Re: [Freesurfer] recon_all hires

2019-08-21 Thread falk.luesebr...@med.ovgu.de 
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Hi Mona,

Potentially you have a bad skull strip resulting in a huge defect which will 
take a long time to correct. Simply fix your skull strip and you should be fine.

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Nasiriavanaki, Zahra
Gesendet: Dienstag, 20. August 2019 16:19
An: Freesurfer support list 
Betreff: [Freesurfer] recon_all hires


Dear Freesurfer experts



I am doing recon-all on one of my subjects and it seems that it's stuck for 
days and not going through. I even re-run it and it's still stuck at the same 
spot as before.

I attached the log file and here is my command:

recon-all -all -s $subj -i /$subj/anat/$run/mT1v2.nii -expert 
expertopts/expert.opts -hires -mail zn025 -parallel

I appreciate any help.



Thanks

Mona





Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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[Freesurfer] Hippocampal mask from the subfields masks

2019-08-21 Thread Ole Johan Evjenth Sørhaug 
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Dear freesurfer experts,

I wish to use the subfield segmentations from the 6.0 version of freesurfer
to have a segmentation of the whole hippocampus. As far as I have
understood, a segmentation of the whole hippocampus is not provided by
default by the subfields module. Would the correct way to obtain this be by
using the command mri_mergelabels on the subfield segmentations, then use
mri_label2vol to create an mgz volume of the whole hippocampus?

Regards
Ole Johan Evjenth Sørhaug
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Re: [Freesurfer] freeview crash -- petsc error when opening volume

2019-08-21 Thread TRISTAN J PAUTSCH 
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Adding more details provided by my user:

The crash only happens when loading surface files, either via the -f flag from 
the CLI or directly through the GUI. Could this be an issue with the surface 
files or the manner in which they are created?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of TRISTAN J PAUTSCH 

Sent: Tuesday, August 20, 2019 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] freeview crash -- petsc error when opening volume


External Email - Use Caution

Greetings all, I'll try to keep this succinct.

I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I 
used the stable 6.0/CentOS 6 download, in addition to the dev version of 
freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have 
ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview 
launches fine and stays open when launched alone, however attempting to open a 
volume (either through the GUI or directly via the CLI) causes a crash and the 
following error about 5-8 seconds after launching (brain images begin to 
populate, then crash):

---

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named xxx by xxx Tue Aug 20 
13:44:15 2019
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)

---

I've seen a number of other posts on the mailing list about this, but all of 
them I could find either end abruptly without a solution or with an unanswered 
request for more info.

Happy to provide any additional information or anything that may aid in the 
resolution of this issue.

Thanks everyone,
~T
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[Freesurfer] mris_pmake on the inflated surface

2019-08-21 Thread Lee, Jeungchan 
Hi,

 

I’m trying to calculate Dijkstra distance between startVertex and endVertex on 
the inflated surface (fsaverage, lh.inflated) using mris_pmake.

I see several options: --surface0, --surface1, --curv0, --curv1

 

I think I can use ‘--surface0 inflated’, but not sure about other options e.g., 
--surface1, --curv0, and --curv1.

I read the instruction (curv0 for curvature, curv1 for height parameter…) but 
was not able to understand what those mean exactly and what to use.

 

Would you explain what the meaning is and what to use?

 

Here is the command line that I have:

Mris_pmake --subject fsaverage --hemi lh --surface0 inflated --curv0 sulc 
--curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs `more 
./input_D.txt` (where input_D.txt says startVertex:8762,endVertex:1, for 
example)

 

Thanks in advance,

 

jeungchan

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Re: [Freesurfer] mris_pmake on the inflated surface

2019-08-21 Thread Rudolph Pienaar 
The in-line help in version 6.0 of FreeSurfer is incorrect
unfortunately. Please try the following for example:

mris_pmake --subjecttestSubject \
   --hemi   lh  \
   --surfacepial\
   --curv   sulc\
   --mpmOverlay euclidean   \
   --mpmProgpathFind\
   --mpmArgsvertexStart:121981,vertexEnd:132633 

to determine the distance on subject 'testSubject' for the lh.pial
surface. Of course, adjust as necessary.

