[Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh resultsDirectory 1, 10 gives error line 22: cd: left: No such file or directory

[Knut J Bjuland]

 Dear Freesurfer experts,


I have processed my subject with recon-all and subfields hippocampal
segmentation. . I have tried to use
kvlQuantifyHippocampalSubfieldSegmentations.sh on a subset of my
subjects. I have these subjects A  B  C  D  E  fsaverage in a folder.
When I try to exclude fsaverage by using this command
kvlQuantifyHippocampalSubfieldSegmentations.sh  ~/subjects/hippo 1 5.  I
get this error message.

cd A/
Quantifying subject A/ left
Doing left side
cd left
/usr/local/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line
22: cd: left: No such file or directory
failed to do cd left
I have issued this command both in tsch and in bash.
However, when I run the command without any options in the same folder,
it works but bails out as expected when it reaches fsaverage-

Best regards,

Knut J. Bjuland
PhD candidate
NTNU
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[Freesurfer] mri_convert crash after updating with tracula add update 2014/05/26 on Ubuntu 14.04 lts

[Knut J Bjuland]

Dear Freesurfer experts,After I added the Tracula update at 
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula,  I have been unable to use 
mri_onvert. Since I have Ubuntu 14.04, I used the Centos 6 x86_64 version found 
at this link. However, when I tried to use mri_convert it segement fault. I 
have added the output when I try to convert a dicom to mgz. I am abel to get 
this segment fault reproducible. 



mri_convert_crash 1/2/1.dcm 001.mgzmri_convert_crash 1/2/1.dcm 001.mgz $Id: 
mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $reading from 
1/2/1.dcm...crypt_gkey = (null)Segmentation fault (core dumped)
I was able to get mri_conver to work by use the old version which was included 
in Freesurfer 5.3.
mri_convert 1/2/1.dcm 001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 
21:55:16 mreuter Exp $reading from 1/2/1.dcm...Getting Series No Scanning 
Directory INFO: Found 162 files in 1/2INFO: Scanning for Series Number 2INFO: 
found 160 files in seriesINFO: loading series header info.
worked with the same command line.
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[Freesurfer] freesurfer-Linux-centos7_x86_64-dev-20150521 on ubuntu 14.04 crash with Illegal instruction (core dumped)

[Knut J Bjuland]

Hi

I have tired the freesurfer-Linux-centos7_x86_64-dev-20150521. When I
start mri_convert on ubuntu 14.04.4 I get this results.

knutjb@dmed4960:/usr/local/freesurfer60$ export FREESURFER_HOME=
/usr/local/freesurfer60
knutjb@dmed4960:/usr/local/freesurfer60$ source
/usr/local/freesurfer60/SetUpFreeSurfer.sh
 freesurfer-Linux-centos7_x86_64-dev-20150521 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer60
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/knutjb/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/share/fsl/5.0
knutjb@dmed4960:/usr/local/freesurfer60$ mri_con
mri_concatmri_concatenate_lta   mri_convert_crash
mri_concatenate_gcam  mri_convert   mri_convert_mdh
knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert --help
Illegal instruction (core dumped)
knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert -h
Illegal instruction (core dumped)
knutjb@dmed4960:/usr/local/freesurfer60$

and in GDB
Starting program: /usr/local/freesurfer60/bin/mri_convert
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".

Program received signal SIGILL, Illegal instruction.
0x006be48f in make_cmd_version_string (argc=argc@entry=1,
argv=argv@entry=0x7fffdd98,
id_string=id_string@entry=0xc6de08 "$Id: mri_convert.c,v 1.221
2015/04/16 18:56:00 greve Exp $",
version_string=version_string@entry=0xc6cd66 "$Name:  $",
return_string=return_string@entry=0x7fffb0e0 "(\rW\366\377\177")
at version.c:215
215version.c: No such file or directory.

Knut Jørgen Bjuland



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Re: [Freesurfer] freesurfer-Linux-centos7_x86_64-dev-20150521 on ubuntu 14.04 crash with Illegal instruction (core dumped)

[Knut J Bjuland]

Hi zeke

Do you know if version that support non Haswell cpu will be available?

Knut Jørgen

On 05/22/2015 06:06 PM, Z K wrote:
> That particular developmental build is compiled with optimization flags 
> for machines containing Intels new Haswell processor and wont run on 
> platforms without it. Although that build is available via our dev 
> download page, it remains an unsupported build that exists primarily for 
> internal experimental purposes only.
>
> -Zeke
>
> On 05/22/2015 11:49 AM, Knut J Bjuland wrote:
>> Hi
>>
>> I have tired the freesurfer-Linux-centos7_x86_64-dev-20150521. When I
>> start mri_convert on ubuntu 14.04.4 I get this results.
>>
>> knutjb@dmed4960:/usr/local/freesurfer60$ export FREESURFER_HOME=
>> /usr/local/freesurfer60
>> knutjb@dmed4960:/usr/local/freesurfer60$ source
>> /usr/local/freesurfer60/SetUpFreeSurfer.sh
>>  freesurfer-Linux-centos7_x86_64-dev-20150521 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /usr/local/freesurfer60
>> FSFAST_HOME   /usr/local/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR  /home/knutjb/subjects
>> MNI_DIR   /usr/local/freesurfer/mni
>> FSL_DIR   /usr/share/fsl/5.0
>> knutjb@dmed4960:/usr/local/freesurfer60$ mri_con
>> mri_concatmri_concatenate_lta   mri_convert_crash
>> mri_concatenate_gcam  mri_convert   mri_convert_mdh
>> knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert --help
>> Illegal instruction (core dumped)
>> knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert -h
>> Illegal instruction (core dumped)
>> knutjb@dmed4960:/usr/local/freesurfer60$
>>
>> and in GDB
>> Starting program: /usr/local/freesurfer60/bin/mri_convert
>> [Thread debugging using libthread_db enabled]
>> Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
>>
>> Program received signal SIGILL, Illegal instruction.
>> 0x006be48f in make_cmd_version_string (argc=argc@entry=1,
>>  argv=argv@entry=0x7fffdd98,
>>  id_string=id_string@entry=0xc6de08 "$Id: mri_convert.c,v 1.221
>> 2015/04/16 18:56:00 greve Exp $",
>>  version_string=version_string@entry=0xc6cd66 "$Name:  $",
>>  return_string=return_string@entry=0x7fffb0e0 "(\rW\366\377\177")
>>  at version.c:215
>> 215version.c: No such file or directory.
>>
>> Knut Jørgen Bjuland
>>
>>
>>
>> ___
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>>
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[Freesurfer] Freeview crash if started with argument from Matlab 2015a on Mac os 11.10.5

[Knut J Bjuland]

Dear FreeSurfer experts









I have downloaded the FreeSurfer tutorials. When I try to load Freeview in 
Matlab with the argument that I found in the group tutorial Freeview will crash 
on Mac OS X 10.10.5, but it worked on Fedora 22. I am using Matlab because 
Freeview do not have FDR. Fdr is calculated using lme_mass_fdr.


I used this matlab command in Matlab 2015a after FDR correction. 








SUBJECTS_DIR=fullfile('Applications','freesurfer','subjects');leftcommand=sprintf('%s/%s/surf/lh.%s:annot=aparc.annot:annot_outline=1:overlay=%s:overlay_threshold=%s',SUBJECTS_DIR,template,surface,leftmgh,fdrtreshold);rightcommand=sprintf('%s/%s/surf/rh.%s:annot=aparc.annot:annot_outline=1:overlay=%s:overlay_threshold=%s
 ',SUBJECTS_DIR,template,surface,rightmgh,fdrtreshold);









commandline=sprintf('freeview -f %s -f %s -viewport 
3d',leftcommand,rightcommand);

freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
 -viewport 3dI got this results.
done freesurfer stuff...dyld: lazy symbol binding failed: Symbol not found: 
___emutls_get_address  Referenced from: 
/Applications/freesurfer//Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address  Referenced from: 
/Applications/freesurfer//Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib
[0]PETSC ERROR: 
[0]PETSC
 ERROR: Caught signal number 5 TRAP[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 darwin12. named Knuts-MacBook-Pro.local by 
knutjorgenbjulan Sun Aug 16 12:32:26 2015[0]PETSC ERROR: Libraries linked from 
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt[0]PETSC
 ERROR: Configure run at Mon Dec 17 15:29:35 2012[0]PETSC ERROR: Configure 
options --with-debugging=no --with-cc=gcc --with-fc=0 
--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) - 
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[Freesurfer] update mri_glmfit

[Knut J Bjuland]

Hi

I saw an updated version of mri_glmfit in 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/.
 

Should I update this file in my freesurfer installation.
What do this fix? Is is not in the release notes?



Knut J
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[Freesurfer] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?

[Knut J Bjuland]

   How can I get 300 dpi resolution or about when saving tiff files in 
tksurfer?
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Re: [Freesurfer] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?

[Knut J Bjuland]

Hi Bruce,
Do you upsample the tiffs from tksurfer when making image for 
publications? Or do you use another program in FreeSurfer suite?


Knut J


On 12/06/2012 10:22 PM, Bruce Fischl wrote:
> Hi Knut
> the tiffs written by tksurfer are 600x600 regardless of what DPI you 
> set. You can change the dpi with convert (or photoshop), but it won't 
> change the # of pixels.
>
> cheers
> Bruce
>
>
> On Thu, 6 Dec 2012, Knut J Bjuland wrote:
>
>>
>>   How can I get 300 dpi resolution or about when saving tiff files in
>> tksurfer?
>> ___
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>
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[Freesurfer] fixed version of mri_glmfit and mri_glmfit-sim

[Knut J Bjuland]

Hi

I saw an updated version of mri_glmfit in
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/.

Should I update this file in my freesurfer installation.
What do this fix? Is is not in the release notes? Along with mri_glmfir-sim 
from Doug Greve ftp site.



Knut J

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Re: [Freesurfer] regarding use-mritotal

[Knut J Bjuland]

Hi,
Talairach.xfm is a text file which contains a transformation matrix. 
Though there is small numerical difference between two transformation 
matrix made using mritotal and the default Talairach registration. The 
process of calculation the ICV may amplify this difference since it used 
the determinate of the transformation matrix to calculate ICV. The 
differences in ICV may depend on how different the numerical values of 
the Talairach transformation matrix are.


Best regrards
Knut J

On 12/14/2012 09:06 PM, Eric Cunningham wrote:

Hi,

this link:
http://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1
discusses a solution to bad talairach.xfm transforms, the 
-use-mritotal flag.


this link:
http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV
mentions that the talairach.xfm is used to calculate the total 
intracranial volume.


is using mritotal likely to result in significantly different 
intracranial volumes even if the talairach.xfm does not appear to be 
very different when viewed?


thanks much,
-eric




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[Freesurfer] None segmentation

[Knut J Bjuland]

Hi,

How can I calculate the number of None segmentation in right or left 
hippocampus or another structure in Matlab or in Freesufer?  

Knut J
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[Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19

[Knut J Bjuland]

When I run recon-all using freesurfer 5.2 latest beta it will segment 
crash.


Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 
x86_64 x86_64 x86_64 GNU/Linux

/home/knutjbj/freesurfer/ernie

 mri_convert /usr/local/freesurfer/subjects/sample-001.mgz 
/home/knutjbj/freesurfer/ernie/mri/orig/001.mgz


mri_convert /usr/local/freesurfer/subjects/sample-001.mgz 
/home/knutjbj/freesurfer/ernie/mri/orig/001.mgz

Segmentation fault
Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 
2013 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013

For more details, see the log file 
/home/knutjbj/freesurfer/ernie/scripts/recon-all.log
To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Knut J
--
SUBJECT ernie
DATE ti. 29. jan. 19:28:17 +0100 2013
USER knutjbj
HOST mypc 
PROCESSOR x86_64
OS Linux
Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 
x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.379.2.54 2013/01/15 22:31:19 nicks Exp $
/usr/local/freesurfer/bin/recon-all
PWD /home/knutjbj/freesurfer/ernie
CMD mri_convert /usr/local/freesurfer/subjects/sample-001.mgz 
/home/knutjbj/freesurfer/ernie/mri/orig/001.mgz
ti. 29. jan. 19:28:13 +0100 2013
/home/knutjbj/freesurfer/ernie
/usr/local/freesurfer/bin/recon-all
-i /usr/local/freesurfer/subjects/sample-001.mgz -i /usr/local/freesurfer/subjects/sample-002.mgz -s ernie -debug
subjid ernie
setenv SUBJECTS_DIR /home/knutjbj/freesurfer
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  1024 
maxlocks unlimited
maxsignal192659 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:  24683456   24399144 284312  0 654024   20092400
-/+ buffers/cache:3652720   21030736
Swap: 49337340   3796   49333544


program versions used
$Id: recon-all,v 1.379.2.54 2013/01/15 22:31:19 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/01/29-18:28:13-GMT  BuildTimeStamp: Jan 17 2013 00:19:38  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: knutjbj  Machine: mypc  Platform: Linux  PlatformVersion: 3.7.4-204.fc18.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/01/29-18:28:13-GMT  BuildTimeStamp: Jan 17 2013 00:19:38  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: knutjbj  Machine: mypc  Platform: Linux  PlatformVersion: 3.7.4-204.fc18.x86_64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/01/29-18:28:13-GMT  BuildTimeStamp: Jan 17 2013 00:19:38  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: knutjbj  Machine: mypc  Platform: Linux  PlatformVersion: 3.7.4-204.fc18.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/01/29-18:28:13-GMT  BuildTimeStamp: Jan 17 2013 00:19:38  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $  User: knutjbj  Machine: mypc  Platform: Linux  PlatformVersion: 3.7.4-204.fc18.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/01/29-18:28:13-GMT  BuildTimeStamp: Jan 17 2013 00:19:38  CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $  User: knutjbj  Machine: mypc  Platform: Linux  PlatformVersion: 3.7.4-204.fc18.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/01/29-18:28:13-GMT  BuildTimeStamp: Jan 17 2013 00:19:38  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: knutjbj  Machine: mypc  Platform: Linux  PlatformVersion: 3.7.4-204.fc18.x86_64  CompilerNam

Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19

[Knut J Bjuland]

Hi Nick

I reran dicom import from /usr/local/freesurfer/subject/sample*. I had 
24254940 kB free memory but I still got a segmentation error.I used 
sample data from /usr/local/freesurfer/subject. Do you think it is a 
glibc bug in Fedora 18. It contain glibc-2.16-28.fc18.x86_64.



This error showed up in my dmesg log.

[  175.413292] mri_convert[1350]: segfault at 0 ip 0037e092fbda sp 
7fff0a9dc2c8 error 4 in libc-2.16.so[37e080+1ad000]



Knutj



On 29. jan. 2013 19:47, Nick Schmansky wrote:

Knut,

I noticed in the log that there was only 284KB of free memory available,
which is not enough to run freesurfer, although it would seem like it
should be enough to run the mri_convert command.  Can you free-up more
memory and re-run?   Also, I noticed that you're running the Centos6
build, what OS are you running? Fedora 18?  Does the v5.2 Centos4
freesurfer build work on that?

Nick

On Tue, 2013-01-29 at 19:30 +0100, Knut J Bjuland wrote:

When I run recon-all using freesurfer 5.2 latest beta it will segment
crash.

Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
/home/knutjbj/freesurfer/ernie

   mri_convert /usr/local/freesurfer/subjects/sample-001.mgz
/home/knutjbj/freesurfer/ernie/mri/orig/001.mgz

mri_convert /usr/local/freesurfer/subjects/sample-001.mgz
/home/knutjbj/freesurfer/ernie/mri/orig/001.mgz
Segmentation fault
Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC
2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013

For more details, see the log file
/home/knutjbj/freesurfer/ernie/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Knut J
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Tue Jan 29 20:26:29 CET 2013
/home/knutjbj/freesurfer/ernie
/usr/local/freesurfer/bin/recon-all
-i /usr/local/freesurfer/subjects/sample-001.mgz -i /usr/local/freesurfer/subjects/sample-002.mgz -s ernie
subjid ernie
setenv SUBJECTS_DIR /home/knutjbj/freesurfer
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  192659 
maxlocks unlimited
maxsignal192659 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:  24683456 455644   24227812  0  66580  77648
-/+ buffers/cache: 311416   24372040
Swap: 49337340  0   49337340


program versions used
$Id: recon-all,v 1.379.2.54 2013/01/15 22:31:19 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/01/29-19:26:29-GMT  BuildTimeStamp: Jan 17 2013 00:19:38  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: root  Machine: super-knut  Platform: Linux  PlatformVersion: 3.7.4-204.fc18.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/01/29-19:26:29-GMT  BuildTimeStamp: Jan 17 2013 00:19:38  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: root  Machine: super-knut  Platform: Linux  PlatformVersion: 3.7.4-204.fc18.x86_64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/01/29-19:26:29-GMT  BuildTimeStamp: Jan 17 2013 00:19:38  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: root  Machine: super-knut  Platform: Linux  PlatformVersion: 3.7.4-204.fc18.x86_64  CompilerName

Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19

[Knut J Bjuland]

On 29. jan. 2013 21:16, Nick Schmansky wrote:
> does v5.1 work on this system?
no

> does the centos4_x86_64 v5.2 build work?
no.


I have filed a bug report on 
https://bugzilla.redhat.com/show_bug.cgi?id=905638 . It might be problem 
with mri_convert and glibc interaction.

