[Freesurfer] fwd: Re: Re: problem display tksurfer in vmware

[Pedro Paulo de Magalhaes Oliveira Jr]

-Msg original-
De: Giacomo Mandruzzato
Enviado:  14/10/2009 06:22:24
Assunto:  Re: Re: [Freesurfer] problem display tksurfer in vmware

Hi,
I have a question about a probabilistic segmentation of gray matter with
freesurfer. How can I do it?
if I binarize like this:

mri_binarize --i aparc+aseg.mgz --min 999.5 --o ctx.mgz

I obtain only a mask 0-1. Can I obtain a probablistic map like I obtained
with SPM and FSL of the gray matter?
thank you in advance

Giacomo



2009/9/28 Pedro Paulo de Magalhães Oliveira Junior 

> Have you installed the VirtualBox that comes from the FreeSurfer Wiki?
>  VirtualBox 3.x?
>
> ---
> Pedro Paulo de M. Oliveira Junior
> Diretor de Operações
> Netfilter & SpeedComm Telecom
> --- Novo Netfilter 3.2 www.Netfilter.com.br
> --- Novo Netfilter Small Business
>
>
>
> 2009/9/28 Giacomo Mandruzzato 
>
> Hi,
>> now I have installed Virtual Box with freesurfer, but I have same problem
>> with tksurfer and a library problem with qdec (it can't find libtiff.so.3
>> file, and in the folder I see only libtiff.so.3 file!)
>> Giacomo
>>
>> 2009/9/26 Giacomo Mandruzzato 
>>
>> thankyou for your help and your rapid answer.
>>>
>>> I use bash and i set doublebufferflag=1 but the problem persists!
>>>
>>>
>>> 2009/9/26 Pedro Paulo de Magalhaes Oliveira Jr 
>>>
 In csh use setenv doublebufferflag 1

 In bash export doublebufferflag=1


 --
 Enviado do meu celular Nokia E71
 -Msg original-
 De: Giacomo Mandruzzato
 Enviado:  26/09/2009 09:33:26
 Para: p...@netfilter.com.br
 Assunto:  Re: [Freesurfer] problem display tksurfer in vmware

 Yes, I know but I have problem with VirtualBox in the first boot that I
 do!
 Can I use freesurfer (and so tksurfer) with vmware? Or Is there any
 solution
 for my problem?
 thank you

 2009/9/26 Pedro Paulo de Magalhaes Oliveira Jr 

 > Use the official FreeSurfer distribution for Virtualbox
 >
 > --
 > Enviado do meu celular Nokia E71
 > -Msg original-
 > De: Giacomo Mandruzzato
 > Enviado:  26/09/2009 08:22:55
 > Para: freesurfer@nmr.mgh.harvard.edu
 > Assunto:  [Freesurfer] problem display tksurfer in vmware
 >
 > Hi,
 > I'm Giacomo Mandruzzato, a student of Bioengineering at Padova (DIE)
 and
 > I'm
 > working on my Thesis with Freesurfer (last version). I am using a
 virtual
 > machine Vmware 2.5.3 with Cent0S 5.1 running FSL virtual disk in
 Windows
 > Vista Home premium,
 > I installed freesurfer and tkmedit e qdec run correctly but when run
 > tksurfer (i.e. tksurfer bert rh pial, like website suggests) display
 an
 > error :
 >
 >
 > > [r...@localhost ~]# tksurfer bert rh pial
 > > surfer: current subjects dir: /usr/local/freesurfer/subjects
 > > surfer: not in "scripts" dir ==> using cwd for session root
 > > surfer: session root data dir ($session) set to:
 > >
 > > surfer: /root
 > > surfer: all rgb files written to /root
 > > surfer: Reading header info from /usr/local/freesurfer/
 > subjects/bert/mri/T1.mgz
 > > surfer: vertices=131860, faces=263716
 > >
 > >
 > > WARNING: No colortable found!
 > >
 > >
 > >
 > > surfer: single buffered window
 > > surfer: tkoInitWindow(bert)
 > > surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
 > > Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
 > > Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
 > >
 > > Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
 > > Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
 > > Successfully parsed tksurfer.tcl
 > > reading white matter vertex locations...
 > > %
 > >
 > >
 >
 > Tksurfer open and I can see only a little piece of brain.
 > I have update the video card's driver and I tried to use another vm,
 like
 > VirtualBox but I left the idea because I found some problem with boot
 of
 > it.
 > I have found a similar problem in internet, but without solution:
 >
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07389.html(I
 > am not using a Nvidia video card).
 >
 >
 > characteristic of my notebook:
 > Olidata , Intel core duo T2450 @ 2 x 2.00 Ghz,
 > Ram 2 GB, Windows Vista Home Premium 32bit SP2 updated.
 > Video card: Mobile Intel 945 Express Chipset Family
 >
 > I apologize for bad English and little knowledge of Unix OS.
 > Please, if somebody can help I am grateful.
 >
 > Best Regards,
 >
 > Giacomo Mandruzzato
 > giacomo.man...@gmail.com
 >
 >