best



On Wed, 2019-08-21 at 14:35 -0400, Lee, Jeungchan wrote:
> Hi,
> 
>  
> 
> I’m trying to calculate Dijkstra distance between startVertex and
> endVertex on the inflated surface (fsaverage, lh.inflated) using
> mris_pmake.
> 
> I see several options: --surface0, --surface1, --curv0, --curv1
> 
>  
> 
> I think I can use ‘--surface0 inflated’, but not sure about other
> options e.g., --surface1, --curv0, and --curv1.
> 
> I read the instruction (curv0 for curvature, curv1 for height
> parameter…) but was not able to understand what those mean exactly
> and what to use.
> 
>  
> 
> Would you explain what the meaning is and what to use?
> 
>  
> 
> Here is the command line that I have:
> 
> Mris_pmake --subject fsaverage --hemi lh --surface0 inflated --curv0
> sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs 
> `more ./input_D.txt` (where input_D.txt says
> startVertex:8762,endVertex:1, for example)
> 
>  
> 
> Thanks in advance,
> 
>  
> 
> jeungchan
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 
Rudolph Pienaar, Dr.Eng  
__

Staff Scientist 
  Boston Children's Hospital
Department of Radiology
   mailstop: BCH3181
  300 Longwood Avenue
   Boston, MA, 02115
__
  Technical Director 
 Fetal-Neonatal Neuroimaging and Developmental Science Center
Landmark Center, 401 Park Drive 
  Office LM7092 (East)
   Boston, MA, 02215
__
mailto:rudolph.pien...@childrens.harvard.edu 
http://fnndsc.babymri.org
-o- +1-857-218-5139
-f- +1-617-730-4671

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[Freesurfer] ERROR reading //fsaverage/label/lh.BA1_exvivo.label

2019-08-21 Thread liuxingze1993 
External Email - Use Caution

Hello，Dear FreeSurfer Developers,

 

I’m a doctoral student from Xiangya 2nd Hospital of Central South University, 
and also a beginner to FreeSurfer. I'm attempting to follow the steps 
descripted on ‘Practice Working with Data’ 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice) with our own 
data, but I’ve met the same problem several times when I programing the command 
‘recon-all -all -i 61492283 -s Sub219’:

(**ps: 61492283 is the T1 file I found after programing the command 'dcmunpack 
-src . -scanonly.log')

 

SUBJECTS_DIR   /media/dell/AA32E/Data_prac/219/20181211/1947

(**PS: 1947 is the folder where the T1 located)

 

FREESURFER_HOME  /usr/local/freesurfer

 

Loading source label

 

Invalid argument

 

ERROR reading  
/media/dell/AA32E/Data_prac/219/20181211/1947/fsaverage/label/lh.BA1_exvivo.label

 

recon-all -s Sub219 exited with ERRORS at 

 

 

I've searched the ‘lh.BA1_exvivo.label’ file in the related path and no such 
file here.  

 

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2) Platform: Ubuntu14.04 LTS

3) uname -a: Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 
UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

4) recon-all.log: see attached

 

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Re: [Freesurfer] ERROR reading //fsaverage/label/lh.BA1_exvivo.label

2019-08-21 Thread Greve, Douglas N.,Ph.D. 
There is no file attached. Can you send?

On 8/21/2019 10:25 PM, liuxingze1993 wrote:

External Email - Use Caution
Hello， Dear FreeSurfer Developers,

I’m a doctoral student from Xiangya 2nd Hospital of Central South University, 
and also a beginner to FreeSurfer. I'm attempting to follow the steps 
descripted on ‘Practice Working with Data’ 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice) with our own 
data, but I’ve met the same problem several times when I programing the command 
‘recon-all -all -i 61492283 -s Sub219’:
(**ps: 61492283 is the T1 file I found after programing the command 'dcmunpack 
-src . -scanonly.log')

SUBJECTS_DIR   /media/dell/AA32E/Data_prac/219/20181211/1947
(**PS: 1947 is the folder where the T1 located)

FREESURFER_HOME  /usr/local/freesurfer

Loading source label

Invalid argument

ERROR reading  
/media/dell/AA32E/Data_prac/219/20181211/1947/fsaverage/label/lh.BA1_exvivo.label

recon-all -s Sub219 exited with ERRORS at 


I've searched the ‘lh.BA1_exvivo.label’ file in the related path and no such 
file here.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu14.04 LTS
3) uname -a: Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 
UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached

Thank u for viewing, and I will be waiting here for your professional advice !