Knut J
>
> n.
>
> On Tue, 2013-01-29 at 20:33 +0100, Knut J Bjuland wrote:
>> Hi Nick
>>
>> I reran dicom import from /usr/local/freesurfer/subject/sample*. I had
>> 24254940 kB free memory but I still got a segmentation error.I used
>> sample data from /usr/local/freesurfer/subject. Do you think it is a
>> glibc bug in Fedora 18. It contain glibc-2.16-28.fc18.x86_64.
>>
>>
>> This error showed up in my dmesg log.
>>
>> [  175.413292] mri_convert[1350]: segfault at 0 ip 0037e092fbda sp
>> 7fff0a9dc2c8 error 4 in libc-2.16.so[37e080+1ad000]
>>
>>
>> Knutj
>>
>>
>>
>> On 29. jan. 2013 19:47, Nick Schmansky wrote:
>>> Knut,
>>>
>>> I noticed in the log that there was only 284KB of free memory available,
>>> which is not enough to run freesurfer, although it would seem like it
>>> should be enough to run the mri_convert command.  Can you free-up more
>>> memory and re-run?   Also, I noticed that you're running the Centos6
>>> build, what OS are you running? Fedora 18?  Does the v5.2 Centos4
>>> freesurfer build work on that?
>>>
>>> Nick
>>>
>>> On Tue, 2013-01-29 at 19:30 +0100, Knut J Bjuland wrote:
>>>> When I run recon-all using freesurfer 5.2 latest beta it will segment
>>>> crash.
>>>>
>>>> Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013
>>>> x86_64 x86_64 x86_64 GNU/Linux
>>>> /home/knutjbj/freesurfer/ernie
>>>>
>>>> mri_convert /usr/local/freesurfer/subjects/sample-001.mgz
>>>> /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz
>>>>
>>>> mri_convert /usr/local/freesurfer/subjects/sample-001.mgz
>>>> /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz
>>>> Segmentation fault
>>>> Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC
>>>> 2013 x86_64 x86_64 x86_64 GNU/Linux
>>>>
>>>> recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013
>>>>
>>>> For more details, see the log file
>>>> /home/knutjbj/freesurfer/ernie/scripts/recon-all.log
>>>> To report a problem, see
>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>>
>>>> Knut J
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> 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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Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19

[Knut J Bjuland]

NIck

The MRI_convert with debug information ran correctly aside from the leaks 
detected by valgrind. I manage to import sample-001,mgz into ernie using 
mri_convert with debuginfo.

There is more updated info athttps://bugzilla.redhat.com/show_bug.cgi?id=905638.

Knut




On 30. jan. 2013 17:52, Nick Schmansky wrote:
> Knut,
>
> thanks for testing the other two builds and for filing the report.  i
> noticed they had you run valgrind.  if you want, i've put a debug build of
> mri_convert here:
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
>
> running it in valgrind i think would output source code line numbers of
> where its going wrong, which would be a big help.
>
> Nick
>
>
>> On 29. jan. 2013 21:16, Nick Schmansky wrote:
>>> does v5.1 work on this system?
>> no
>>
>>> does the centos4_x86_64 v5.2 build work?
>> no.
>>
>>
>> I have filed a bug report on
>> https://bugzilla.redhat.com/show_bug.cgi?id=905638 . It might be problem
>> with mri_convert and glibc interaction.
>>
>> Knut J
>>> n.
>>>
>>> On Tue, 2013-01-29 at 20:33 +0100, Knut J Bjuland wrote:
>>>> Hi Nick
>>>>
>>>> I reran dicom import from /usr/local/freesurfer/subject/sample*. I had
>>>> 24254940 kB free memory but I still got a segmentation error.I used
>>>> sample data from /usr/local/freesurfer/subject. Do you think it is a
>>>> glibc bug in Fedora 18. It contain glibc-2.16-28.fc18.x86_64.
>>>>
>>>>
>>>> This error showed up in my dmesg log.
>>>>
>>>> [  175.413292] mri_convert[1350]: segfault at 0 ip 0037e092fbda sp
>>>> 7fff0a9dc2c8 error 4 in libc-2.16.so[37e080+1ad000]
>>>>
>>>>
>>>> Knutj
>>>>
>>>>
>>>>
>>>> On 29. jan. 2013 19:47, Nick Schmansky wrote:
>>>>> Knut,
>>>>>
>>>>> I noticed in the log that there was only 284KB of free memory
>>>>> available,
>>>>> which is not enough to run freesurfer, although it would seem like it
>>>>> should be enough to run the mri_convert command.  Can you free-up more
>>>>> memory and re-run?   Also, I noticed that you're running the Centos6
>>>>> build, what OS are you running? Fedora 18?  Does the v5.2 Centos4
>>>>> freesurfer build work on that?
>>>>>
>>>>> Nick
>>>>>
>>>>> On Tue, 2013-01-29 at 19:30 +0100, Knut J Bjuland wrote:
>>>>>> When I run recon-all using freesurfer 5.2 latest beta it will segment
>>>>>> crash.
>>>>>>
>>>>>> Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013
>>>>>> x86_64 x86_64 x86_64 GNU/Linux
>>>>>> /home/knutjbj/freesurfer/ernie
>>>>>>
>>>>>>  mri_convert /usr/local/freesurfer/subjects/sample-001.mgz
>>>>>> /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz
>>>>>>
>>>>>> mri_convert /usr/local/freesurfer/subjects/sample-001.mgz
>>>>>> /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz
>>>>>> Segmentation fault
>>>>>> Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC
>>>>>> 2013 x86_64 x86_64 x86_64 GNU/Linux
>>>>>>
>>>>>> recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100
>>>>>> 2013
>>>>>>
>>>>>> For more details, see the log file
>>>>>> /home/knutjbj/freesurfer/ernie/scripts/recon-all.log
>>>>>> To report a problem, see
>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>>>>
>>>>>> Knut J
>>>>>> ___
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>> 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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[Freesurfer] cvs freesurfer cvs [checkout aborted]: cannot expand modules

[Knut J Bjuland]

Hi

could you please add  information about how to download from cvs?

cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot 
checkout -P -r  dev

Give this error message

cvs [checkout aborted]: must specify at least one module or directory

Knut J
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[Freesurfer] read only cvs server is down

[Knut J Bjuland]

When I tries to download Freesurfer 5.2.0 beta source I get this error message.

cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P 
dev
cvs server: cannot find module `dev' - ignored
cvs [checkout aborted]: cannot expand modules


Knut J
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[Freesurfer] surface area mesurment and qatools

[Knut J Bjuland]

Hi

What would be the best way to measure cortical surface either the white 
surface area or pial surface? Is the total surface area calculated by 
mris_anatomical the same pial surface?
When using QA tool which article should I cite?

Knut J
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[Freesurfer] Updated info for freesurfer 5.2 on Fedora 18. update from Bugzilla. Freesurfer used unsupported, nonstandard salt to crypt()

[Knut J Bjuland]

HI

I have copied the info from Bugzilla.


Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=905638 Patsy 
Franklin  changed: What |Removed |Added 
 
Flags|needinfo?(pfrankli@redhat.c | |om) | 
Flags|needinfo?(pfrankli@redhat.c | |om) | --- Comment #27 from Patsy 
Franklin  --- The most immediate solution is for 
the application to be changed to use a compliant crypt salt value. After 
further investigation, we found that the application is passing 
unsupported, nonstandard salt to crypt(). This will result in crypt() 
returning NULL and setting errno to EINVAL. It does not appear that the 
application is checking for a NULL return value from crypt. It also 
appears that the application is using this NULL return value in a 
subsequent function call resulting in a segmentation fault. Previously 
glibc would accept unsupported salt values, but newer versions of the 
library have become stricter. We are currently reviewing the 
implementation to see if the accepted salt values can be expanded while 
still meeting our standards compliance requirements.
--

Knut J
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Re: [Freesurfer] mri_info crashing (bits stored vs bits allocated?)

[Knut J Bjuland]

HI

I have similar problem and filled a bug report at.


Product: Fedorahttps://bugzilla.redhat.com/show_bug.cgi?id=905638  Patsy
Franklin  changed: What |Removed |Added

Flags|needinfo?(pfrankli@redhat.c  | |om) |
Flags|needinfo?(pfrankli@redhat.c  | |om) | --- Comment #27 from Patsy
Franklin  --- The most immediate solution is for
the application to be changed to use a compliant crypt salt value. After
further investigation, we found that the application is passing
unsupported, nonstandard salt to crypt(). This will result in crypt()
returning NULL and setting errno to EINVAL. It does not appear that the
application is checking for a NULL return value from crypt. It also
appears that the application is using this NULL return value in a
subsequent function call resulting in a segmentation fault. Previously
glibc would accept unsupported salt values, but newer versions of the
library have become stricter. We are currently reviewing the
implementation to see if the accepted salt values can be expanded while
still meeting our standards compliance requirements.
--

Knut J











On 03/20/2013 09:59 PM, Bruce Fischl wrote:
> Hi John
>
> if you email it to me I'll take a look
> Bruce
> On Wed, 20 Mar 2013, Ostuni, John
> (NIH/NINDS) [E] wrote:
>
>> We have a data set that mri_info cannot work with.
>>
>> We've tried multiple architectures and freesurfer versions, but mri_info 
>> either crashes with segmentation fault or generates errors such as
>> *** glibc detected *** mri_info: free(): invalid pointer: 0x006b 
>> ***
>>
>> One feature of the data set is that the bits stored(12) is different than 
>> the bits allocated(16).
>> Could this be the problem?
>>
>> I have an anonymized version of the data set I can upload if that helps.
>>
>> Thanks for any assistance,
>>John
>>
>>
>>
>> ___
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>>
>>
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> at
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> properly
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[Freesurfer] subj: Undefined variable.

[Knut J Bjuland]

Hi

Strange error in tracula 5.1. When I use a dmric file that have worked 
before I now get
subj: Undefined variable.
I may have uppgrade tcsh. Is there any fix to get tracula-preproc to use 
the id from dmric files


Knut J
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Re: [Freesurfer] CUDA Error when runnign freesurfer

[Knut J Bjuland]

Hi

can you send part of recon-all.log and do recon-all -i 242.nii.gz -s 
242_FS -nuintensitycor-3T -nocanorm -openmp 8 -use-cuda -hippo-subfields 
-all -debug



Knut J

On 06/29/2013 06:06 PM, Salil Soman wrote:

Hi,

I am running freesurfer 5.3 on an ubuntu 13.04 with a nvidia card and 
the the CUDA drivers installed. I am getting the following error when 
I try using the use-cuda command:


Testing for CUDA device:
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVIDIA Corporation
Built on Fri_Sep_21_17:28:58_PDT_2012
Cuda compilation tools, release 5.0, V0.2.1221

Acquiring CUDA device
Using default device
ERROR: Unable to acquire a CUDA device!
Linux Baldrick 3.5.0-27-generic #46-Ubuntu SMP Mon Mar 25 19:58:17 UTC 
2013 x86_64 x86_64 x86_64 GNU/Linux


I am running the following freesurfer command:

recon-all -i 242.nii.gz -s 242_FS -nuintensitycor-3T -nocanorm -openmp 
8 -use-cuda -hippo-subfields -all


Any suggestions on how I can fix this problem?

Best wishes,

Sal


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[Freesurfer] Crash in mri_register_ca during recon-all -base id -tp id1 -tp id2 -all

[Knut J Bjuland]

Hi,
I have some trouble running recon-all longitudinal pipelines. When 
recon-all comes to mri_register_ca it crashes without giving a message, 
even tough 8g ram was available. I have run the program with -debug. Is 
there any other option I may use? The system is running Rocks 6.0 
(Mamba), and it uses Slurm queue system.

Can I use the FreeSurfer 5.3 longitudinal process with data processed 
with FreeSurfer 5.1? I wish to use the new Longitudinal linear mixed 
effects model  MATLAB tools.

Knut J
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[Freesurfer] crash during longitudinal process when it run mri_ca_register

[Knut J Bjuland]

Hi,
I have run recon-al longitudinal process on abel cluster with this command 
recon-all -base @filename@_template -tp @filename@ -tp @filename@v2 -all 
-debug. However, it crashed or is killed when it ran mri_ca_register. 
 I have looked through the log, and I have not found a reason for it being 
killed even tough I added -debug. The cluster is running sbatch and CentOS 
release 6.4. Are there any debug options I can add or are there any 
debugversion of mri_ca_register I can download? This happen every time I run 
the program. I have asked for 8g ram when ran the program.

Best regards
Knut Jørgen Bjuland
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Re: [Freesurfer] crash during longitudinal process when it run mri_ca_register during CA reg.

[Knut J Bjuland]

When I run recon-all -base 1_template -tp 1_first -tp 1_secon -all 
-debug. It crash during CA Reg Thu Sep 12 19:59:01 CEST 2013. I can send 
the rest of the log.

Knut J




#--
#@# CA Reg Thu Sep 12 19:59:01 CEST 2013
/cluster/home/kjbjuland/freesurfer/long/NTNU_PRE_023_template/mri

 mri_ca_register -nobigventricles -T transforms/talairach.lta 
-align-after -mask
 brainmask.mgz norm.mgz 
/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_a

ll_2008-03-26.gca transforms/talairach.m3z

not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log


 === NUMBER OF OPENMP THREADS = 1 ===
reading input volume 'norm.mgz'...
reading GCA 
'/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'...

label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.55 (predicted orig area = 5.2)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
 pass 1 of 1 
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
: dt=0.000, rms=0.932, neg=0, invalid=96777











On 09/12/2013 10:14 AM, Knut J Bjuland wrote:

Hi,
I have run recon-al longitudinal process on abel cluster with this 
command recon-all -base @filename@_template -tp @filename@ -tp 
@filename@v2 -all -debug. However, it crashed or is killed when it ran 
mri_ca_register.
 I have looked through the log, and I have not found a reason for it 
being killed even tough I added -debug. The cluster is running sbatch 
and CentOS release 6.4. Are there any debug options I can add or are 
there any debugversion of mri_ca_register I can download? This happen 
every time I run the program. I have asked for 8g ram when ran the 
program.


Best regards
Knut Jørgen Bjuland


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Re: [Freesurfer] Resolved, crash during longitudinal process when it run mri_ca_register during CA reg.

[Knut J Bjuland]

Closed, not bug in Freesurfer.


On 09/12/2013 10:31 PM, Knut J Bjuland wrote:
When I run recon-all -base 1_template -tp 1_first -tp 1_secon -all 
-debug. It crash during CA Reg Thu Sep 12 19:59:01 CEST 2013. I can 
send the rest of the log.

Knut J




#--
#@# CA Reg Thu Sep 12 19:59:01 CEST 2013
/cluster/home/kjbjuland/freesurfer/long/NTNU_PRE_023_template/mri

 mri_ca_register -nobigventricles -T transforms/talairach.lta 
-align-after -mask
 brainmask.mgz norm.mgz 
/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_a

ll_2008-03-26.gca transforms/talairach.m3z

not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log


 === NUMBER OF OPENMP THREADS = 1 ===
reading input volume 'norm.mgz'...
reading GCA 
'/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'...

label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.55 (predicted orig area = 5.2)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
 pass 1 of 1 
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
: dt=0.000, rms=0.932, neg=0, invalid=96777











On 09/12/2013 10:14 AM, Knut J Bjuland wrote:

Hi,
I have run recon-al longitudinal process on abel cluster with this 
command recon-all -base @filename@_template -tp @filename@ -tp 
@filename@v2 -all -debug. However, it crashed or is killed when it 
ran mri_ca_register.
 I have looked through the log, and I have not found a reason for it 
being killed even tough I added -debug. The cluster is running sbatch 
and CentOS release 6.4. Are there any debug options I can add or are 
there any debugversion of mri_ca_register I can download? This happen 
every time I run the program. I have asked for 8g ram when ran the 
program.


Best regards
Knut Jørgen Bjuland


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[Freesurfer] freesurfer map with low efftive size

[Knut J Bjuland]

How to detect group differences between groups with low group size like 
for instant n=8 vs n=50?
  Are there any statistics measures I could use like looking at 
interaction between group and gender, or should I use doss? Is it 
feasible to design a custom based design matrix?

Knut J
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[Freesurfer] longitudinal 5.3 used with baseline fs 5.1 recon-all

[Knut J Bjuland]

Hi,we have finished cross sectional scanworkups in Freesurfer 5.1 and gone 
through qa. Can we use these scanworkups for further processing in the 
longitudinal stream in Freesurfer 5.3? 
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Re: [Freesurfer] TRACULA exists uncompleted

[Knut J Bjuland]

Hi

You should do cat -n 
$RAW_DATA/Bled_Jean_Jacques/TENSEUR_50_directions_ASSET_10/20121113_141004COMA201210s010a1001.bvec 
and cat -n set bvalfile = 
$RAW_DATA/Bled_Jean_Jacques/TENSEUR_50_directions_ASSET_10/20121113_141004COMA201210s010a1001.bval 
to look for empty lines. Trac-all -prep -c runscript crashed because 
bvecs and bvals don't have the same number of entries.



Knut J


On 11/22/2013 10:34 PM, Emad Ahmadi wrote:

Hello,

I'm using TRACULA for analyzing a number of cases, and I've made a file to
successively run the three stages of pre-processing, model fitting, and
pathways reconstruction which is attached (ter1.tcsh). I've also attached
the configuration file I'm using (dmrircTer1.cshell).

The problem is that TRACULA exists uncompleted. I've attached the log
files. I'd really appreciate it if you let me know where I'm making some
sort of a mistake.

All the best,
Emad


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Re: [Freesurfer] Fwd: Problems with longitudinal analysis

[Knut J Bjuland]

Hi Jorge

I have tried both methods. I now get image more like the one in your 
paper.  Can you take a look at my script please? I have used fwhm at 30 mm.
 How did you make the figure in Spatiotemporal Linear Mixed Effects 
Modeling for the Mass-univariate Analysis of Longitudinal?

