Still the same error
UN:~> mri_surf2vol --surfval surf/rh.thickness.paint --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness.paint
Best Regards,
Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:20:43 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
try adding "paint" after "surf/rh.thickness". The -surfval switch takes an optional format parameter after the file name I think
cheers Bruce
On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Hi Bruce, I have tried to convert by using the following commands but still some error occur.
UN:~> set subj=/home/naveed/freesurfer/subjects/CHR01/ UN:~> mri_surf2vol --surfval surf/rh.thickness --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.nii gdiagno = -1 ERROR: cannot recognize the type of surf/rh.thickness
Can you help me. Thank you.
Best Regards, Muhammad Naveed Iqbal Qureshi
Date: Tue, 7 Jan 2014 08:13:45 -0500 From: fischl@nmr.mgh.harvard.edu To: mniqureshi@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 119, Issue 6
Hi Muhammad
have you looked at the help? It's pretty extensive. If you have trouble post again and Doug should be able to guide you
cheers Bruce On Tue, 7 Jan 2014, Muhammad Naveed Iqbal Qureshi wrote:
Thank you Bruce,
Please guide me how can I use mri_surf2vol command on lh/rh.thickness
files
to get the output as lh/rh.ribbon.nii for AFNI SUMA. Thank you
Best Regards, Muhammad Naveed Iqbal Qureshi
From: freesurfer-request@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 119, Issue 6 To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 6 Jan 2014 10:51:33 -0500
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Today's Topics:
- erroneuos segmentation labeling of skull outside of brain
(Yuliya Yoncheva) 2. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 3. Re: Motion correction for SPACE FLAIR (Bruce Fischl) 4. Re: erroneuos segmentation labeling of skull outside of brain (Yuliya Yoncheva) 5. Re: erroneuos segmentation labeling of skull outside of brain (Bruce Fischl) 6. Re: recon-all exited w/errors (Bruce Fischl) 7. ROI masks created in FreeSurfer used in FSL?? (Frank Hsieh) 8. converting .thickness files of T1 MRI from FreeSurfer into AFNI (Muhammad Naveed Iqbal Qureshi) 9. brain orientation in qdec (L. Schweren) 10. Re: converting .thickness files of T1 MRI from FreeSurfer into AFNI (Bruce Fischl) 11. recon-all error (Emad Ahmadi) 12. Fwd: Anatomical segmentation - question (Rotem Saar)
Message: 1 Date: Sun, 5 Jan 2014 15:14:39 -0500 From: Yuliya Yoncheva yuliya.yoncheva@gmail.com Subject: [Freesurfer] erroneuos segmentation labeling of skull outside of brain To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGE5uFc2uD9pMefXjRZE0LQP+GcfhHKWeVkHxOGwDzV1=jYrQA@mail.gmail.com 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?
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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
>> 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.
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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
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.
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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 -------------- next part -------------- An HTML attachment was scrubbed... URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/201401
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