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[Freesurfer] ERROR reading //fsaverage/label/lh.BA1_exvivo.label with recon-all.log

2019-08-21 Thread liuxingze1993 
External Email - Use Caution

Hello，Dear FreeSurfer Developers,

 

I’m a doctoral student from Xiangya 2nd Hospital of Central South University, 
and also a beginner to FreeSurfer. I'm attempting to follow the steps 
descripted on ‘Practice Working with Data’ 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice) with our own 
data, but I’ve met the same problem several times when I programing the command 
‘recon-all -all -i 61492283 -s Sub219’:

(**ps: 61492283 is the T1 file I found after programing the command 'dcmunpack 
-src . -scanonly.log')

 

SUBJECTS_DIR   /media/dell/AA32E/Data_prac/219/20181211/1947

(**PS: 1947 is the folder where the T1 located)

 

FREESURFER_HOME  /usr/local/freesurfer

 

Loading source label

 

Invalid argument

 

ERROR reading  
/media/dell/AA32E/Data_prac/219/20181211/1947/fsaverage/label/lh.BA1_exvivo.label

 

recon-all -s Sub219 exited with ERRORS at 

 

 

I've searched the ‘lh.BA1_exvivo.label’ file in the related path and no such 
file here.  

 

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2) Platform: Ubuntu14.04 LTS

3) uname -a: Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 
UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

4) recon-all.log: see attached

 

Thank u for viewing, and I will be waiting here for your professional advice !





 Tue Apr 28 01:24:00 EDT 2009
/autofs/space/minerva_001/users/nicks/dev/distribution/average/fsaverage
/space/minerva/1/users/nicks/freesurfer/bin/recon-all
-s fsaverage -cortparc
subjid fsaverage
setenv SUBJECTS_DIR 
/autofs/space/minerva_001/users/nicks/dev/distribution/average
FREESURFER_HOME /space/minerva/1/users/nicks/freesurfer
Actual FREESURFER_HOME /autofs/space/minerva_001/users/nicks/freesurfer
build-stamp.txt: freesurfer-x86_64-redhat-linux-gnu-dev4-20090216
Linux minerva 2.6.9-78.0.13.ELsmp #1 SMP Wed Jan 14 15:55:36 EST 2009 x86_64 
x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize10240 kbytes
coredumpsize unlimited
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 32 kbytes
maxproc  65536 

 total   used   free sharedbuffers cached
Mem:   74031286807536 595592  0 1330406185568
Swap: 16386292224   16386068


program versions used
$Id: recon-all,v 1.201 2009/04/22 22:24:48 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.8 2008/02/29 20:14:51 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2009/04/28-05:24:00-GMT  BuildTimeStamp: Jan 14 2009 16:52:12  
CVS: $Id: mri_convert.c,v 1.156 2009/01/28 20:04:23 fischl Exp $  User: nicks  
Machine: minerva  Platform: Linux  PlatformVersion: 2.6.9-78.0.13.ELsmp  
CompilerName: GCC  CompilerVersion: 30400 
FLIRT version 5.4.2b
$Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $
mri_convert --version 
dev build (use --all-info flag for full version info)
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2009/04/28-05:24:00-GMT  BuildTimeStamp: Jan 14 2009 
16:52:12  CVS: $Id: tkregister2.c,v 1.104 2009/02/13 21:36:16 greve Exp $  
User: nicks  Machine: minerva  Platform: Linux  PlatformVersion: 
2.6.9-78.0.13.ELsmp  CompilerName: GCC  CompilerVersion: 30400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva 
(x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2009/04/28-05:24:01-GMT  BuildTimeStamp: Jan 14 2009 16:52:12  
CVS: $Id: mri_normalize.c,v 1.56 2008/12/06 18:22:09 fischl Exp $  User: nicks  
Machine: minerva  Platform: Linux  PlatformVersion: 2.6.9-78.0.13.ELsmp  
CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2009/04/28-05:24:01-GMT  BuildTimeStamp: Jan 14 2009 16:52:12  
CVS: $Id: mri_watershed.cpp,v 1.72 2007/11/18 22:40:49 nicks Exp $  User: nicks 
 Machine: minerva  Platform: Linux  PlatformVersion: 2.6.9-78.0.13.ELsmp  
CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2009/04/28-05:24:02-GMT  BuildTimeStamp: Jan 14 2009 16:52:12  
CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks Exp $  User: nicks  
Machine: minerva  Platform: Linux  PlatformVersion: 2.6.9-78.0.13.ELsmp  
CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2009/04/28-05:24:02-GMT  BuildTimeStamp: Jan 14 2009 
16:52:12  CVS: $Id: mri_label2label.c,v 1.37 2008/12/01 20:02:01 greve Exp $  
User: nicks  Machine: minerva  Platform: Linux  PlatformVersion: 
2.6.9-78.0.13.ELsmp  Co