>>>
>>
>


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[Freesurfer] Fwd: probabilistic segmentation of gray matter

[Giacomo Mandruzzato]

-- Forwarded message --
From: Giacomo Mandruzzato 
Date: 2009/10/14
Subject: probabilistic segmentation of gray matter
To: freesurfer@nmr.mgh.harvard.edu



Hi,
I have a question about a probabilistic segmentation of gray matter with
freesurfer. How can I do it?
if I binarize like this:

mri_binarize --i aparc+aseg.mgz --min 999.5 --o ctx.mgz

I obtain only a mask 0-1. Can I obtain a probablistic map like I obtained
with SPM and FSL of the gray matter?
thank you in advance

Giacomo Mandruzzato
Student of Bioengineering
Universiti of Padova
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Re: [Freesurfer] Fwd: probabilistic segmentation of gray matter

[Bruce Fischl]

Hi Giacomo,

we don't write out the probabilities by default. To get them you would 
need to add -write_probs  to the mri_ca_label command 
line (you can find it in recon-all.log for each subject).

cheers
Bruce
On Wed, 14 Oct 
2009, Giacomo Mandruzzato wrote:

> -- Forwarded message --
> From: Giacomo Mandruzzato 
> Date: 2009/10/14
> Subject: probabilistic segmentation of gray matter
> To: freesurfer@nmr.mgh.harvard.edu
>
>
>
> Hi,
> I have a question about a probabilistic segmentation of gray matter with
> freesurfer. How can I do it?
> if I binarize like this:
>
> mri_binarize --i aparc+aseg.mgz --min 999.5 --o ctx.mgz
>
> I obtain only a mask 0-1. Can I obtain a probablistic map like I obtained
> with SPM and FSL of the gray matter?
> thank you in advance
>
> Giacomo Mandruzzato
> Student of Bioengineering
> Universiti of Padova
>
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Re: [Freesurfer] using freeview

[Bruce Fischl]

yes, that looks right
On Wed, 14 Oct 2009, Ahmed, F, Me  
wrote:

> Hello,
>
> I had problems with the "sliver" problem with Tkmedit and tried all of the 
> possible solutions to try and correct it, to no avail. My last resort was 
> using freeview. I tried the example commands Nick wrote on the wiki site for 
> this problem:
>
> cd 
> freeview --volume mri/T1.mgz \
>  --surface surf/lh.white \
>  --surface surf/rh.white \
>  --surface surf/lh.pial:annot=aparc.annot \
>  --surface surf/rh.pial:annot=aparc.annot
>
> And I got the following output, I just wanted to know if what I'm seeing is 
> correct. And if this is what freeview looks like?
>
>
>
>
>
>
>
>
> Thank you
>
>
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Re: [Freesurfer] Fwd: probabilistic segmentation of gray matter