Can you please send me link to the matlab scripts?


Best
Knut Jørgen


On 12/05/2013 08:43 PM, jorge luis wrote:


Hi Knut

There are a few confusing things in your question post. First, it 
seems that your attached images are depicting /p-values/. We usually 
use /-log10(pvalue)/ format for visualization in tksurfer. The sig.mgh 
file saved by lme should be in that format. However we didn't use 
tksurfer to build the figures for the paper you mentioned. We instead 
just used matlab-based geometric objects and figures. Second, for 
mass-univariate analyses the contrast matrix is given to lme as a 
matlab structure /CM.C = [0 0 1 0 0 0] /not a plain matrix C. Perhaps 
you should try first the vertex-wise lme model to ensure that all your 
parameters (design matrix, data matrix, contrast matrix, etc...) are 
right and then give it a try to the more complex spatio-temporal lme 
model using the same parameters.


eg./lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex);/

/Then you can compare the results to have a better idea about what is 
going on. /


/Best/
/-Jorge/


El Jueves 5 de diciembre de 2013 13:29, Martin Reuter 
 escribió:


Hi Jorge,

this was on the freesurfer list. Do you know what is going on ?

Best, Martin


 Original Message 
Subject:[Freesurfer] Problems with longitudinal analysis
Date:   Wed, 4 Dec 2013 22:04:07 +0100
From:   Knut J Bjuland 
<mailto:knutjor...@outlook.com>
To: freesurfer 
<mailto:freesurfer@nmr.mgh.harvard.edu>



Hi,

I have used a linear mixed model for longitudinal data analysis on a
FreeSurfer 5.3, Matlab 2013b on a system with Ubuntu 12.04.

I used mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi
lh --meas thickness --out lh.thickness.mgh to concatenate thickness surf
files, and smoothed with mri_surf2surf --hemi lh --s fsaverage --sval
lh.thickness.mgh --tval lh.thickness_sm30.mgh --fwhm-trg 30 --cortex
–noreshape.

I then used the same command and options in a Matlab script, as shown at
http://freesurfer.net/fswiki/LinearMixedEffectsModel  found in the
example for mass-univariate data analyses.

.

I used this design matrix: interception, time, group, group*time,
gender, gender*time, and I used two random effect on interception and
time. I did not compare the two random effect models with one random
effect model.

I used this contrast vector C=[0 0 1 0 0] for these images which are
included in the email.

The script ran fine but when I looked at sig.mgh, it contained many
visible quadrate shapes boxes even after FDR correction, and the
image looks quite different than the image in the paper in Neuroimage
(Spatiotemporal Linear Mixed Effects Modeling for the Mass-univariate
Analysis of Longitudinal ).


Any idea what went wrong here?


Thank you!

Best regards,
Knut Jørgen



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function[F_stats,detvtx,sided_pval]=runlme3(hemi,sel,contrast,out_dir,qdecname)
sel=6;



dir1=sprintf('~/ANALYSIS/lme/%s',out_dir);
%
%http://www.mathworks.com/help/techdoc/ref/exist.html
if exist(dir1,'dir')
display('folder exist')
else
mkdir(dir1)
end






[Y,mri]=fs_read_Y(sprintf('%s.long_thickness.30.mgh',hemi));

% The fsaverage's spherical surface (lh.sphere) and cortex label (lh.cortex.label) were read with:
sphere=fs_read_surf(sprintf('$FREESURFER_HOME/subjects/fsaverage/surf/%s.sphere',hemi));
cortex=fs_read_label(sprintf('$FREESURFER_HOME/subjects/fsaverage/label/%s.cortex.label',hemi));


% read Qdec dat file
Qdec=fReadQdec(qdecname);
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);

Qdec = rmQdecCol(Qdec,1);



label=Qdec(1,:);





X = [ones(length(M),1), M(:,1),M(:,1).^2,M(:,2),M(:,2).*M(:,1),M(:,3) ];
% interception, time, time^2, group, group*time, gender
%contrast
field = 'C';
value=[0 0 0 0 1 0];
% interception, time, time^2, group, group*time, gender
CM=struct(field,value);











[M,Y,ni]=sortData(M,1,Y,sID);



%reads in mgh file
%;
%Thus, our design matrix X was built from matrix M to represent the previo

[Freesurfer] reporting bhvat value from lme

[Knut J Bjuland]

Dear Freesurfers

We are now finishing an article, where we have used linear mixed models 
included in FreeSurfer 5.3 for longitudinal changes between two-time 
points. We have used this model.

Intercept(RF) + centered time+ group + group*centered time + sex(gender).

Everything is clear except for one thing. When we used this contrast 
vector [0 1 0 1 0] to get longitudinal change for the study group, we 
get two bhvat values. How can we calculate these two bhvat values to one 
bhvat vaule in position two and four? Should we just add them together 
after we have been multiple them with the contrast vector, or add them 
as sqrt(a^2+b^2)?


Best regards
Knut Jørgen Bjuland
NTNU
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Re: [Freesurfer] Reporting bhvat value from lme with contrast vector 0 1 0 1 0

[Knut J Bjuland]

Dear freesurfers
We have found a way to calculate the beta for this contrast vector [0 1 
0 1 0].  We multiple the contrast vector with the bhvat collum vector [ 
0 3 4 5 0]T and got  3+5=8. Is this correct?


 How is the information stored in stats.CovBhat?  What is the 
recommended way to present data from univariate lme?


Knut Jørgen













On 02/08/2014 04:10 AM, Knut J Bjuland wrote:

Dear Freesurfers

We are now finishing an article, where we have used linear mixed 
models included in FreeSurfer 5.3 for longitudinal changes between 
two-time points. We have used this model.

Intercept(RF) + centered time+ group + group*centered time + sex(gender).

Everything is clear except for one thing. When we used this contrast 
vector [0 1 0 1 0] to get longitudinal change for the study group, we 
get two bhvat values. How can we calculate these two bhvat values to 
one bhvat vaule in position two and four? Should we just add them 
together after we have been multiple them with the contrast vector, or 
add them as sqrt(a^2+b^2)?


Best regards
Knut Jørgen Bjuland
NTNU


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[Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message

[Knut J Bjuland]

 flirt.fsl 
-ref/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii-in/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii-bins
 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90-searchrz -90 90 
-verbose 0 
-omat/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fsl.mat-init/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fslmat0.trans.mat-schedule
 /usr/local/freesurfer/bin/flirt.newdefault.20080811.schterminate called after 
throwing an instance of'NEWMAT::SingularException'Abort (core dumped) ERROR: 
flirtFedora 
24glibc-2.23.1-8.fc24.x86_64gcc-6.1.1-3.fc24.x86_64libstdc++-6.1.1-3.fc24.x86_64ldd
 /usr/local/freesurfer/bin/flirt.fsl linux-vdso.so.1 (0x7ffe8b6c8000)   
 libz.so.1 => /lib64/libz.so.1 (0x7feaeba06000)libstdc++.so.6 => 
/lib64/libstdc++.so.6(0x7feaeb67e000)libm.so.6 => /lib64/libm.so.6 
(0x7feaeb374000)libgcc_s.so.1 => /lib64/libgcc_s.so.1 
(0x7feaeb15d000)libc.so.6 => /lib64/libc.so.6 (0x7feaead9a000)
/lib64/ld-linux-x86-64.so.2 (0x557ba6f46000)Knut Jørgen Bjuland 
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Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message

[Knut J Bjuland]

Hi  Anastasia

Thanks. I am sending my entire trac-all.log

Knut Jøgen


On 07/12/2016 11:19 PM, Anastasia Yendiki wrote:


Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks!

a.y

On Mon, 11 Jul 2016, Knut J Bjuland wrote:






flirt.fsl -ref
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii 


-in
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii 


-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90
-searchrz -90 90 -verbose 0 -omat
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fsl.mat 


-init
/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fslmat0.trans.mat 


-schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch

terminate called after throwing an instance of
'NEWMAT::SingularException'

Abort (core dumped)

ERROR: flirt





Fedora 24


glibc-2.23.1-8.fc24.x86_64

gcc-6.1.1-3.fc24.x86_64


libstdc++-6.1.1-3.fc24.x86_64

ldd /usr/local/freesurfer/bin/flirt.fsl

linux-vdso.so.1 (0x7ffe8b6c8000)

libz.so.1 => /lib64/libz.so.1 (0x7feaeba06000)

libstdc++.so.6 => /lib64/libstdc++.so.6
(0x7feaeb67e000)

libm.so.6 => /lib64/libm.so.6 (0x7feaeb374000)

libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x7feaeb15d000)

libc.so.6 => /lib64/libc.so.6 (0x7feaead9a000)

/lib64/ld-linux-x86-64.so.2 (0x557ba6f46000)







Knut Jørgen Bjuland






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Wed Jul 13 16:32:42 CEST 2016
/home/knutjbj/subjects
/usr/local/freesurfer/bin/trac-all
-prep -c dmric.4_test
Subject 4_test
SUBJECTS_DIR /home/knutjbj/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer60
build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20160706-3f44648
knutjbj
loalhost
Linux loalhost 4.6.3-300.fc24.x86_64 #1 SMP Fri Jun 24 20:52:41 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  127405 
maxlocks unlimited
maxsignal127405 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   32845380 962006816527136  169380 669817622482108
Swap:  71678968   071678968


Program versions:
$Id: trac-all,v 1.60 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2016/07/13-14:32:42-GMT  BuildTimeStamp: Jul  6 2016 17:01:27  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: knutjbj  Machine: loalhost  Platform: Linux  PlatformVersion: 4.6.3-300.fc24.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2016/07/13-14:32:42-GMT  BuildTimeStamp: Jul  6 2016 17:01:27  CVS:   User: knutjbj  Machine: loalhost  Platform: Linux  PlatformVersion: 4.6.3-300.fc24.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2016/07/13-14:32:42-GMT  BuildTimeStamp: Jul  6 2016 17:01:27  CVS:   User: knutjbj  Machine: loalhost  Platform: Linux  PlatformVersion: 4.6.3-300.fc24.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2016/07/13-14:32:42-GMT  BuildTimeStamp: Jul  6 2016 17:01:27  CVS:   User: knutjbj  Machine: loalhost  Platform: Linux  PlatformVersion: 4.6.3-300.fc24.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2016/07/13-14:32:42-GMT  BuildTimeStamp: Jul  6 2016 17:01:27  CVS:   User: knutjbj  Machine: loalhost  Platform: Linux  PlatformVersion: 4.6.3-300.fc24.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-in

[Freesurfer] Reproducibility of freesurfer analyses across different version of linux

[Knut J Bjuland]

Dear FreeSurfer experts,I found this paper about named “Reproducibility of 
neuroimaging analyses across operating systems” (Glatard et al., 2015).   There 
were differences in cortical morphometry like cortical thicknes between  images 
proscced in the same version of freesurfer with different version of Linux or 
glibc for Freesurfer, and according to the paper, it was caused by how 
different version of glibc handles small single precssion floating numbers. I 
have therefore some questions.
Are there plans for freesurfer to use double floating numbers in steps that may 
be affected by numerical stability? Or can this problem be solved by using 
staticall linking glibc into Freesurfer?
Best regards
Knut Jørgen BjulandPhD candidateNTNU  ___
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Re: [Freesurfer] Reproducibility of freesurfer analyses across different version of linux

[Knut J Bjuland]

On 08/28/2016 05:57 PM, R Edgar wrote:

On 28 August 2016 at 06:59, Knut J Bjuland  wrote:


I found this paper about named “Reproducibility of neuroimaging analyses
across operating systems” (Glatard et al., 2015).   There were differences
in cortical morphometry like cortical thicknes between  images proscced in
the same version of freesurfer with different version of Linux or glibc for
Freesurfer, and according to the paper, it was caused by how different
version of glibc handles small single precssion floating numbers. I have
therefore some questions.

Are there plans for freesurfer to use double floating numbers in steps that
may be affected by numerical stability? Or can this problem be solved by
using staticall linking glibc into Freesurfer?

Freesurfer does use double precision numbers extensively on the CPU
side (on the GPU side of things, I generally went back to singles).
The issue is not one of numeric stability, and going to all-double (or
all-quad) would not remove the differences - they are fundamental to
how floating point arithmetic works. Put simply, for floating point
numbers:
a+(b+c) != (a+b)+c
Any attempt to ignore this fact is going to come to grief at some point.

Freesurfer often has to do things such as "find voxels exceeding
threshold" or "find most likely label for voxel." Operations like this
are always going to be vulnerable to differences in the least
significant bit.

Speaking from a numerical background (I have no experience in
neuroscience), I would suggest embracing this behaviour rather than
trying avoid it (arguably a fool's errand). Use the differences
between different library versions (not just libc, but all the other
numerical libraries Freesurfer uses) to provide an estimate of the
confidence levels/error bounds on your Freesurfer runs. If your
conclusion depends critically on using version x.y.z of a library,
rather than x.y.z+1, then unless you can point to a specific bug in
the library, you probably don't really have a conclusion.

Regards,

Richard

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Hi


Thanksfortheanswer.

Isitpossibletouseascripttoextractinformation 
aboutwhichlibrarythatisusedforeachrecons? 
Orarethereanyothermeanstogetthisinformation?


How do you? "Use the differences between different library versions (not 
just libc, but all the other


numerical libraries Freesurfer uses) to provide an estimate of the confidence 
levels/error bounds on your Freesurfer runs"


Regards

Knut Jørgen



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Re: [Freesurfer] trac-all -path Segmentation fault

[Knut J Bjuland]

Hei

Er det id 2 og 3 du har problemer med? Det ser ut som at du ikke har kjørt 
bedpostx på disse to idene og jeg ser at du ikke har kjørt trac-all -prep 
utifra logfilen
.
[/work/projects/nn9208k/subjects/LMR/dtitracula/2]: ls
dlabel  dmri  dpath  scripts

[/work/projects/nn9208k/subjects/LMR/dtitracula/3]: ls
dlabel  dmri  dpath  scripts

Hilsen

Knut Jørgen


On 21 Sep 2016, at 11:14, Lars M. Rimol 
mailto:lari...@gmail.com>> wrote:

trac-paths exited with ERRORS

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[Freesurfer] trouble with mailing list

[Knut J Bjuland]

Hi

I have posted two posts to the FreeSurfer mailing list that does not appear in 
the archive. Are there any trouble with the list or are there a trouble with my 
mailing client?



Knut Jørgen Bjuland PhD
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Re: [Freesurfer] trouble with mailing list

[Knut J Bjuland]

Are there trouble with messages that contains attachments like jpgs? I have 
sent two questions with pictures that I have received post acknowledgment, but 
they do no appear in the mailing list.

Thanks
Knut Jørgen



On 21 Nov 2016, at 17:34, Z K 
mailto:zkauf...@nmr.mgh.harvard.edu>> wrote:

This seems to be an issue as there are other recently confirmed cases of
emails missing from the archive. In these instances, messages are
distributed to the freesurfer support list, but do not show up on the
mail-archives.com<http://mail-archives.com> website.

We will look into the matter but it appears to be more of an issue with
the mail-archives.com<http://mail-archives.com> website (which is out of out 
hands) than the
Freesurfer support list. Hopefully the issue will be resolved shortly.

Thanks,
-Zeke



On 11/21/2016 11:24 AM, Knut J Bjuland wrote:
Hi

I have posted two posts to the FreeSurfer mailing list that does not appear in 
the archive. Are there any trouble with the list or are there a trouble with my 
mailing client?




Knut Jørgen Bjuland PhD


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[Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.

[Knut J Bjuland]

Hi, 

I would like to to obtain FA data from the white matter ROIs in 
WMParcStatsLUT.txt. or FreeSurferColorLUT.txt. So would it work to coregister a 
DWI file, either produced by  dt_recon (or perhaps better - from Tracula) and 
an anatomy file in atlas space and then use WMParcStatsLUT.txt or 
FreeSurferColorLUT.txt  (not sure which) to obtain the wm ROIs containing FA 
data. And then register the aparc+aseg.mgz to the FA image and use mri_segstats 
to retrieve FA data from the white matter ROIs. 

I have done this: 
# Register DTI file to individual anatomy space
1) dt_recon --i 1/dti/1.dcm --s 001 --b 1/dti/bval 1/dti/bvec --o 1/dtrecon

# Register fa.nii to wmparc.mgz and aparc+aseg.mgz 
2) 
mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 
001v4/mri/wmparc.mgz   --inv --interp nearest --o 1/mri/aseg2DTI.mgz
   --no-save-reg
mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 
001v4/mri/aparc+aseg.mgz --inv --interp nearest --o 1/mri/aparc-aseg2DTI.mgz 
--no-save-reg

3) It works for wmparc, in that I get data that range from 0.0 to 0.4 with mean 
= 0.04 (which is a little low for FA values): 
mri_segstats --seg 1/mri/wmparc2DTI.mgz --ctab 
/usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i   1/dtrecon/fa.nii 
--sum fa.stats_wm-lh-medialorbitofrontal

But for aparc+aseg, it doesn't produce any data:
mri_segstats --seg 1/mri/aparc-aseg2DTI.mgz --ctab 
/usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i   1/dtrecon/fa.nii 
--sum fa.stats_wm-lh-medialorbitofrontal

output:
Found   1 segmentations
Computing statistics for each segmentation
  0   3014  wm-lh-medialorbitofrontal   0   0.000

Reporting on   0 segmentations
mri_segstats done



Questions: 
1) Am I right to use FreeSurferColorLUT.txt   and not WMParcStatsLUT.txt? 
2) In order to get FA data from the wm regions corresponding to cortical ROIs, 
should I use the FA registrated to wmparc.mgz  or aparc+aseg.mgz?
3) If I want to use Tracula DTI files instead, which file do I choose: Is it 
FA_ditifit.nii?


sincerely yours,

Knut Jørgen Bjuland PhD


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Re: [Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.

