New subject: Freesurfer Digest, Vol 119, Issue 6

7 Jan 2014

      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)
Re: erroneuos segmentation labeling of skull outside of	brain
(Bruce Fischl)
Re: Motion correction for SPACE FLAIR (Bruce Fischl)
Re: erroneuos segmentation labeling of skull outside	of brain
(Yuliya Yoncheva)
Re: erroneuos segmentation labeling of skull outside of brain
(Bruce Fischl)
Re: recon-all exited w/errors (Bruce Fischl)
ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh)
converting .thickness files of T1 MRI from FreeSurfer	into
AFNI (Muhammad Naveed Iqbal Qureshi)
brain orientation in qdec (L. Schweren)
Re: converting .thickness files of T1 MRI from FreeSurfer
into AFNI (Bruce Fischl)
recon-all error (Emad Ahmadi)
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.
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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?.

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
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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.
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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
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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

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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
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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
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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
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End of Freesurfer Digest, Vol 119, Issue 6

Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6

Emad Ahmadi, MD

Emad Ahmadi, MD

Emad Ahmadi, MD