure brush info (for choosing brush size) > > > > > > > > > > click on edit voxels: click in MIDDLE for adding voxels,
RIGHT
for
> > > > removing > > > > > voxels : slice by slice. > > > > > > > > > > when finish, click: File-> save main volume > > > > > > > > > > sisxt step: (cp for correcting segmentation) > > > > > > > > > > *tkmedit FOLDER-NAME brainmask.mgz lh.white -aux T1.mgz -aux-surface > > > > > rh.white* > > > > > > > > > > seventh step: (done) > > > > > > > > > > *recon-all -autorecon2-cp -autorecon3 -s FOLDER-NAME* > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Rotem Saar-Ashkenazy > > > > > Department of Brain and Cognitive Science > > > > > Ben Gurion University of the Negev > > > > > Beer-Sheva 84105 > > > > > Israel > > > > > -------------- next part -------------- > > > > > An HTML attachment was scrubbed... > >>>>URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201
4
0
1 > > 06/3 > > > > df4f7b3/attachment.html > > > > > -------------- next part -------------- > > > > > A non-text attachment was scrubbed... > > > > > Name: 3.png > > > > > Type: image/png > > > > > Size: 299694 bytes > > > > > Desc: not available > > >>>Url:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/2014
0
1
06/ > > 3 > > > > df4f7b3/attachment.png > > > > > > > > > > ------------------------------ > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > > > > > > End of Freesurfer Digest, Vol 119, Issue 6 > > > > > ****************************************** > > > > > > > > > > > >