[Knut J Bjuland]

Hi  Anastasia

If I want to use Tracula DTI files instead, which file do I choose: Is it 
FA_ditifit.nii?

Best

Knut Jørgen



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[Freesurfer] Topup before trac-all

[Knut J Bjuland]

Hi,

I would like to preprocess my dti data with topup (from FSL) before running 
trac-all. Is this a sensible approach? When I tried  running trac-all -prep 
with the output file from topup (*_hifi_nodif.nii.gz) I got an error message:


mv -f /usit/abel/<>/topuop/146/dmri/bvecs 
/usit/abel/<...>/topuop/146/dmri/bvecs.norot
xfmrot /usit/abel/<...>/topuop/146/dmri/dwi.ecclog 
/usit/abel/<...>topuop/146/dmri/bvecs.norot 
/usit/abel/<...>/topuop/146/dmri/bvecs

R: Subscript out of range.



It seems that there's a problem with bvecs and bvals. Should I reorganise my 
bvec and bvals?


Thank you!


Knut J Bjuland
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[Freesurfer] How can I use mri_vol2surf to map the white matter volume cortical surface in order to generate a white matter map that is similar to the gray matter volume map produced by mris_preproc?

[Knut J Bjuland]

DearFreeSurferexperts,

HowcanIusemri_vol2surftomapthewhitemattervolumecorticalsurfaceinordertogenerateawhitemattermapthatissimilartothegraymattervolumemapproducedbymris_preproc? 



ShouldIusebinarymaskcreatedinMatlabtoremovelabelsthatarenotwhitematter?


Best regards

KnutJørgenBjuland

NTNU

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[Freesurfer] follow up on question asked during freesurfer course

[Knut J Bjuland]

Hi 

To compare data different version of Freesurfer I was advised to bring it into 
the same version, and the subjects are the same.
 I used recon-all  –make –all –s to convert from Freesurfer 4.30 to Freesurfer 
5.1. The results are now more similar but there are some differences for weak 
correlations. When I use mri_glmfit I get a different output fwhm with the two 
different dataset using Freesurfer 5.1.  Would you recommend me to rerun the 
converted subject using recon-all –all? I usually get similar result on 
hemisphere and results that are more similar than before on the other 
hemisphere. 
I am enclosing two representative jpg files. I have used smoothing at   fwhm 60 
mm. 

Best regards
Knut J Bjuland 

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[Freesurfer] What effect will it give if software is used to change flip angle on a dicom image? Can Freesurfer change flip angle?

[Knut J Bjuland]

Hi
I have problem with two dataset processed with different version of 
Freesurfer but with the same subject. I am able to import the data set 
proceed with Freesurfer 4.30 into Freesurfer 5.1. But there was used 
some proprietary programs at FS 430 data for motion correction and 
contrast enhancement before the dicom files was input into Freesurfer. 
These proprietary programs change the flip angle from 7 degrees to 
401.07 degrees.
I am able to replicate findings that survive FDR but I get quite 
different result for findings that do not survive FDR. My theory is that 
the proprietary programs change the dicom in such manner that it gives a 
new dicom files. Is this correct? I do not have access to these programs 
anymore.
What effect will it give if software is used to change flip angle on a 
dicom image? Can I use Freesurfer to force the flip angle back to 7 
degree? I converted the files from Freesurfer 4.30 to Freesurfer 5.1 
using recon –make all –s {subject}. I am enclosing the mri_info of the 
first files in Freesurfer pipeline.


The vox to ras and ras to voxel is also changed. What effect will this 
have?



Knut J
Volume information for 007_fs51/mri/orig/001.mgz
  type: MGH
dimensions: 256 x 256 x 128
   voxel sizes: 1., 1., 1.3300
  type: SHORT (4)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -85.1, zend: 85.1
TR: 2730.00 msec, TE: 3.45 msec, TI: 1000.00 msec, flip angle: 7.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =   0.0349, y_r =  -0.0035, z_r =  -0.9994, c_r = 4.7335
  : x_a =  -0.9994, y_a =  -0.0001, z_a =  -0.0349, c_a =28.6033
  : x_s =  -0., y_s =  -1., z_s =   0.0035, c_s =   -19.5607

talairach xfm : 
Orientation   : PIL
Primary Slice Direction: sagittal

voxel to ras transform:
0.0349  -0.0035  -1.329285.7802
   -0.9994  -0.0001  -0.0464   159.5116
   -0.  -1.   0.0046   108.1415
0.   0.   0. 1.

voxel-to-ras determinant -1.33

ras to voxel transform:
0.0349  -0.9994  -0.   156.4207
   -0.0035  -0.0001  -1.   108.4594
   -0.7514  -0.0262   0.002668.3587
0.   0.   0. 1.
Volume information for 007/mri/orig/001.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 256.000
   dof: 1
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2730.00 msec, TE: 3.45 msec, TI: 1000.00 msec, flip angle: 
401.07 degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 1.
  : x_a =   0., y_a =   0., z_a =   1., c_a =-1.
  : x_s =   0., y_s =  -1., z_s =   0., c_s = 1.

talairach xfm : 
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0.   129.
0.   0.   1.  -129.
0.  -1.   0.   129.
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0.   129.
   -0.  -0.  -1.   129.
   -0.   1.  -0.   129.
0.   0.   0. 1.
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Re: [Freesurfer] Newbie question: mean/stddev for volumes and thicknesses in an atlas

[Knut J Bjuland]

Hi 

I use this script to extract mean cortical thickness. The script is available  
under GNU GPL3.


Knut J Bjuland

> From: souheil.in...@nih.gov
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Mon, 16 Jan 2012 23:04:09 -0500
> Subject: [Freesurfer] Newbie question: mean/stddev for volumes and
> thicknesses in an atlas
> 
> Hi All,
> 
> I have a very small set of patients and I would like to compare the volumes 
> of subcortical structures and thickness across the cortex to those of a large 
> normative set.  I don't need all the underlying data, just means and standard 
> deviations.  Is such a set of measures available?
> 
> Thanks,
> Souheil
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global_thickness.sh
Description: application/shellscript
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[Freesurfer] update version of tksurfer and freeview

[Knut J Bjuland]

Hi

When I was at the Freesurfer course in December we used an updated version if 
Tksurfer and Freeview. Is it possible to get a download link to thesse new 
version of Tksurfer and Freeview please?

Cheers
Knut J
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[Freesurfer] autmatic image with panel of hemisphere made by script

[Knut J Bjuland]

I have used Tksurfer to make image from cross subject statistics maps in 
mgh files. Is it possible to use a script to make image with both 
hemisphere in lateral and medial view.  I would also like to display p 
values as 10^-log(p). Is this possible? Can I use Matlat or FDR? How can 
I produce image with 500 dpi in tksurfer?

Knut J
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Re: [Freesurfer] autmatic image with panel of hemisphere made by script

[Knut J Bjuland]

Hi

Thanks.

Python was the first programing languages that I learned along with Java.

Cheers
Knut Jørgen

On 08. feb. 2012 06:42, Michael Waskom wrote:

Hi,

On the off chance that you are comfortable with Python, you may find 
that PySurfer <http://pysurfer.github.com/> provides a more pleasant 
scripting environment than the tcl-based TkSurfer interface :)


Best,
Michael

On Tue, Feb 7, 2012 at 12:46 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


Hi Knut, you can check out my script called tksnap (uses accopanying
mytks.tcl). It will take pics in different orientations. Note: this is
not a supported script, so it's up to you to figure out what it
does and
how it does it. I provide it as a way to help you figure this
stuff out.
If you don't know csh and tcl, then it's not going to be much use to
you. Good luck!
doug

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tksnap
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mytks.tcl


Knut J Bjuland wrote:
> Hi Bruce
>
>
> Is it possible to use ascript to create a similar figure to the jpg
> file I am  attaching?
>
> Knut J
>
>
>
> On 07. feb. 2012 15:09, Bruce Fischl wrote:
>> Hi Knut
>>
>> you can use  a tcl script in tksurfer if you want. You are probably
>> better off doing the 10^-log(p) on your own and saving it as a
>> separate overlay. There are plenty of tcl scripts in the
distribution
>> as examples. A simple one would be:
>>
>> set val $home/$subject/label/$hemi.your_overlay.mgz
>> puts "loading overlay $val"
>> sclv_read_binary_values sclv_current_field
>> redraw
>> save_tiff $odir/$hemi.your_overlay.lateral.tif
>> rotate_brain_y 180
>> redraw
>> save_tiff $odir/$hemi.your_overlay.medial.tif
>>
>>
>> put that in a file named something.tcl then load tksurfer with -tcl
>> something.tcl
>>
>> I don't know about the 500dpi though, sorry.
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Tue, 7 Feb 2012, Knut J Bjuland wrote:
>>
>>> I have used Tksurfer to make image from cross subject statistics
>>> maps in
>>> mgh files. Is it possible to use a script to make image with both
>>> hemisphere in lateral and medial view.  I would also like to
display p
>>> values as 10^-log(p). Is this possible? Can I use Matlat or
FDR? How
>>> can
>>> I produce image with 500 dpi in tksurfer?
>>>
>>> Knut J
>>> ___
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
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>>>
>>>
>>>
>>
>>
>> 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
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Compliance
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>>
>>
>>
>
>
>

>
>

>
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Re: [Freesurfer] How do I compile a table from several hundred "wmparc.stats" files?

[Knut J Bjuland]

Hi

You could try to use use python or similar languages to combine several 
text files to one files with wmparc.stats.


Knut J

On 09. feb. 2012 21:57, Tracy Abildskov wrote:
> Hello surfers:
>
> I was wondering if there is a command like "aparcstats2table" or
> "asegstats2table" that would work with data in the "wmparc.stats"
> files. If I needed to compile the data on just a few scans I would not
> post this question. The problem is I need to compile this list on
> several hundred analyzed scans.
>
> Thank you, in advance, for any help you can offer.
>
> BA
>
> P.S. I know that wmparc.stats is not as good as aseg.ststs however it
> is the only place I can find some of this types of data.
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[Freesurfer] How to access information in gamma.mgh and gammavar.mgh?

[Knut J Bjuland]

Dear Sirs/Madams

How to access information in gamma.mgh and gammavar.mgh? Which command 
should I use? Since it not explained in the tutorial. I want to use it 
to calculate effective population size? How large population size is 
needed to demonstrate a deviation between to population in cortical 
thickness?

Best regards

Knut J
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[Freesurfer] small difference in recon-all for Ubuntu 11.10 and Centos 5.7

[Knut J Bjuland]

Hi

I used recon-all on two different system one with Ubuntu 11.10 and a 
cluster with Centos 5.7. When I compare the recon-all of these two 
recon-all run I see that there is a small difference. Is this difference 
caused by difference in math libraries, and difference in the way 
floating point is handle? Is there any way to get around this problem 
and get Freesurfer to behave is similar way on Centos 5.7 system as it 
did on the Ubuntu 11.10.


Knut J

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Re: [Freesurfer] Trac-all on a cluster with PBS/torque

[Knut J Bjuland]

Hi Anastasia


I think this hack was also added

##  Steinar, steinar, commnet out this to fool the program to run under PBS
##  date 20 april 2012
##  hack

#if ($?PBS_JOBID) then
#  echo "ERROR: Do not submit $ProgName as a job with pbsubmit or qsub."
#  echo "ERROR: Run it directly on the command line."
#  echo "ERROR: If run on the cluster, $ProgName will submit the jobs 
for you."
#  echo "ERROR: Each subject listed in your dmrirc will be submitted as 
a job."
#  exit 1
#endif

## end hack

Should I revert those changes? I changed to fsl_sub because the cluster 
I am using had my modifcation to fsl_sub. Should I change back?

Knut J







On 04/27/2012 05:06 PM, Anastasia Yendiki wrote:
>
> Hi Knut - If I understand correctly, your modification was replacing 
> "fsl_sub_seychelles" with "fsl_sub"?
>
> a.y
>
> On Fri, 27 Apr 2012, Knut J Bjuland wrote:
>
>> Hi
>>
>> I am trying to run Trac-all on a cluster with PBS/torque. The 
>> trac-all scripts was modified to run with qsub, but
>> the second stage in Trac-all crash without getting finished. This is 
>> tested with the tutorial data. I am
>> enclosing the modified trac-all script.
>>
>> Best regard
>>
>> Knut J Bjuland
>> NTNU
>>
>>
>
>
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> it is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
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>

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[Freesurfer] submitt job with either interactive qsub or nested qusub with PBS

[Knut J Bjuland]

I have used trac-all on the cluster where I have an account. I am able to start 
both prep and post part as qsub process. Are there anyone who has modifed 
trac-all to be used with qsub in such a manner that a single node then submits 
jobs to other nodes? Or is there a path I should use to make trac-all work with 
PBS/torque. I have been able to use trac-all from the frontend of the cluster. 


Knut J


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[Freesurfer] copy of pbsubmit

[Knut J Bjuland]

Hi

I am trying to setup a local pc as cluster to debug trac-all. Is it 
possible to get a copy of pbsubmit? I think I could use it as wrapper 
fro qsub on my pc.


Best regards

Knut J
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[Freesurfer] correlation coefficient

[Knut J Bjuland]

Hi

I am trying to calculate correlation coefficient using freesurfer GLM for 
associations between volumes and IQ. I found this ealier answar, but the matlab 
script but the link appear to be dead.

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html

Best regards

Knut J


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[Freesurfer] total brain volume or intra crainal volume as estimated for total brain volume

[Knut J Bjuland]

Hello,

We would like to  calculate a Total Brain Volume based on data in aseg.stat 
generated from version 5.1.0. Can I use intra crainal volume as estimated for 
total brain volume? Or should I just add total grey volume with subcortical 
grey volume with total white matter volume? 

Thanks,
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Re: [Freesurfer] total brain volume or intra crainal volume as estimated for total brain volume

[Knut J Bjuland]

Hi Doug

I have run recon-all -segstats -s subject on all my subjects, but I can not see 
total brain volume label. 
Should I use intra cranial volume?


Knut J

> Date: Mon, 4 Jun 2012 10:09:16 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] total brain volume or intra crainal volume as 
> estimated for total brain volume
> 
> Hi Knut, you can copy the following file into 
> $FREESURFER_HOME/bin/mri_segstats
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
> (assuming you're using linux)
> The run
> recon-all -segstats -s subject
> This will create a new aseg.stats file with total brain volume based on 
> adding up the values in the segmentation.
> doug
> 
> 
> 
> On 06/04/2012 05:20 AM, Knut J Bjuland wrote:
> > Hello,
> >
> > We would like to  calculate a Total Brain Volume based on data in 
> > aseg.stat generated from version 5.1.0. Can I use intra crainal volume 
> > as estimated for total brain volume? Or should I just add total grey 
> > volume with subcortical grey volume with total white matter volume?
> >
> > Thanks,
> > Knut Jørgen
> >
> >
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> -- 
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
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Re: [Freesurfer] Qdec pre-smoothed

[Knut J Bjuland]

HI

I believe that recon-all -s  -qcache
will pre-cache smoothing from 0 through 25 fwhm. You can howevere select 
a small subjection of this by issuing recon-all

-s  -qcache  -fwhm .

-measure  can follow -qcache, where  is one of: 
thickness,

curv, sulc, area, jacobian_white or any surface measure. Multiple instances
of -measure  is supported.

Knut J



-s  -qcache


Knut J

  -qcache


On 06/20/2012 06:23 PM, mdkrue...@uwalumni.com wrote:

Freesurfers-

For pre-smoothing subject surfaces for qdec using:

recon-all -s  -qcache
Is it necessary to have all the variations of smoothing done (ie - 
fwhm 0,5,10,15,20,25) or is it possible to run with only a subsection 
of these?


Best-
Michael
--
Michael D. Kruepke
PhD - University of Illinois at Urbana-Champaign
BA - Psych - University of Wisconsin-Madison
mdkrue...@gmail.com 
(262)-483-7449



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[Freesurfer] Freesurfer GLM vs SPSS for voulme analysis

[Knut J Bjuland]

Hi,
I have calculated the group differences  for volume using both 
FreeSurfer GLM and SPSS GLM. I have used gender and group as fixed 
factor and intercranial volume and age at MRI scan as covariate.

GroupDescriptorFile 1
Title  group_difference_between_group1_and_group2_gender_age
DeMeanFlag 1
Class Group2Male
Class Group2Female
Class Group1Male
Class Group1Female
Variables ICU Age

I used this as fsgd heading, and I used this contrast vector 0.5 0.5 
-0.5 -0.5 0 0 0 0 0 0 0 0 to be able to control for gender difference 
and difference due to age and ICU. I get difference results between SPSS 
and Freesurfer.  I think this is strange since I used the same data both 
in FreeSurfer GLM and SPSS glm. Is there anything I have done wrong? I 
have used both univariate and multivariate in SPSS glm.