[Giacomo Mandruzzato]

Thank you for the answer but sorry, I don't know how use mri_ca_label
function!
I have aparc+aseg.mgz volume segmentation and I would have a probabilistic
segmentation of gray matter cortical in ctx.mgz file.
How can I do?
I am a beginner freesurfer user!

best

Giacomo

2009/10/14 Bruce Fischl 

> Hi Giacomo,
>
> we don't write out the probabilities by default. To get them you would need
> to add -write_probs  to the mri_ca_label command line (you
> can find it in recon-all.log for each subject).
>
> cheers
> Bruce
>
> On Wed, 14 Oct 2009, Giacomo Mandruzzato wrote:
>
>  -- Forwarded message --
>> From: Giacomo Mandruzzato 
>> Date: 2009/10/14
>> Subject: probabilistic segmentation of gray matter
>> To: freesurfer@nmr.mgh.harvard.edu
>>
>>
>>
>> Hi,
>> I have a question about a probabilistic segmentation of gray matter with
>> freesurfer. How can I do it?
>> if I binarize like this:
>>
>> mri_binarize --i aparc+aseg.mgz --min 999.5 --o ctx.mgz
>>
>> I obtain only a mask 0-1. Can I obtain a probablistic map like I obtained
>> with SPM and FSL of the gray matter?
>> thank you in advance
>>
>> Giacomo Mandruzzato
>> Student of Bioengineering
>> Universiti of Padova
>>
>>
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Re: [Freesurfer] [martinos-tech] surfcluster & simulations

[Frida Polli]

so doug we ran them using qdec. can you expand?

On Tue, Oct 13, 2009 at 6:00 PM, Douglas N Greve
wrote:
>
>>
>>
>> It depends on which program you ran and how you ran it.
>>
>>
>> Frida Polli wrote:
>> >
>> >
>> > hey bruce, nick, doug
>> >
>> > when we use qdec to generate simulations to find CWP, the cluster
>> > sizes that we get are smaller area than if we make a label from the
>> > cluster and use label_area to determine the size of the cluster.
>> >
>> > im just wondering if the CWP value that we get is therefore correct?
>> > and what could be the cause of this discrepancy?
>> >
>> > i feel like i might have seen this before with surfcluster and fMRI
>> > data but i dont totally remember.
>> >
>> > thnx, frida
>> >
>> >
>> > --
>> > Frida E. Polli, PhD
>> > Postdoctoral Fellow
>> > Brain & Cognitive Sciences, MIT
>> > 43 Vassar St., Room 46-4033
>> > Cambridge, MA 02139
>> > email: fpo...@mit.edu  
>> > > >
>> > tel: (617) 324 2897
>> >
>> >
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> In order to help us help you, please follow the steps in:
>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>>  __._,_.___
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Re: [Freesurfer] Fwd: probabilistic segmentation of gray matter

[Bruce Fischl]

Hi Giacomo,

all the freesurfer commands are stored in the subject's recon-all.log 
file. You should be able to find the mri_ca_label command in there and 
modify it.

cheers
Bruce
On Wed, 14 Oct 2009, Giacomo Mandruzzato wrote:

