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/20140
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/201401
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/20140
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/20140
1
05/a
552481b/attachment-0001.html > > ------------------------------ > > Message: 8 > Date: Mon, 6 Jan 2014 17:11:54 +0900 > From: Muhammad Naveed Iqbal Qureshi mniqureshi@hotmail.com > 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/20140
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/20140
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/201401
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/201401
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/20140
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/201401
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 > ******************************************