Best regards
Knut J
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Re: [Freesurfer] Freesurfer GLM vs SPSS for voulme analysis

[Knut J Bjuland]

HI,

I solve my problem. The FreeSurfer GLM model is easier to use than SPSS 
GLM. I had force SPSS to look at my model by selecting group differences 
between group1 and group2 and  look at interactions between the three 
groups. I then got similar results as in FreeSurfer glm for the group 
differences


Best regards

Knut J


On 07/31/2012 09:37 AM, Knut J Bjuland wrote:
> Hi,
> I have calculated the group differences  for volume using both
> FreeSurfer GLM and SPSS GLM. I have used gender and group as fixed
> factor and intercranial volume and age at MRI scan as covariate.
>
> GroupDescriptorFile 1
> Title  group_difference_between_group1_and_group2_gender_age
> DeMeanFlag 1
> Class Group2Male
> Class Group2Female
> Class Group1Male
> Class Group1Female
> Variables ICU Age
>
> I used this as fsgd heading, and I used this contrast vector 0.5 0.5
> -0.5 -0.5 0 0 0 0 0 0 0 0 to be able to control for gender difference
> and difference due to age and ICU. I get difference results between SPSS
> and Freesurfer.  I think this is strange since I used the same data both
> in FreeSurfer GLM and SPSS glm. Is there anything I have done wrong? I
> have used both univariate and multivariate in SPSS glm.
>
> Best regards
> Knut J
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[Freesurfer] unable to download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol

[Knut J Bjuland]

HI

I am unable to download 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol. 
Could you pleas add the file back.

Knut J
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Re: [Freesurfer] unable to download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol

[Knut J Bjuland]

Hi

I have tired using wget but I am still not able to download 
mri_label2vol. There may be permission error.


u/transfer/outgoing/flat/greve/mri_label2vol
--2012-08-10 14:56:12-- 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol
=> `mri_label2vol'
Resolving surfer.nmr.mgh.harvard.edu... 132.183.202.158
Connecting to surfer.nmr.mgh.harvard.edu|132.183.202.158|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /transfer/outgoing/flat/greve ... done.
==> SIZE mri_label2vol ... done.
==> PASV ... done.==> RETR mri_label2vol ...
No such file `mri_label2vol'.


Knut J









On 08/09/2012 09:25 PM, Douglas N Greve wrote:
> ok, try now
>
> On 08/09/2012 02:28 PM, Knut J Bjuland wrote:
>> HI
>>
>> I am unable to download
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.
>> Could you pleas add the file back.
>>
>> Knut J
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>

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[Freesurfer] Freesurfer 5.2 or new trac_all

[Knut J Bjuland]

When will FreeSurfer 5.2 be release. Is is possible to download the news 
version of trac-all and fsl_sub and use them in FreeSurfer 5. since I am 
using fsl 4.1.9.


Knut Jørgen



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Re: [Freesurfer] trac-all -path unable to open merged_ph1samples.nii.gz

[Knut J Bjuland]

Hi Anastasia

This files do not exist in dmri.bedpostX directory. I am now running 
bedpostx on the directory.


Knut J

On 08/17/2012 05:35 PM, Anastasia Yendiki wrote:
>
> Hi Knut - Does merged_ph1samples.nii.gz exist in your dmri.bedpostX 
> directory? It's one of the bedpostx output files. If not, it means 
> bedpostx did not finish running properly. You can try running bedpostx 
> directly on the dmri directory, not through trac-all -bedp.
>
> Output files of bedpostx are listed here:
> http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html
>
> a.y
>
> On Fri, 17 Aug 2012, Knut J Bjuland wrote:
>
>> The Tracula script has been modifed and adopted to a local cluster. I 
>> am now
>> able to run trac-all -prep, but trac-all bails out when I am running
>> trac-all -bedp. Is there any work around since I am using FSL 4.1.9 with
>> Fressurfer 5.1 I am not able to see what went wrong when I am running
>> trac-all -bedp., but when I ran trac-all -path I get this error 
>> niiRead():
>> error opening file  merged_ph1samples.nii.gz. Should I adjust the 
>> patch I
>> have used to get around this error or should I run bedpostx ro another
>> command before running trac-all -path? Will I be able to use Tracula 
>> from
>> Freesurfer 5.2 with recon-all data used with Freesurfer 5.1?
>>
>>
>
>
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> 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 
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[Freesurfer] sub field hippo segment fault in kvlSegmentHippocampalSubfields.sh: line 18

[Knut J Bjuland]

When I run recon-all for subfield segmentation I get a segmentation 
error? I get the error message below.
Cheers

Knut J


Bad trial move (maximal deformation: 278.205, lambda: 12.021)
 Cost going from 433597 to 1.79769e+308
Transforming mesh
Done transforming mesh
 Increasing lambda from 12.021 to 24.0421 and trying again.
Transforming mesh
Done transforming mesh
Calculating Levenberg-Marquardt step with lambda 24.0421...
Time taken to solve the Levenberg-Marquardt system of equations: 0.621659
...done!
maximalDeformation: 348.155
Transforming mesh
Done transforming mesh
Rasterizing Levenberg-Marquardt...

Done transforming mesh
Rasterizing Levenberg-Marquardt...
/global/apps/freesurfer/5.1.0/bin/kvlSegmentHippocampalSubfields.sh: 
line 18: 21317 Segmentation fault  kvlSegmentWithoutGUI 
configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt
failed to do kvlSegmentWithoutGUI 
configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt
Linux c4-1.local 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:50:31 EDT 2010 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s subject_id exited with ERRORS at Sat Aug 18 19:00:37 CEST 2012

For more details, see the log file 
/home/kjbjuland/freesurfer/20_ucsd_automatic/023/scripts/recon-all.log
To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] sub field hippo recon-all crash without getting finsihed

[Knut J Bjuland]

when I tun the recon-all -sub -hippo-subfields. I get a crash at line 17 in

kvlSegmentHippocampalSubfields.sh:. Should I edit the line to prevent 
kvlSegmentHippocampalSubfields.sh
  from bailing out by changin exit -1 to #exit -1. I run recon-all 
-hippo-subfields with 3 gb ram on the cluster and I have set the wall time to 
48 hours. The cluster use PBS on Rock centos distribution.



Knut J







On 08/18/2012 07:55 PM, Knut J Bjuland wrote:
> When I run recon-all for subfield segmentation I get a segmentation
> error? I get the error message below.
> Cheers
>
> Knut J
>
>
> Bad trial move (maximal deformation: 278.205, lambda: 12.021)
>   Cost going from 433597 to 1.79769e+308
> Transforming mesh
> Done transforming mesh
>   Increasing lambda from 12.021 to 24.0421 and trying again.
> Transforming mesh
> Done transforming mesh
> Calculating Levenberg-Marquardt step with lambda 24.0421...
> Time taken to solve the Levenberg-Marquardt system of equations: 0.621659
> ...done!
> maximalDeformation: 348.155
> Transforming mesh
> Done transforming mesh
> Rasterizing Levenberg-Marquardt...
>
> Done transforming mesh
> Rasterizing Levenberg-Marquardt...
> /global/apps/freesurfer/5.1.0/bin/kvlSegmentHippocampalSubfields.sh:
> line 18: 21317 Segmentation fault  kvlSegmentWithoutGUI
> configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt
> failed to do kvlSegmentWithoutGUI
> configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt
> Linux c4-1.local 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:50:31 EDT 2010
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s subject_id exited with ERRORS at Sat Aug 18 19:00:37 CEST 2012
>
> For more details, see the log file
> /home/kjbjuland/freesurfer/20_ucsd_automatic/023/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
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[Freesurfer] crash repport automatic hippocampus segmentation failed

[Knut J Bjuland]

When I run subfield segmentation for some of the subject, I get segmentation 
error. Is there any known workaround these problems as recon-all is ran on a 
cluster? I usually get this error Rasterizing 
Levenberg-Marquardt.../global/apps/freesurfer/5.1.0/bin/kvlSegmentHippocampalSubfields.sh:
 line 18:  9231 Segmentation fault  kvlSegmentWithoutGUI 
configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txtfailed 
to do kvlSegmentWithoutGUI 
configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txtCan I 
edit kvlSegmentHippocampalSubfields.sh to ensure that it does not exit the loop 
at line 18.Knut J___
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[Freesurfer] cortical volume and ortical jacobian_whitematter

[Knut J Bjuland]

Hi,I have looked into cortical surface volume and cortical 
jacobian_whitematter. Can I use these measure a in similar way as cortical 
thickness? Do jacobian_whitematter represent the whitematter thickness in the 
cortex? How reliable are cortical volumes compared to cortical thickness?Best 
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Re: [Freesurfer] errors Quantifying Hippocampal Subfield Segmentations

[Knut J Bjuland]

Hi

kvlQuantifyHippocampalSubfieldSegmentations.sh "expected that the 
"-hippo-subfields" flag has been used for each subject in $SUBJECTS_DIR; 
if this is not the case the 
"kvlQuantifyHippocampalSubfieldSegmentations.sh" script will fail and no 
(or incomplete) output files will be generated". from 
http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation.


Cheers
Knut J



On 08/30/2012 07:56 PM, Carolina Valencia wrote:

Hi Freesurfer community:


I run hippocampal subfields command succesfully

recon-all -s CORBIC_vol15 finished without error at Thu Aug 30 
11:29:16 COT 2012

done

but when I run  kvlQuantifyHippocampalSubfieldSegmentations.sh

the terminal shows some errors:

resultsDirectory /home/cvalencia/freesurfer/subjects/volumetria
cd /home/cvalencia/freesurfer/subjects/volumetria
resultsDirectory /home/cvalencia/freesurfer/subjects/volumetria
startIndex: 1
endIndex: 5
cd CORBIC_vol15/
Quantifying subject CORBIC_vol15/ left
Doing left side
cd mri
kvlQuantifyPosteriorProbabilityImages 
/home/cvalencia/freesurfer/data/GEMS/compressionLookupTable_left.txt   
  posterior_Left-Hippocampus.mgz 
posterior_left_presubiculum.mgz posterior_left_CA1.mgz 
posterior_left_CA2-3.mgz posterior_left_fimbria.mgz 
posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz 
posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt

cd ..
Quantifying subject CORBIC_vol15/ right
Doing right side
cd mri
kvlQuantifyPosteriorProbabilityImages 
/home/cvalencia/freesurfer/data/GEMS/compressionLookupTable.txt   
  posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz 
posterior_right_CA1.mgz posterior_right_CA2-3.mgz 
posterior_right_fimbria.mgz posterior_right_subiculum.mgz 
posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz 
> volumeStats_right.txt

cd ..
cd ..
cd fsaverage/
Quantifying subject fsaverage/ left
Doing left side
cd mri
kvlQuantifyPosteriorProbabilityImages 
/home/cvalencia/freesurfer/data/GEMS/compressionLookupTable_left.txt   
  posterior_Left-Hippocampus.mgz 
posterior_left_presubiculum.mgz posterior_left_CA1.mgz 
posterior_left_CA2-3.mgz posterior_left_fimbria.mgz 
posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz 
posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt

terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  itkMGHImageIO.cxx:216:
itk::ERROR: MGHImageIO(0x9231728): Can't find/open file: 
posterior_Left-Hippocampus.mgz
/home/cvalencia/freesurfer/bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: 
línea 22: 15068 Abortado(`core' generado) 
kvlQuantifyPosteriorProbabilityImages 
/home/cvalencia/freesurfer/data/GEMS/compressionLookupTable_left.txt 
posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz 
posterior_left_CA1.mgz posterior_left_CA2-3.mgz 
posterior_left_fimbria.mgz posterior_left_subiculum.mgz 
posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz > 
volumeStats_left.txt
failed to do kvlQuantifyPosteriorProbabilityImages 
/home/cvalencia/freesurfer/data/GEMS/compressionLookupTable_left.txt   
  posterior_Left-Hippocampus.mgz 
posterior_left_presubiculum.mgz posterior_left_CA1.mgz 
posterior_left_CA2-3.mgz posterior_left_fimbria.mgz 
posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz 
posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt


when I tried to visualize them

cvalencia@cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/volumetria/CORBIC_vol15$ 
 freeview nu.mgz \

>   -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \
>   -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \
>   -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
freeview.bin: No match.

Am I miss something?

Best regards,
--
--
*Carolina Valencia M*


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[Freesurfer] intracranial volume and dicom

[Knut J Bjuland]

Hi,
I have calculated relative volume by dividing each volume by the 
intracranial volume and multiply it with 100. When I add the relative 
volume of total gray matter, cortical white matter, lateral ventricle, 
3rd centricle, 4th ventricle and ventral DC, I get 82-86 %. Can this be 
caused by the fact that the intracranial volume is much larger than the 
brain?
In which way can motion correction affect volume if I have series where 
some subjects have to dicom and other just have one dicom serie?

Knut J
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Re: [Freesurfer] intracranial volume and dicom

[Knut J Bjuland]

On 09/25/2012 03:09 PM, Bruce Fischl wrote:
> check the accuracy of the talairach xform
Hi

I am using Freesurfer version 5.1 with all bug fixes. I have snapshots 
off all talairach xforms made through qa_tools. I have seen on a few 
subjects that the talirach transformation went okay. The pial surface 
and whitematter surface have aligned with the surfaces on each subject. 
Can you please describe how I can report this to you as picture or as a 
text file?


Knut J


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[Freesurfer] error in mri_segstats, important

[Knut J Bjuland]

I have download the latest verion of mri_segstats from the release 
notes. But it does not generate asegstats.


4 x86_64 x86_64 GNU/Linux
#
#@# ASeg Stats Tue Oct  2 07:36:17 CEST 2012
/home/knutjb/freesurfer/20_ucsd_automatic_version2/004

  mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent 
--subcortgray --in mri/norm.mgz --in-intensity-name norm 
--in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray 
--ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 004

ERROR: Option --sum unknown

#--

recon-all -s 004 finished without error at Tue Oct  2 07:36:17 CEST 2012
done

knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats
USAGE: mri_label2vol

  Possible inputs:
--label labelid <--label labelid>
--annot annotfile : surface annotation file
--seg   segpath : segmentation
--aparc+aseg  : use aparc+aseg.mgz in subjectdir as seg

--temp tempvolid : output template volume

--reg regmat : VolXYZ = R*LabelXYZ
--regheader volid : label template volume (needed with --label or 
--annot)
for --seg, use the segmentation volume
--identity : set R=I
--invertmtx : Invert the registration matrix

--fillthresh thresh : between 0 and 1 (def 0)
--labvoxvol voxvol : volume of each label point (def 1mm3)
--proj type start stop delta

--subject subjectid : needed with --proj or --annot
--hemi hemi : needed with --proj or --annot
--surf surface  : use surface instead of white

--o volid : output volume
--hits hitvolid : each frame is nhits for a label
--label-stat statvol : map the label stats field into the vol
--stat-thresh thresh : only use label point where stat > thresh
--offset k : add k to segmentation numbers (good when 0 should not 
be ignored)

--native-vox2ras : use native vox2ras xform instead of tkregister-style
--version : print version and exit
--help

$Id: mri_label2vol.c,v 1.39 2012/06/08 17:29:54 greve Exp $

knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats --sum
ERROR: Option --sum unknown



Knut J
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Re: [Freesurfer] error in mri_segstats, important (resolved)

[Knut J Bjuland]

Hi

I downloaded about Tuesday and this morning. However when I download a 
bit later to day I got a working mri_segstats.It print out  mri_segstats 
--all-infoProgramName: mri_segstats ProgramArguments: --all-info  
ProgramVersion: $Name:  $ TimeStamp: 2012/10/02-19:57:40-GMT  
BuildTimeStamp: Jun 20 2012 12:45:04  CVS: $Id: mri_segstats.c,v 1.86 
2012/07/16 14:39:07 greve Exp $  User: knutjb  Machine: dmed4960  
Platform: Linux PlatformVersion: 3.2.0-32-generic  CompilerName: GCC 
CompilerVersion: 40100

Best regards
Knut J

On 10/02/2012 06:04 PM, Douglas N Greve wrote:
> Hi Knut, when did you download mri_segstats? Can you send me the result of
> mri_segstats --all-info
> doug
>
> On 10/02/2012 01:42 AM, Knut J Bjuland wrote:
>> I have download the latest verion of mri_segstats from the release
>> notes. But it does not generate asegstats.
>>
>>
>> 4 x86_64 x86_64 GNU/Linux
>> #
>> #@# ASeg Stats Tue Oct  2 07:36:17 CEST 2012
>> /home/knutjb/freesurfer/20_ucsd_automatic_version2/004
>>
>> mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
>> mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent
>> --subcortgray --in mri/norm.mgz --in-intensity-name norm
>> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray
>> --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 004
>>
>> ERROR: Option --sum unknown
>>
>> #--
>>
>> recon-all -s 004 finished without error at Tue Oct  2 07:36:17 CEST 2012
>> done
>>
>> knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats
>> USAGE: mri_label2vol
>>
>> Possible inputs:
>>   --label labelid<--label labelid>
>>   --annot annotfile : surface annotation file
>>   --seg   segpath : segmentation
>>   --aparc+aseg  : use aparc+aseg.mgz in subjectdir as seg
>>
>>   --temp tempvolid : output template volume
>>
>>   --reg regmat : VolXYZ = R*LabelXYZ
>>   --regheader volid : label template volume (needed with --label or
>> --annot)
>>   for --seg, use the segmentation volume
>>   --identity : set R=I
>>   --invertmtx : Invert the registration matrix
>>
>>   --fillthresh thresh : between 0 and 1 (def 0)
>>   --labvoxvol voxvol : volume of each label point (def 1mm3)
>>   --proj type start stop delta
>>
>>   --subject subjectid : needed with --proj or --annot
>>   --hemi hemi : needed with --proj or --annot
>>   --surf surface  : use surface instead of white
>>
>>   --o volid : output volume
>>   --hits hitvolid : each frame is nhits for a label
>>   --label-stat statvol : map the label stats field into the vol
>>   --stat-thresh thresh : only use label point where stat>  thresh
>>   --offset k : add k to segmentation numbers (good when 0 should not
>> be ignored)
>>
>>   --native-vox2ras : use native vox2ras xform instead of tkregister-style
>>   --version : print version and exit
>>   --help
>>
>> $Id: mri_label2vol.c,v 1.39 2012/06/08 17:29:54 greve Exp $
>>
>> knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats --sum
>> ERROR: Option --sum unknown
>>
>>
>>
>> Knut J
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Re: [Freesurfer] FS install ubuntu 11.1

[Knut J Bjuland]

Hi

You should reinstall FSL 5.0 since it is missing a file.