> Thank you for the answer but sorry, I don't know how use mri_ca_label
> function!
> I have aparc+aseg.mgz volume segmentation and I would have a probabilistic
> segmentation of gray matter cortical in ctx.mgz file.
> How can I do?
> I am a beginner freesurfer user!
>
> best
>
> Giacomo
>
> 2009/10/14 Bruce Fischl 
>
>> Hi Giacomo,
>>
>> we don't write out the probabilities by default. To get them you would need
>> to add -write_probs  to the mri_ca_label command line (you
>> can find it in recon-all.log for each subject).
>>
>> cheers
>> Bruce
>>
>> On Wed, 14 Oct 2009, Giacomo Mandruzzato wrote:
>>
>>  -- Forwarded message --
>>> From: Giacomo Mandruzzato 
>>> Date: 2009/10/14
>>> Subject: probabilistic segmentation of gray matter
>>> To: freesurfer@nmr.mgh.harvard.edu
>>>
>>>
>>>
>>> Hi,
>>> I have a question about a probabilistic segmentation of gray matter with
>>> freesurfer. How can I do it?
>>> if I binarize like this:
>>>
>>> mri_binarize --i aparc+aseg.mgz --min 999.5 --o ctx.mgz
>>>
>>> I obtain only a mask 0-1. Can I obtain a probablistic map like I obtained
>>> with SPM and FSL of the gray matter?
>>> thank you in advance
>>>
>>> Giacomo Mandruzzato
>>> Student of Bioengineering
>>> Universiti of Padova
>>>
>>>
>
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[Freesurfer] index out of bounds

[Alessandro D. Gagliardi]

Hello FreeSurfers,

I'm trying to analyze some BOLD data where the subject moves through a
dozen or so states over the course of an hour.  None of these repeat
but they are the same for all subjects.  I have a .par file that
specifies the duration of each segment with an integer index for each
one.  I don't need an HRF; a square wave is preferable.  But that
doesn't seem to be an option in mkanalysis-sess so I used a gamma
function with an exponent of 0 and a long dispersion (~300 sec.) which
seems to approximate a square wave well enough.  There is no "resting
state" to speak of, each state is meant to be contrasted against all
the others.  It's a very simple design and yet difficult to fit into
an analysis.  I thought I did it right (or well enough) but when I try
to run it I get a series of errors that Google is of no help in
elucidating:


??? Attempted to access a(1); index out of bounds because numel(a)=0.

Error in ==> fast_st2fir at 121
b(1) = a(1);

Error in ==> flac_desmat at 56
 flacnew.ev(nthev).Xfir = fast_st2fir(st,flac.ntp,flac.TR,ev.psdwin,1);

Error in ==> flac_customize at 272
flacnew = flac_desmat(flacnew);

Error in ==> fast_selxavg3 at 97
flac0 = flac_customize(flac0);

>> --
ERROR: fast_selxavg3() failed\n


Any help figuring this out would certainly be appreciated!

Thank you,

Alessandro D. Gagliardi
Ph.D. Candidate
Integrative Neuroscience Program
Rutgers University Mind Brain Analysis
adfgaglia...@gmail.com
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[Freesurfer] Any way to calculate overlap of labels to atlas regions quickly?

[Laluz, Victor]

Hello,

I'm interested in subdividing some of the standard atlas regions into anterior 
and posterior divisions. Besides creating individual labels for each of the 
labels, is it possible to create a generic anterior label for multiple 
subregions (encompassing an entire lobe at a time), then quickly calculate 
areas of overlap between each individual atlas region and the anterior lobe 
label in order to calculate anterior volumes per region?

Victor Laluz

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[Freesurfer] a question about mri_label_volume -eTIV

[Guang Zeng]

Hi, there,

>From FS Wiki,  eTIV - estimated Total Intracranial Volume, aka ICV,

I read 

 mri_label_volume requires specifying the transform file to use, and the scale 
factor: mri_label_volume -eTIV \
 $sdir/transforms/talairach.xfm 1948 \
 $sdir/aseg.mgz 17 53where $sdir is the path to the subject's mri directory 
(ie, $SUBJECTS_DIR//mri). The
'17' and '53' are label ID's, in this case left and right hippocampus
(see the subjects /stats/aseg.stats file for IDs). The output will look
like: using eTIV from atlas transform of 1528 cm^3
processing label 17...
3822 voxels (3822.0 mm^3) in label 17, %0.250119 of eTIV volume (1528075)
processing label 53...
4410 voxels (4410.0 mm^3) in label 53, %0.288598 of eTIV volume (1528075)>From 
a previous post at FS mailing list, I also read something similar,

Just as an aside, once you have a talairach_with_skull.lta file (whether
from v3 or v4), you can calculate eTIV as scale_factor/determinant(lta),
where the scale_factor employed is 2150.