Knut J


On 10/08/2012 08:05 PM, David Soto wrote:

Hi, just trying to install Fresufer in Ubuntu OneiricOcelot 11.10,

I followed the installation steps in your web and seemed fine

 in one of the last steps I did

wmen-dsoto3:/> source $FREESURFER_HOME/SetUpFreeSurfer.csh
 freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
/usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh: Command not found.
FSL_DIR   /usr/share/fsl/5.0


the thing is that when I test the install by typing

tkmedit

it says command not found & cannot get Freesurfer to start

can you help please?

Thanks!

David
http://www1.imperial.ac.uk/medicine/people/d.soto/


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[Freesurfer] import dicom files with # in name and when to run talairach_avi --i nu.mgz --xfm transforms/talairach.xfm

[Knut J Bjuland]

Hi,

I have two questions about Freesurfer. How can I import dicom files, 
which include "#" as part of the files names into freesurfer witouth 
renaming the files? Recon-all -i seem to cut the files name after "#" so 
that image#1.dcm becomes image.
Would you recommend me to run this command for all my processed 
subjects? As stated in the relase notes? Can I use QA_tools to measure 
the quality of the recons?
cd subjid/mri
talairach_avi --i nu.mgz --xfm transforms/talairach.xfm
recon-all -s subjid -segstats
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Re: [Freesurfer] FS install ubuntu 11.1

[Knut J Bjuland]

This errer message mean that you are missing 
/usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh in your 
/usr/share/fsl/5.0/etc/fslconf. You should get a copy of this file and 
place in /usr/share/fsl/5.0/etc/fslconf/f


knut J


On 10/09/2012 02:00 PM, David Soto wrote:

hi - so the output to  source $FREESURFER_HOME/SetUpFreeSurfer.csh

was:



 freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
/usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh: Command not found.
FSL_DIR   /usr/share/fsl/5.0




On Tue, Oct 9, 2012 at 11:54 AM, Knut J Bjuland <mailto:knut...@hotmail.com>> wrote:


Can you please send me the output again?  The files should not
prevent you from starting since fsl and freesurfer need that file
to be able to set the environment right.


On 10/09/2012 10:41 AM, David Soto wrote:

thanks, I'll try though I have already reinstalled
FSL now I have FSL 5.0.1- should that fine prevent
FS from starting up anyway?
Cheers

On Tue, Oct 9, 2012 at 9:06 AM, Knut J Bjuland
mailto:knut...@hotmail.com>> wrote:

Hi

You should reinstall FSL 5.0 since it is missing a file.

Knut J



On 10/08/2012 08:05 PM, David Soto wrote:

Hi, just trying to install Fresufer in Ubuntu OneiricOcelot
11.10,

I followed the installation steps in your web and seemed fine

 in one of the last steps I did

wmen-dsoto3:/> source $FREESURFER_HOME/SetUpFreeSurfer.csh
 freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR /usr/local/freesurfer/mni
/usr/share/fsl/5.0/etc/fslconf/fslmachtype.sh: Command not
found.
FSL_DIR /usr/share/fsl/5.0


the thing is that when I test the install by typing

tkmedit

it says command not found & cannot get Freesurfer to start

can you help please?

Thanks!

David
http://www1.imperial.ac.uk/medicine/people/d.soto/


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[Freesurfer] QA_tools missing signal to noise calculation

[Knut J Bjuland]

Hi,

I have downloaded the latest QA_tools v1.1 from 
http://surfer.nmr.mgh.harvard.edu/fswiki/QATools. However, when I ran

recon_checker, I did not get a signal to noise calculations. I ran 
recon_checker  with -s-dir subjectfile and -snaps-detailed. Is there any option 
that I missed? Is it possible to download a newer version from cvs?


Knut J

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[Freesurfer] ERROR: inputs have mismatched dimensions! when running recon -i dicom -i dicom -s

[Knut J Bjuland]

Hi,

When I import one subject with recon -i dicom -i dicom -s subjec, I get 
this error message ERROR: inputs have mismatched dimensions! I think it 
is caused by the fact that there is a different number of slices into 
the two series. One series has 256x256x125 white the other has 
256x256x128. How can I detect if there is missing slices in the series 
with 125 slices? What would you recommend me to do? Is is possible to 
ask recon-all to bypass this error message and import both series?

Knut J

output

k_ras = (-1, 0, 0)
writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz...
ERROR: inputs have mismatched dimensions!
/home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100
 
is
256 x 256 x 125 while
/home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235
 
is
256 x 256 x 128
Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 
2012 x86_64 x86_64 x86_64 GNU/Linux

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Re: [Freesurfer] ERROR: inputs have mismatched dimensions! when running recon -i dicom -i dicom -s

[Knut J Bjuland]

Hi Bruce

I converted the dicom into 001.mgz. Then I tried to reslice.

mri_convert -rl -i orig/001.mgz  -o orig/001.mgz
mri_convert -rl -i orig/001.mgz -o orig/001.mgz
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from orig/001.mgz...
TR=2730.00, TE=3.45, TI=1000.00, flip angle=7.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, 0, 0)
reading template info from volume -i...

mri_read(): couldn't determine type of file 
/home/knutjb/freesurfer/expo/test/mri/-i
error reading from volume -i

Could you please give me an example on how to use mri_convert to reslice 
please?


Knut J



On 10/15/2012 12:43 AM, Bruce Fischl wrote:
> Hi Knut
>
> you could mri_convert them into mri/orig/001.mgz and 002.mgz, 
> reslicing the 125 into the 128 geometry (-rl) and go from there.
>
> cheers
> Bruce
>
> On Sun, 14 Oct 2012, Knut J Bjuland wrote:
>
>> Hi,
>>
>> When I import one subject with recon -i dicom -i dicom -s subjec, I get
>> this error message ERROR: inputs have mismatched dimensions! I think it
>> is caused by the fact that there is a different number of slices into
>> the two series. One series has 256x256x125 white the other has
>> 256x256x128. How can I detect if there is missing slices in the series
>> with 125 slices? What would you recommend me to do? Is is possible to
>> ask recon-all to bypass this error message and import both series?
>>
>> Knut J
>>
>> output
>>
>> k_ras = (-1, 0, 0)
>> writing to 
>> /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz...
>> ERROR: inputs have mismatched dimensions!
>> /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100
>>  
>>
>> is
>> 256 x 256 x 125 while
>> /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235
>>  
>>
>> is
>> 256 x 256 x 128
>> Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC
>> 2012 x86_64 x86_64 x86_64 GNU/Linux
>>
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>>
>>
>>
>
>
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> 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
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Re: [Freesurfer] ERROR: inputs have mismatched dimensions! when running recon -i dicom -i dicom -s

[Knut J Bjuland]

I am able to convert using mri_convert, but when I try to reslice with 
mri_convert -rl input output. I get the error message shown below. I 
according to the documentation I could use mri_convert to reslice, but 
it does not mention how I should set an vaule for the -rl input. Should 
I use matlab instead please?

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


mri_convert -rl 001.mgz  001t.mgz
mri_convert -rl 001.mgz 001t.mgz

mri_convert: missing output volume name

type mri_convert -u for usage


Knut J


On 10/15/2012 01:23 PM, Bruce Fischl wrote:
> Don't use the -I, just give it an input (the dicoms) and and output
>
>
>
> On Oct 15, 2012, at 1:23 AM, Knut J Bjuland  wrote:
>
>> Hi Bruce
>>
>> I converted the dicom into 001.mgz. Then I tried to reslice.
>>
>> mri_convert -rl -i orig/001.mgz  -o orig/001.mgz
>> mri_convert -rl -i orig/001.mgz -o orig/001.mgz
>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>> reading from orig/001.mgz...
>> TR=2730.00, TE=3.45, TI=1000.00, flip angle=7.00
>> i_ras = (-0, -1, 0)
>> j_ras = (-0, -0, -1)
>> k_ras = (-1, 0, 0)
>> reading template info from volume -i...
>>
>> mri_read(): couldn't determine type of file 
>> /home/knutjb/freesurfer/expo/test/mri/-i
>> error reading from volume -i
>>
>> Could you please give me an example on how to use mri_convert to reslice 
>> please?
>>
>>
>> Knut J
>>
>>
>>
>> On 10/15/2012 12:43 AM, Bruce Fischl wrote:
>>> Hi Knut
>>>
>>> you could mri_convert them into mri/orig/001.mgz and 002.mgz, reslicing the 
>>> 125 into the 128 geometry (-rl) and go from there.
>>>
>>> cheers
>>> Bruce
>>>
>>> On Sun, 14 Oct 2012, Knut J Bjuland wrote:
>>>
>>>> Hi,
>>>>
>>>> When I import one subject with recon -i dicom -i dicom -s subjec, I get
>>>> this error message ERROR: inputs have mismatched dimensions! I think it
>>>> is caused by the fact that there is a different number of slices into
>>>> the two series. One series has 256x256x125 white the other has
>>>> 256x256x128. How can I detect if there is missing slices in the series
>>>> with 125 slices? What would you recommend me to do? Is is possible to
>>>> ask recon-all to bypass this error message and import both series?
>>>>
>>>> Knut J
>>>>
>>>> output
>>>>
>>>> k_ras = (-1, 0, 0)
>>>> writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz...
>>>> ERROR: inputs have mismatched dimensions!
>>>> /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100
>>>> is
>>>> 256 x 256 x 125 while
>>>> /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235
>>>> is
>>>> 256 x 256 x 128
>>>> Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC
>>>> 2012 x86_64 x86_64 x86_64 GNU/Linux
>>>>
>>>> ___
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>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>>
>>> 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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>>>
>>
>

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Re: [Freesurfer] ERROR: inputs have mismatched dimensions! when running recon -i dicom -i dicom -s

[Knut J Bjuland]

Hi

I think i understood it. Should i use mri_convert -rl template input output


from mri_convert.c
printf("reading template info from volume %s...\n",
  reslice_like_name);
   template = MRIreadInfo(reslice_like_name);
   if(template == NULL)
   {
 fprintf(stderr, "error reading from volume %s\n",
 reslice_like_name);
 exit(1);



Knut J



On 10/15/2012 02:22 PM, Knut J Bjuland wrote:
> I am able to convert using mri_convert, but when I try to reslice with
> mri_convert -rl input output. I get the error message shown below. I
> according to the documentation I could use mri_convert to reslice, but
> it does not mention how I should set an vaule for the -rl input. Should
> I use matlab instead please?
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert
>
>
> mri_convert -rl 001.mgz  001t.mgz
> mri_convert -rl 001.mgz 001t.mgz
>
> mri_convert: missing output volume name
>
> type mri_convert -u for usage
>
>
> Knut J
>
>
> On 10/15/2012 01:23 PM, Bruce Fischl wrote:
>> Don't use the -I, just give it an input (the dicoms) and and output
>>
>>
>>
>> On Oct 15, 2012, at 1:23 AM, Knut J Bjuland  wrote:
>>
>>> Hi Bruce
>>>
>>> I converted the dicom into 001.mgz. Then I tried to reslice.
>>>
>>> mri_convert -rl -i orig/001.mgz  -o orig/001.mgz
>>> mri_convert -rl -i orig/001.mgz -o orig/001.mgz
>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>>> reading from orig/001.mgz...
>>> TR=2730.00, TE=3.45, TI=1000.00, flip angle=7.00
>>> i_ras = (-0, -1, 0)
>>> j_ras = (-0, -0, -1)
>>> k_ras = (-1, 0, 0)
>>> reading template info from volume -i...
>>>
>>> mri_read(): couldn't determine type of file 
>>> /home/knutjb/freesurfer/expo/test/mri/-i
>>> error reading from volume -i
>>>
>>> Could you please give me an example on how to use mri_convert to reslice 
>>> please?
>>>
>>>
>>> Knut J
>>>
>>>
>>>
>>> On 10/15/2012 12:43 AM, Bruce Fischl wrote:
>>>> Hi Knut
>>>>
>>>> you could mri_convert them into mri/orig/001.mgz and 002.mgz, reslicing 
>>>> the 125 into the 128 geometry (-rl) and go from there.
>>>>
>>>> cheers
>>>> Bruce
>>>>
>>>> On Sun, 14 Oct 2012, Knut J Bjuland wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> When I import one subject with recon -i dicom -i dicom -s subjec, I get
>>>>> this error message ERROR: inputs have mismatched dimensions! I think it
>>>>> is caused by the fact that there is a different number of slices into
>>>>> the two series. One series has 256x256x125 white the other has
>>>>> 256x256x128. How can I detect if there is missing slices in the series
>>>>> with 125 slices? What would you recommend me to do? Is is possible to
>>>>> ask recon-all to bypass this error message and import both series?
>>>>>
>>>>> Knut J
>>>>>
>>>>> output
>>>>>
>>>>> k_ras = (-1, 0, 0)
>>>>> writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz...
>>>>> ERROR: inputs have mismatched dimensions!
>>>>> /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100
>>>>> is
>>>>> 256 x 256 x 125 while
>>>>> /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235
>>>>> is
>>>>> 256 x 256 x 128
>>>>> Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC
>>>>> 2012 x86_64 x86_64 x86_64 GNU/Linux
>>>>>
>>>>> ___
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>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>>
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>>>> 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
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Re: [Freesurfer] QA_tools missing signal to noise calculation

[Knut J Bjuland]

Hi Louis

I manage to replicate the error by using  wm-anat-snr directly on bert 
in /usr/local/freesurfer/subjects. I think think the error is in 
wm-anat-snr and it interactions with mri_segstats.


mri_segstats -all-info
ProgramName: mri_segstats  ProgramArguments: -all-info ProgramVersion: 
$Name:  $  TimeStamp: 2012/10/15-19:39:47-GMT BuildTimeStamp: Jun 20 
2012 12:45:04  CVS: $Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve 
Exp $  User: knutjb  Machine: dmed5549  Platform: Linux  
PlatformVersion: 3.5.0-17-generic CompilerName: GCC  CompilerVersion: 40100


Knut J

On 10/15/2012 04:50 PM, Louis Nicholas Vinke wrote:

Hi Knut,
It should run by default.  Did you check the summary log file, 
$SUBJECTS_DIR/QA/recon_checker.ALL.summary.log?  Otherwise, could you 
send

 the terminal output when you run QAtools on a single subject?
-Louis

On Sun, 14 Oct 2012, Knut J Bjuland wrote:


Hi,

I have downloaded the latest QA_tools v1.1 from
http://surfer.nmr.mgh.harvard.edu/fswiki/QATools. However, when I ran

recon_checker, I did not get a signal to noise calculations. I ran 
recon_checker  with -s-dir subjectfile and -snaps-detailed. Is there 
any option that I missed? Is it possible to download a newer version 
from cvs?



Knut J

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Mon Oct 15 21:36:38 CEST 2012

setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
cd /usr/local/freesurfer/subjects
/usr/local/freesurfer/bin/wm-anat-snr --s bert --debug --force

subject bert
/usr/local/freesurfer
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux dmed5549 3.5.0-17-generic #26 SMP Fri Oct 12 11:52:17 CEST 2012 x86_64 
x86_64 x86_64 GNU/Linux
$Id: wm-anat-snr,v 1.2 2011/01/21 23:11:47 greve Exp $
UpdateOnly 0
mri_binarize --i /usr/local/freesurfer/subjects/bert/mri/aparc+aseg.mgz --o 
/usr/local/freesurfer/subjects/bert/tmp/wmeroded.mgh --erode 3 --match 2 41 7 
46 251 252 253 254 255 77 78 79

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /usr/local/freesurfer/subjects
cmdline mri_binarize --i /usr/local/freesurfer/subjects/bert/mri/aparc+aseg.mgz 
--o /usr/local/freesurfer/subjects/bert/tmp/wmeroded.mgh --erode 3 --match 2 41 
7 46 251 252 253 254 255 77 78 79 
sysname  Linux
hostname dmed5549
machine  x86_64
user knutjb

input  /usr/local/freesurfer/subjects/bert/mri/aparc+aseg.mgz
frame  0
nErode3d   3
nErode2d   0
output /usr/local/freesurfer/subjects/bert/tmp/wmeroded.mgh
Binarizing based on matching values
nMatch 12
 0 2
 141
 2 7
 346
 4   251
 5   252
 6   253
 7   254
 8   255
 977
1078
1179
binval1
binvalnot 0
Found 514097 values in range
Eroding 3 voxels in 3d
Counting number of voxels
Found 53426 voxels in final mask
mri_binarize done
mri_segstats --snr --seg /usr/local/freesurfer/subjects/bert/tmp/wmeroded.mgh 
--sum /usr/local/freesurfer/subjects/bert/tmp/wmeroded.sum --i 
/usr/local/freesurfer/subjects/bert/mri/norm.mgz --excludeid 0

$Id: mri_segstats.c,v 1.86 2012/07/16 14:39:07 greve Exp $
cwd 
cmdline mri_segstats --snr --seg 
/usr/local/freesurfer/subjects/bert/tmp/wmeroded.mgh --sum 
/usr/local/freesurfer/subjects/bert/tmp/wmeroded.sum --i 
/usr/local/freesurfer/subjects/bert/mri/norm.mgz --excludeid 0 
sysname  Linux
hostname dmed5549
machine  x86_64
user knutjb
UseRobust  0
Loading /usr/local/freesurfer/subjects/bert/tmp/wmeroded.mgh
Loading /usr/local/freesurfer/subjects/bert/mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   2 segmentations
Computing statistics for each segmentation
  1 1  0  0

Reporting on   0 segmentations

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[Freesurfer] Cortical thickness percent difference surface maps howto

[Knut J Bjuland]

Hi

Is it possible to generate surface maps for the percent difference in cortical 
thickness between 2 groups within with Freesurfer 5.1? Could you please give 
link to how to use Matlab to compute the differences
as described in  
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07433.html?

Cheers
Knut J

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[Freesurfer] calculate percent from two different mgh files

[Knut J Bjuland]

How can I dived a gamma.mgh with another gamma.mgh to get new mgh 
structure? Is there any Freesurfer Matlab function that I should use. I 
am able to use Matlab to calculate the difference for vol.



n=size(gamm.vol(2))

for i=1:n;
 test=gamma.mgh.vol(i)/gamma.mgh(i)
end

I am trying to follow this howto at 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07433.html.


Knut J

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[Freesurfer] Cortical thickness percent difference surface maps script in matlab feedback wanted.

[Knut J Bjuland]

Dear Freesurfer expert

I have produce a script to make percent difference in cortical thickens using 
information from the mailing list.
Could you please take look if this script is correct, or if there is a better 
way to do it?


function [ out ] = diff_map( difference, average )
%percent difference  Summary of this function goes here
%   This function takes two gamma.mgh from group differences 1 -1 and divide
%   with gamma.mgh from 0.5 0.5 to produce a new mgh with percent
%   difference between two groups.
% Copyright Knut Jørgen Bjuland 
% Freesurfer license
mat=fast_vol2mat(difference.vol);
n=size(mat);

for i=1:n(2),
mat(i)=difference.vol(i)*100/average.vol(i);
end

out=difference;
out.vol=fast_mat2vol(mat,out.volsize);

end

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Re: [Freesurfer] error while compiling utils

[Knut J Bjuland]

Hi Kim

You are missing some packages. 
https://help.ubuntu.com/community/CompilingEasyHowTo


You should install teh essential package for compiling in ubuntu by

sudo apt-get install build-essential and sudo apt-get install linux-libc-dev to 
get Linux headers in /usr/include/linux.

When building you should ensure that you meet the dependency before 
compiling.


Cheers

Knut J



On 10/18/2012 11:10 PM, Kim, Daniel wrote:

Hi Freesurfer users,

I'm trying to compile utils on my Ubuntu 10.04 64 bit machine and I am getting 
a considerable amount of error while compiling afni.c

- I am using gcc-4.4.3, g++-4.4.3 for compilers
- I have successfully installed VXL and MNI as per the developer's guide (I am 
not building any GUI apps)
- Had to add "-I/usr/src/linux-headers-2.6.32-43/include" under CFLAGS in 
utils/Makefile since without it, it would spit out error message saying it cannot find 

- under the utils folder, "make" gives an error along the lines of "expected 
specifier-qualifier-list before 'size_t'" (attaching error log file)
- tried using older compiler gcc-3.3, g++3.3 but problems seems worse

I'm a bit stuck here and hoping that someone has had experience similar to this 
who can lend me some help?

Thanks very much!

cheers

Danny Kim
Children's Brain Mapping Centre
BC Children's Hospital


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[Freesurfer] Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0

[Knut J Bjuland]

Dear FreeSurfer expert,



I have compared the aseg volume between FreeSurfer 5.3 and FreeSurfer 6.0 with 
asegstatsdiff from FreeSurfer 6.0 for each subject in my data set. I have 
enclosed the range for some of the volume. I found the largest differences in 
subcortical structures, especially in Corpus callosum(CC). I found that 
FreeSurfer 6.0 CC posterior volume was 525.51 % larger than in FreeSurfer 5.3. 
Nevertheless, these differences were much smaller for lhCortex, but also here 
FreeSurfer 6.0 was on average larger than FreeSurfer 5.3. I ran the FreeSurfer 
6.0 using the same option as FreeSurfer 5.30. Both versions of FreeSurfer were 
run on Centos. I am also enclosing a table with mean values along with min and 
max  for differences between FreeSurfer 5.3 and FreeSurfer 6.0 aseg volumes.





Best regards

Knut Jørgen Bjuland PhD

NTNU



Left-Lateral-Ventricle


7.4  (-0.13,130.72)


Left-Cerebellum-White-Matter


0.64  (-22.9,56.15)


Left-Cerebellum-Cortex


7.56  (-10.3,19.17)


Left-Thalamus-Proper


0.12  (-16.31,32.42)


Left-Caudate


-4.25  (-12,33.64)


Left-Putamen


-16.72  (-27.99,8.3)


Left-Pallidum


16.23  (-22.94,84.75)


Left-Hippocampus


-1.74  (-13.53,15.93)


Left-Amygdala


2.29  (-19.28,41.04)


Right-Lateral-Ventricle


4.6  (-24.77,102.12)


Right-Cerebellum-White-Matter


-3.2  (-20.87,49.37)


Right-Cerebellum-Cortex


4.88  (-12.99,14.36)


Right-Thalamus-Proper


1.06  (-22.34,19.99)


Right-Caudate


-6.08  (-14.59,6.13)


Right-Putamen


-12.87  (-31.37,10.17)


Right-Pallidum


14.01  (-27.79,89.19)


Right-Hippocampus


-1.71  (-9.29,12.02)


Right-Amygdala


3.74  (-18.6,51.01)


Right-Accumbens-area


-9.14  (-37.89,61.02)


CC_Posterior


22.07  (-47.04,525.51)


CC_Mid_Posterior


53.59  (-11.3,537.3)


CC_Central


36.77  (-21.36,317.24)


CC_Mid_Anterior


24.09  (-18.86,128.31)


CC_Anterior


10.64  (-33.71,152.33)


lhCortexVol


3.13  (-1.31,12.37)


rhCortexVol


3.16  (-0.36,14.2)


CortexVol


3  (-4.47,13.26)


EstimatedTotalIntraCranialVol


0.65  (-0.05,26.52)


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Re: [Freesurfer] Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0

[Knut J Bjuland]

Hi Bruce

I found some filled-in occipital horn and some in the anterior parts. I can 
upload nu.mgz and aseg.mgz for a subject with problems with lateral ventricle.

Cheers
Knut Jørgen




On 4 May 2017, at 16:54, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi Knut

where is it being filled? If it is the occipital horn we may soon have a patch 
for it

cheers
Bruce
On Thu, 4 May 2017, Knut J Bjuland wrote:

Hi
Are there any options that I can use in Freesurfer 6.0 that can prevent lef
t lateral ventricle from being filled with WM? Should I send the MPRAGE seq
uence information?
Knut Jørgen

 On 2 May 2017, at 17:57, Douglas Greve
 mailto:gr...@nmr.mgh.harvard.edu>> wrote:
This is a test we do before we release. The averages don't look out of
line. Putamen should be smaller because we now try to remove
claustrum. Small structures may have some large percent differences.
Some structures are not that meaningful (like the CC because it has no
real boundaries). The left lateral ventricle may be a problem. I've
seen cases where it totally gets filled in with WM in v6. Others are
hard to define -- when I would look at the scans there would not be a
good case for rejecting one and accepting the other (eg, pallidum and
thalamus don't have good contrast at typical mprage acq parameters).
On 5/2/17 3:56 AM, Knut J Bjuland wrote:
 Dear FreeSurfer experts,

When I ran Freesurfer 5.3 and Freesurfer 6.0 I ran with default settings us
ing this command. recon-all -s (id) -all for both Freesurfer 5.3 and FreeSu
rfer 6.0.
Are these differences larger than one would expect? I think that 100% may b
e a little high? The difference in volume between Freesurfer 5.3 and Freesu
rfer 6.0 is shown in the table below calculated using asegstatsdiff.

Knut Jørgen Bjuland
Volume name
Mean(range)
Left-Lateral-Ventricle
7.4  (-0.13,130.72)
Left-Cerebellum-White-Matter
0.64  (-22.9,56.15)
Left-Cerebellum-Cortex
7.56  (-10.3,19.17)
Left-Thalamus-Proper
0.12  (-16.31,32.42)
Left-Caudate
-4.25  (-12,33.64)
Left-Putamen
-16.72  (-27.99,8.3)
Left-Pallidum
16.23  (-22.94,84.75)
Left-Hippocampus
-1.74  (-13.53,15.93)
Left-Amygdala
2.29  (-19.28,41.04)
Right-Lateral-Ventricle
4.6  (-24.77,102.12)
Right-Cerebellum-White-Matter
-3.2  (-20.87,49.37)
Right-Cerebellum-Cortex
4.88  (-12.99,14.36)
Right-Thalamus-Proper
1.06  (-22.34,19.99)
Right-Caudate
-6.08  (-14.59,6.13)
Right-Putamen
-12.87  (-31.37,10.17)
Right-Pallidum
14.01  (-27.79,89.19)
Right-Hippocampus
-1.71  (-9.29,12.02)
Right-Amygdala
3.74  (-18.6,51.01)
Right-Accumbens-area
-9.14  (-37.89,61.02)
CC_Posterior
22.07  (-47.04,525.51)
CC_Mid_Posterior
53.59  (-11.3,537.3)
CC_Central
36.77  (-21.36,317.24)
CC_Mid_Anterior
24.09  (-18.86,128.31)
CC_Anterior
10.64  (-33.71,152.33)
lhCortexVol
3.13  (-1.31,12.37)
rhCortexVol
3.16  (-0.36,14.2)
CortexVol
3  (-4.47,13.26)
EstimatedTotalIntraCranialVol
0.65  (-0.05,26.52)

 On 21 Apr 2017, at 20:01, Knut J Bjuland
 mailto:knutjor...@outlook.com>> wrote:
Dear FreeSurfer expert,

I have compared the aseg volume between FreeSurfer 5.3 and FreeSurfer 6.0 w
ith asegstatsdiff from FreeSurfer 6.0 for each subject in my data set. I ha
ve enclosed the range for some of the volume. I found the largest differenc
es in subcortical structures, especially in Corpus callosum(CC). I found th
at FreeSurfer 6.0 CC posterior volume was 525.51 % larger than in FreeSurfe
r 5.3. Nevertheless, these differences were much smaller for lhCortex, but
?? ?also here FreeSurfer 6.0 was on average larger than FreeSurfer 5.3. I ran t
he FreeSurfer 6.0 using the same option as FreeSurfer 5.30. Both versions o
f FreeSurfer were run on Centos. I am also enclosing a
table with mean values along with min and max  for
differences between FreeSurfer 5.3 and FreeSurfer 6.0 aseg
volumes.


Best regards
Knut Jørgen Bjuland PhD
NTNU
Left-Lateral-Ventricle
7.4  (-0.13,130.72)
Left-Cerebellum-White-Matter
0.64  (-22.9,56.15)
Left-Cerebellum-Cortex
7.56  (-10.3,19.17)
Left-Thalamus-Proper
0.12  (-16.31,32.42)
Left-Caudate
-4.25  (-12,33.64)
Left-Putamen
-16.72  (-27.99,8.3)
Left-Pallidum
16.23  (-22.94,84.75)
Left-Hippocampus
-1.74  (-13.53,15.93)
Left-Amygdala
2.29  (-19.28,41.04)
Right-Lateral-Ventricle
4.6  (-24.77,102.12)
Right-Cerebellum-White-Matter
-3.2  (-20.87,49.37)
Right-Cerebellum-Cortex
4.88  (-12.99,14.36)
Right-Thalamus-Proper
1.06  (-22.34,19.99)
Right-Caudate
-6.08  (-14.59,6.13)
Right-Putamen
-12.87  (-31.37,10.17)
Right-Pallidum
14.01  (-27.79,89.19)
Right-Hippocampus
-1.71  (-9.29,12.02)
Right-Amygdala
3.74  (-18.6,51.01)
Right-Accumbens-area
-9.14  (-37.89,61.02)
CC_Posterior
22.07  (-47.04,525.51)
CC_Mid_Posterior
53.59  (-11.3,537.3)
CC_Central
36.77  (-21.36,317.24)
CC_Mid_Anterior
24.09  (-18.86,128.31)
CC_Anterior
10.64  (-33.71,152.33)
lhCortexVol
3.13  (-1.31,12.37)
rhCortexVol
3.16  (-0.36,14.2)
CortexVol
3  (-4.47,13.26)
EstimatedTotalIntraCranialVol
0.65  (-0.05,26.52)
_

Re: [Freesurfer] Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0

[Knut J Bjuland]

Hi Bruce

Where should I upload  orig.mgz, nu.mgz, aseg.mgz and voxel cords?

Knut Jørgen

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Friday, May 5, 2017 4:44:49 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Differences in aseg volumes between FreeSurfer 5.3.0 
and FreeSurfer 6.0

Include the orig.mgz and voxel cords and I'll see if I have already fixed it

On May 5, 2017, at 10:11 AM, Knut J Bjuland 
mailto:knutjor...@outlook.com>> wrote:

Hi Bruce

I found some filled-in occipital horn and some in the anterior parts. I can 
upload nu.mgz and aseg.mgz for a subject with problems with lateral ventricle.

Cheers
Knut Jørgen




On 4 May 2017, at 16:54, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi Knut

where is it being filled? If it is the occipital horn we may soon have a patch 
for it

cheers
Bruce
On Thu, 4 May 2017, Knut J Bjuland wrote:

Hi
Are there any options that I can use in Freesurfer 6.0 that can prevent lef
t lateral ventricle from being filled with WM? Should I send the MPRAGE seq
uence information?
Knut Jørgen

 On 2 May 2017, at 17:57, Douglas Greve
 mailto:gr...@nmr.mgh.harvard.edu>> wrote:
This is a test we do before we release. The averages don't look out of
line. Putamen should be smaller because we now try to remove
claustrum. Small structures may have some large percent differences.
Some structures are not that meaningful (like the CC because it has no
real boundaries). The left lateral ventricle may be a problem. I've
seen cases where it totally gets filled in with WM in v6. Others are
hard to define -- when I would look at the scans there would not be a
good case for rejecting one and accepting the other (eg, pallidum and
thalamus don't have good contrast at typical mprage acq parameters).
On 5/2/17 3:56 AM, Knut J Bjuland wrote:
 Dear FreeSurfer experts,

When I ran Freesurfer 5.3 and Freesurfer 6.0 I ran with default settings us
ing this command. recon-all -s (id) -all for both Freesurfer 5.3 and FreeSu
rfer 6.0.
Are these differences larger than one would expect? I think that 100% may b
e a little high? The difference in volume between Freesurfer 5.3 and Freesu
rfer 6.0 is shown in the table below calculated using asegstatsdiff.

Knut Jørgen Bjuland
Volume name
Mean(range)
Left-Lateral-Ventricle
7.4  (-0.13,130.72)
Left-Cerebellum-White-Matter
0.64  (-22.9,56.15)
Left-Cerebellum-Cortex
7.56  (-10.3,19.17)
Left-Thalamus-Proper
0.12  (-16.31,32.42)
Left-Caudate
-4.25  (-12,33.64)
Left-Putamen
-16.72  (-27.99,8.3)
Left-Pallidum
16.23  (-22.94,84.75)
Left-Hippocampus
-1.74  (-13.53,15.93)
Left-Amygdala
2.29  (-19.28,41.04)
Right-Lateral-Ventricle
4.6  (-24.77,102.12)
Right-Cerebellum-White-Matter
-3.2  (-20.87,49.37)
Right-Cerebellum-Cortex
4.88  (-12.99,14.36)
Right-Thalamus-Proper
1.06  (-22.34,19.99)
Right-Caudate
-6.08  (-14.59,6.13)
Right-Putamen
-12.87  (-31.37,10.17)
Right-Pallidum
14.01  (-27.79,89.19)
Right-Hippocampus
-1.71  (-9.29,12.02)
Right-Amygdala
3.74  (-18.6,51.01)
Right-Accumbens-area
-9.14  (-37.89,61.02)
CC_Posterior
22.07  (-47.04,525.51)
CC_Mid_Posterior
53.59  (-11.3,537.3)
CC_Central
36.77  (-21.36,317.24)
CC_Mid_Anterior
24.09  (-18.86,128.31)
CC_Anterior
10.64  (-33.71,152.33)
lhCortexVol
3.13  (-1.31,12.37)
rhCortexVol
3.16  (-0.36,14.2)
CortexVol
3  (-4.47,13.26)
EstimatedTotalIntraCranialVol
0.65  (-0.05,26.52)

 On 21 Apr 2017, at 20:01, Knut J Bjuland
 mailto:knutjor...@outlook.com>> wrote:
Dear FreeSurfer expert,

I have compared the aseg volume between FreeSurfer 5.3 and FreeSurfer 6.0 w
ith asegstatsdiff from FreeSurfer 6.0 for each subject in my data set. I ha
ve enclosed the range for some of the volume. I found the largest differenc
es in subcortical structures, especially in Corpus callosum(CC). I found th
at FreeSurfer 6.0 CC posterior volume was 525.51 % larger than in FreeSurfe
r 5.3. Nevertheless, these differences were much smaller for lhCortex, but
?? ?also here FreeSurfer 6.0 was on average larger than FreeSurfer 5.3. I ran t
he FreeSurfer 6.0 using the same option as FreeSurfer 5.30. Both versions o
f FreeSurfer were run on Centos. I am also enclosing a
table with mean values along with min and max  for
differences between FreeSurfer 5.3 and FreeSurfer 6.0 aseg
volumes.