Just want to know where dose this scale factor number 1948 and 2150 come from?


Thanks a lot!

Guang 


  
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Re: [Freesurfer] a question about mri_label_volume -eTIV

[Nick Schmansky]

see:

http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV

also note that mri_segstats is easier to use for getting etiv.

nick

On Wed, 2009-10-14 at 14:22 -0500, Guang Zeng wrote:
> Hi, there,
> 
> From FS Wiki,  eTIV - estimated Total Intracranial Volume, aka ICV,
> 
> I read 
> 
> mri_label_volume requires specifying the transform file to use, and
> the scale factor: 
> mri_label_volume -eTIV \
>  $sdir/transforms/talairach.xfm 1948 \
>  $sdir/aseg.mgz 17 53
> 
> where $sdir is the path to the subject's mri directory (ie,
> $SUBJECTS_DIR//mri). The '17' and '53' are label ID's, in this
> case left and right hippocampus (see the subjects /stats/aseg.stats
> file for IDs). The output will look like: 
> 
> using eTIV from atlas transform of 1528 cm^3
> processing label 17...
> 3822 voxels (3822.0 mm^3) in label 17, %0.250119 of eTIV volume (1528075)
> processing label 53...
> 4410 voxels (4410.0 mm^3) in label 53, %0.288598 of eTIV volume (1528075)
> From a previous post at FS mailing list, I also read something
> similar,
> Just as an aside, once you have a talairach_with_skull.lta file (whether
> from v3 or v4), you can calculate eTIV as scale_factor/determinant(lta),
> where the scale_factor employed is 2150.
> 
> Just want to know where dose this scale factor number 1948 and 2150
> come from?
> 
> 
> Thanks a lot!
> 
> Guang 
> 
> 
> 
> 
> __
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Re: [Freesurfer] isxconcat-sess

[Maximilien Chaumon]

Hi freesurfers,

I've been running isxconcat-sess with this line

chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf
subjlist.txt -analysis Analyse_Simple_Confidence -c
High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08

I was expecting to find a directory called osgm in the specified analysis
directory with which I could feed data to mri_glmfit, but I can't find it.
/homes/11/chaumon/bomba/AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor

The log file is attached. I don't find "error" in the text.

Where am I wrong?
Is there any mri_glmfit-sess like script somewhere? It's going to be pretty
tough to find each parameter to feed to mri_glmfit...

Thanks,
Max
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[Freesurfer] process dying during longitudinal reconstruction

[Dana W. Moore]

Hi everyone,

I am trying to run the longitudinal stream on some images.  I have 3 
timepoints, and 2 of them finished the stream just fine, but a third quits 
during autorecon1 during the 3rd and final longitudinal step.  There is no 
error message or anything, it just stops.  The log file is attached--any 
insight into what is going wrong will be appreciated.

Thanks,
Dana


Wed Oct 14 18:18:06 EDT 2009
/home/gfs06/dwm2003/FS/NC/NC2-CBIC.long.NC2-3T-base
/share/apps/freesurfer/bin/recon-all
-long NC2-CBIC NC2-3T-base -all
subjid NC2-CBIC.long.NC2-3T-base
setenv SUBJECTS_DIR /home/gfs06/dwm2003/FS/NC
FREESURFER_HOME /share/apps/freesurfer
Actual FREESURFER_HOME /share/apps/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0
Linux compute-3-16.v4linux 2.6.18-53.el5 #1 SMP Wed Oct 10 16:34:19 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize10240 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 32 kbytes
maxproc  137216 

 total   used   free sharedbuffers cached
Mem:  164393481225236   15214112  0 107636 919464
-/+ buffers/cache: 198136   16241212
Swap:  8385920  08385920