Best regards
Knut Jørgen Bjuland PhD
NTNU
Left-Lateral-Ventricle
7.4  (-0.13,130.72)
Left-Cerebellum-White-Matter
0.64  (-22.9,56.15)
Left-Cerebellum-Cortex
7.56  (-10.3,19.17)
Left-Thalamus-Proper
0.12  (-16.31,32.42)
Left-Caudate
-4.25  (-12,33.64)
Left-Putamen
-16.72  (-27.99,8.3)
Left-Pallidum
16.23  (-22.94,84.75)
Left-Hippocampus
-1.74  (-13.53,15.93)
Left-Amygdala
2.29  (-19.28,41.04)
Right-Lateral-Ventricle
4.6  (-24.77,102.12)
Right-Cerebellum-White-Matter
-3.2  (-20.87,49.37)
Right-Cerebellum-Cortex
4.88  (-12.99,14.36)
Right-Thalamus-Proper
1.06  (-22.34,19.99)
Right-Caudate
-6.08  (-14.59,6.13

Re: [Freesurfer] Differences in aseg volumes between FreeSurfer 5.3.0 and FreeSurfer 6.0

[Knut J Bjuland]

Hi Bruce

I have uploaded the subject as subject_7.tar.gz and subject_7.zip at 
transfer/incoming on 
surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/>
I can also upload the same subject where I used fs53.


Thanks
Knut Jørgen

On 7 May 2017, at 16:26, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi Knut

the best would be if you can just tar and gzip the entire subject dir and 
upload it according to these dirs:

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange

cheers
Bruce
On Sat, 6 May 2017, Knut J Bjuland wrote:

Hi Bruce
Where should I upload  orig.mgz, nu.mgz, aseg.mgz and voxel cords?
Knut Jørgen

From: freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Bruce Fischl

Sent: Friday, May 5, 2017 4:44:49 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Differences in aseg volumes between FreeSurfer
5.3.0 and FreeSurfer 6.0
Include the orig.mgz and voxel cords and I'll see if I have already fixed it
On May 5, 2017, at 10:11 AM, Knut J Bjuland  wrote:

 Hi Bruce
I found some filled-in occipital horn and some in the anterior parts. I can
 upload nu.mgz and aseg.mgz for a subject with problems with lateral ventri
cle.
Cheers
Knut Jørgen

 On 4 May 2017, at 16:54, Bruce Fischl
  wrote:
Hi Knut
where is it being filled? If it is the occipital horn we may
soon have a patch for it
cheers
Bruce
On Thu, 4 May 2017, Knut J Bjuland wrote:

 Hi
Are there any options that I can use in Freesurfer 6.0 that can prevent lef
t lateral ventricle from being filled with WM? Should I send the MPRAGE seq

 uence information?
 Knut Jørgen

  On 2 May 2017, at 17:57, Douglas Greve
   wrote:
 This is a test we do before we release. The averages
 don't look out of
 line. Putamen should be smaller because we now try
 to remove
 claustrum. Small structures may have some large
 percent differences.
 Some structures are not that meaningful (like the CC
 because it has no
 real boundaries). The left lateral ventricle may be
 a problem. I've
 seen cases where it totally gets filled in with WM
 in v6. Others are
 hard to define -- when I would look at the scans
 there would not be a
 good case for rejecting one and accepting the other
 (eg, pallidum and
 thalamus don't have good contrast at typical mprage
 acq parameters).
 On 5/2/17 3:56 AM, Knut J Bjuland wrote:
  Dear FreeSurfer experts,

When I ran Freesurfer 5.3 and Freesurfer 6.0 I ran with default settings us
ing this command. recon-all -s (id) -all for both Freesurfer 5.3 and FreeSu

 rfer 6.0.
Are these differences larger than one would expect? I think that 100% may b
e a little high? The difference in volume between Freesurfer 5.3 and Freesu

 rfer 6.0 is shown in the table below calculated using asegstatsdiff.

 Knut Jørgen Bjuland
 Volume name
 Mean(range)
 Left-Lateral-Ventricle
 7.4  (-0.13,130.72)
 Left-Cerebellum-White-Matter
 0.64  (-22.9,56.15)
 Left-Cerebellum-Cortex
 7.56  (-10.3,19.17)
 Left-Thalamus-Proper
 0.12  (-16.31,32.42)
 Left-Caudate
 -4.25  (-12,33.64)
 Left-Putamen
 -16.72  (-27.99,8.3)
 Left-Pallidum
 16.23  (-22.94,84.75)
 Left-Hippocampus
 -1.74  (-13.53,15.93)
 Left-Amygdala
 2.29  (-19.28,41.04)
 Right-Lateral-Ventricle
 4.6  (-24.77,102.12)
 Right-Cerebellum-White-Matter
 -3.2  (-20.87,49.37)
 Right-Cerebellum-Cortex
 4.88  (-12.99,14.36)
 Right-Thalamus-Proper
 1.06  (-22.34,19.99)
 Right-Caudate
 -6.08  (-14.59,6.13)
 Right-Putamen
 -12.87  (-31.37,10.17)
 Right-Pallidum
 14.01  (-27.79,89.19)
 Right-Hippocampus
 -1.71  (-9.29,12.02)
 Right-Amygdala
 3.74  (-18.6,51.01)
 Right-Accumbens-area
 -9.14  (-37.89,61.02)
 CC_Posterior
 22.07  (-47.04,525.51)
 CC_Mid_Posterior
 53.59  (-11.3,537.3)
 CC_Central
 36.77  (-21.36,317.24)
 CC_Mid_Anterior
 24.09  (-18.86,128.31)
 CC_Anterior
 10.64  (-33.71,152.33)
 lhCortexVol
 3.13  (-1.31,12.37)
 rhCortexVol
 3.16  (-0.36,14.2)
 CortexVol
 3  (-4.47,13.26)
 EstimatedTotalIntraCranialVol
 0.65  (-0.05,26.52)

  On 21 Apr 2017, at 20:01, Knut J Bjuland
   wrote:
 Dear FreeSurfer expert,

I have compared the aseg volume between FreeSurfer 5.3 and FreeSurfer 6.0 w
ith asegstatsdiff from FreeSurfer 6.0 for each subject in my data set. I ha
ve enclosed the range for some of the volume. I found the largest differenc
es in subcortical structures, especially in Corpus callosum(CC). I found th
at FreeSurfer 6.0 CC posterior volume was 525.51 % larger than in FreeSurfe

 r 5.3. Nevertheless, these differences were much smaller for lhCortex, but
???also here FreeSurfer 6.0 was on av

[Freesurfer] Tksurfer will not accept key input in Ubuntu 14.04

[Knut J Bjuland]

Bug report
I am unable to enter number using the keyboard when using Tksurfer under 
Ubuntu 14.04. I have tried to enter a number in overlay configuration 
and smooth overlay.  Is there any workaround? I have this bug on two 
different system with Ubuntu 14.04.

Best regards
Knut J  Bjuland
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[Freesurfer] Longitudinal recon-all –localGI after error on cross recon-all –localGI and optimal smoothing

[Knut J Bjuland]

Hi
Due to aberrantly high for a few of the subjects, I ran recon-all 
-autorecon2-wm -randomness -autorecon3  –hemi ?h before, calculating the 
localGI index.  However, I intended to use these data in a longitudinal 
stream.   These subject that were reprocessed using recon-all  
-autorecon2-wm -randomness -autorecon3 , and should I rerun the 
longitudinal stream for these subjects before doing I use recon-all 
–long id base_id –localGI?
What are the optimal smoothing when using the linear mixed models?

Best regards
Knut J Bjuland

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Re: [Freesurfer] FDR correction in Matlab

[Knut J Bjuland]

Hi

help lme_mass_FDR

and

help /lme_mass_FDR2/

For help with input and output?

Knut J



On 05/26/2014 11:24 AM, Nandita Vijayakumar wrote:

Hi FS team,

I was wondering if you could help me with FDR correction for linear 
mixed models within Matlab. I have run FDR2 correction using the 
following command:
/dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0); 
/However, dvtx was empty, so I would like to try lme_mass_FDR instead. 
Could you please help me with the command for FDR correction, as well 
as how to visualise the corrected significance map in FreeSurfer?


Thank you,

Nandi Vijayakumar

MPsych (Clinical Neuropsychology) / PhD Candidate
ADAPT | Adolescent Development and Psychopathology Team
Melbourne School of Psychological Sciences
University of Melbourne
Email: _n.vijayaku...@student.unimelb.edu.au 
_



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Re: [Freesurfer] Longitudinal recon-all –localGI after error on cross recon-all –localGI and optimal smoothing

[Knut J Bjuland]

Hi Marie

Thank you for your reply.  I have one additional question. Is there any 
difference in results when using Matlab 2012a compared to Matlab 2013b 
for localGI?
Best regards,
Knut J




On 05/29/2014 11:05 PM, Marie Schaer wrote:
> Hi Knut,
>
> Basically as you reprocessed totally your surfaces, yes it is safer to 
> reprocess the longitudinal stream to make sure that everything is coherent.
>
> As for the smoothing, lGI is already inherently very smoothed, so you 
> definitely have to take a lower FWHM than for thickness. When you run qdec, 
> it computes for you automatically the level of "smoothedness" in your data. 
> You'll see that with thickness this level is more or less similar to the FWHM 
> you used, whereas with lGI it definitely is higher. So you can play with the 
> FWHM until you reach the level of smoothedness that you want. I'd say that 
> with linear mixed model you want the same level of smoothing that you have in 
> equivalent cross-sectional analyses (i.e. most usually 10-15mm).
>
> Hope this helps,
>
> Marie
>
>
> On May 29, 2014, at 1:29 PM, Knut J Bjuland 
>   wrote:
>
>> Hi
>> Due to aberrantly high for a few of the subjects, I ran recon-all
>> -autorecon2-wm -randomness -autorecon3  –hemi ?h before, calculating the
>> localGI index.  However, I intended to use these data in a longitudinal
>> stream.   These subject that were reprocessed using recon-all
>> -autorecon2-wm -randomness -autorecon3 , and should I rerun the
>> longitudinal stream for these subjects before doing I use recon-all
>> –long id base_id –localGI?
>> What are the optimal smoothing when using the linear mixed models?
>>
>> Best regards
>> Knut J Bjuland
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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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>
>


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[Freesurfer] aberrantly high LGI value with localGI on longitudinal subjects, What is the best curse of action?

[Knut J Bjuland]

Dear Freesurfers,

I have run localGI on longitudinal data. However, I got three 
longitudinal subject with value is aberrantly high LGI value. What is 
the best curse of action? Should I rerun the cross section with recon 
-all -s id -autorecon-2-wm -autorecon3 -randomness, and then recreate 
the base before running the localGI again? Or is there any other options?

regards

Knut J Bjuland
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[Freesurfer] tksurfer bug report, input from keyboard is not accepted in ubuntu 14.04

[Knut J Bjuland]

Dear freesurfer
I have used tksurfer on Ubunt 14.04. However, I have one problem. 
Tksurfer does not respond to any input from the keyboard when I am 
running it. I can only access it though the mouse. For instance, I can 
enter threshold values, in overlay configuration option? Are there any 
workaround?
Knut J Bjuland
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[Freesurfer] mri_convert WARNING: files are not found to be different and cannot be sorted and cannot fit in 256^3 mm^3 volume.

[Knut J Bjuland]

Dear FreeSurfers,

I have imported several dicom files with recon-all -i -subjid id. All 
files were imported correctly, apart from one subjects. When I try to 
convert it direcelty with mri_convert -ot mgz dicom//1.dcm -s 

I get this error message.

WARNING: files are not found to be different and cannot be sorted
File1: ../../../../dicom//162.dcm
File2: ../../../../dicom//2.dcm

When I process the subject with recon-all -s  -all. I got this message.

WARNING 
=====
The physical sizes are (240.00 mm, 240.00 mm, 384.00 mm), which cannot 
fit in 256^3 mm^3 volumes.
The resulting volume will have 384 slices.
If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu)


Can you please advise me how to import the dicom files? Should I convert 
them to nifti. Will this affect the end results compared to the other 
subjects that were imported correctly?


Knut J


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Re: [Freesurfer] mri_convert WARNING: files are not found to be different and cannot be sorted and cannot fit in 256^3 mm^3 volume.

[Knut J Bjuland]

Cut-and-paste the following info into your FreeSurfer problem report:
-

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Debian version: jessie/sid

Kernel info: Linux 3.13.0-30-generic x86_64

-
Please include the following additional information in your report:

   1) subject name
   2) the entire command-line executed
   3) the error message generated
   4) optionally include the subject's /script/recon-all.log

See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

recon-all -i dicom//1.dcm -s 


cd /mri/orig
and mri_convert -ot mgz /pat/dicom//1.dcm 001.mgz with the same results

knut j





On 07/05/2014 12:36 PM, Knut J Bjuland wrote:
> Dear FreeSurfers,
>
> I have imported several dicom files with recon-all -i -subjid id. All
> files were imported correctly, apart from one subjects. When I try to
> convert it direcelty with mri_convert -ot mgz dicom//1.dcm -s 
>
> I get this error message.
>
> WARNING: files are not found to be different and cannot be sorted
> File1: ../../../../dicom//162.dcm
> File2: ../../../../dicom//2.dcm
>
> When I process the subject with recon-all -s  -all. I got this message.
>
> WARNING
> =====
> The physical sizes are (240.00 mm, 240.00 mm, 384.00 mm), which cannot
> fit in 256^3 mm^3 volumes.
> The resulting volume will have 384 slices.
> If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu)
>
>
> Can you please advise me how to import the dicom files? Should I convert
> them to nifti. Will this affect the end results compared to the other
> subjects that were imported correctly?
>
>
> Knut J
>
>
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>
>
> 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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Re: [Freesurfer] mri_convert WARNING: files are not found to be different and cannot be sorted and cannot fit in 256^3 mm^3 volume.

[Knut J Bjuland]

/dicom//305.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//146.dcm
File2: /home/freesurfer/subjects/dicom//306.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//147.dcm
File2: /home/freesurfer/subjects/dicom//307.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//148.dcm
File2: /home/freesurfer/subjects/dicom//308.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//149.dcm
File2: /home/freesurfer/subjects/dicom//309.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//150.dcm
File2: /home/freesurfer/subjects/dicom//310.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//151.dcm
File2: /home/freesurfer/subjects/dicom//311.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//152.dcm
File2: /home/freesurfer/subjects/dicom//312.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//153.dcm
File2: /home/freesurfer/subjects/dicom//313.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//154.dcm
File2: /home/freesurfer/subjects/dicom//314.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//155.dcm
File2: /home/freesurfer/subjects/dicom//315.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//156.dcm
File2: /home/freesurfer/subjects/dicom//316.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//157.dcm
File2: /home/freesurfer/subjects/dicom//317.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//158.dcm
File2: /home/freesurfer/subjects/dicom//318.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//159.dcm
File2: /home/freesurfer/subjects/dicom//319.dcm
WARNING: files are not found to be different and cannot be sorted
File1: /home/freesurfer/subjects/dicom//160.dcm
File2: /home/freesurfer/subjects/dicom//320.dcm
INFO: (192 192 320), nframes = 1, ismosaic=0
PE Dir ROW ROW
AutoAlign matrix detected
AutoAlign Matrix -
  1.000   0.000   0.000   0.000;
  0.000   1.000   0.000   0.000;
  0.000   0.000   1.000   0.000;
  0.000   0.000   0.000   1.000;

Volume information for 1.dcm
   type: siemens_dicom
 dimensions: 192 x 192 x 320
voxel sizes: 1.2500, 1.2500, 1.2000
   type: SHORT (4)
fov: 192.000
dof: 0
 xstart: -96.0, xend: 96.0
 ystart: -96.0, yend: 96.0
 zstart: -160.0, zend: 160.0
 TR: 2400.00 msec, TE: 3.61 msec, TI: 1000.00 msec, flip 
angle: 8.00 degrees
nframes: 1
PhEncDir: ROW
ras xform present
 xform info: x_r =  -0.1052, y_r =   0.0617, z_r =  -0.9925, c_r =   
-87.9477
   : x_a =  -0.9944, y_a =  -0.0065, z_a =   0.1050, c_a 
=32.3012
   : x_s =  -0., y_s =  -0.9981, z_s =  -0.0620, c_s =   
-29.8398
Orientation   : PIL
Primary Slice Direction: sagittal

voxel to ras transform:
-0.1315   0.0771  -1.1910   107.8465
-1.2431  -0.0082   0.1260   132.2527
-0.  -1.2476  -0.0744   101.8353
 0.   0.   0. 1.

voxel-to-ras determinant -1.875

ras to voxel transform:
-0.0842  -0.7956  -0.   114.2937
 0.0493  -0.0052  -0.798576.6815
-0.8271   0.0875  -0.051782.8883
 0.   0.   0. 1.




On 07/05/2014 03:46 PM, Bruce Fischl wrote:
> Hi Knut
>
> can you run mri_info on that dicom file?
>
> thanks
> Bruce
> On Sat, 5 Jul 2014, Knut J Bjuland
> wrote:
>
>> Cut-and-paste the following info into your FreeSurfer problem report:
>> -
>>
>> FREESURFER_HOME: /usr/local/freesurfer
>>
>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>
>> Debian version: jessie/sid
>>
>> Kernel info: Linux 3.13.0-30-generic x86_64
>>
>> -
>> Please include the following additional information in your report:
>>
>>1) subject name
>>2) the entire command-line executed
>>3) the error message generated
>