program versions used
$Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable4 $  TimeStamp: 2009/10/14-22:18:07-GMT  BuildTimeStamp: Aug 11 2009 07:36:05  CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $  User: dwm2003  Machine: compute-3-16.v4linux  Platform: Linux  PlatformVersion: 2.6.18-53.el5  CompilerName: GCC  CompilerVersion: 30400 
FLIRT version 5.5
$Id: talairach_avi,v 1.4.2.1 2009/07/30 19:22:07 nicks Exp $
mri_convert --version 
stable4
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable4 $  TimeStamp: 2009/10/14-22:18:07-GMT  BuildTimeStamp: Aug 11 2009 07:36:05  CVS: $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $  User: dwm2003  Machine: compute-3-16.v4linux  Platform: Linux  PlatformVersion: 2.6.18-53.el5  CompilerName: GCC  CompilerVersion: 30400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by ni...@minerva (x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable4 $  TimeStamp: 2009/10/14-22:18:07-GMT  BuildTimeStamp: Aug 11 2009 07:36:05  CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $  User: dwm2003  Machine: compute-3-16.v4linux  Platform: Linux  PlatformVersion: 2.6.18-53.el5  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable4 $  TimeStamp: 2009/10/14-22:18:07-GMT  BuildTimeStamp: Aug 11 2009 07:36:05  CVS: $Id: mri_watershed.cpp,v 1.67.2.5 2009/05/05 19:17:42 nicks Exp $  User: dwm2003  Machine: compute-3-16.v4linux  Platform: Linux  PlatformVersion: 2.6.18-53.el5  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable4 $  TimeStamp: 2009/10/14-22:18:07-GMT  BuildTimeStamp: Aug 11 2009 07:36:05  CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $  User: dwm2003  Machine: compute-3-16.v4linux  Platform: Linux  PlatformVersion: 2.6.18-53.el5  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable4 $  TimeStamp: 2009/10/14-22:18:07-GMT  BuildTimeStamp: Aug 11 2009 07:36:05  CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $  User: dwm2003  Machine: compute-3-16.v4linux  Platform: Linux  PlatformVersion: 2.6.18-53.el5  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable4 $  TimeStamp: 2009/10/14-22:18:07-GMT  BuildTimeStamp: Aug 11 2009 07:36:05  CVS: $Id: mri_em_register.c,v 1.57.2.2 2008/12/29 17:22:03 nicks Exp $  User: dwm2003  Machine: compute-3-16.v4linux  Platform: Linux  PlatformVersion: 2.6.18-53.el5  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable4 $  TimeStamp: 2009/10/14-22:18:07-GMT  BuildTimeStamp: Aug 11 2009 07:36:05  CVS: $Id: mri_ca_normalize.c,v 1.38.2.3 2009/08/02 15:00:46 nicks Exp $  User: dwm2003  Machine: compute-3-16.v4linux  Platform: Linux  PlatformVersion: 2.6.18-53.el5  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable4 $  TimeStamp: 2009/10/14-22:18:07-GMT  BuildTimeStamp: Aug 11 2009 07:36:05  CVS: $Id: mri_ca_register.c,v 1.63.2.3 2009/07

Re: [Freesurfer] process dying during longitudinal reconstruction

[Nick Schmansky]

What happens if you restart it?  The log terminates in an odd place that
I've never seen before.

Nick

On Wed, 2009-10-14 at 22:36 +, Dana W. Moore wrote:
> Hi everyone,
> 
> I am trying to run the longitudinal stream on some images.  I have 3
> timepoints, and 2 of them finished the stream just fine, but a third
> quits during autorecon1 during the 3rd and final longitudinal step.
> There is no error message or anything, it just stops.  The log file is
> attached--any insight into what is going wrong will be appreciated.
> 
> Thanks,
> Dana
> 
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