date:20180921

[Freesurfer] Freeview error

2018-09-21 Thread Md. Mamun Al-Amin

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Dear Experts
I have been encountered a problem opening Freeview window in Mac Terminal.
Could you please help me troubleshooting this problem?
Here is the screenshot.

Thanks in advance.

-- 

Kind regards

Md. Mamun Al-Amin
--
*PhD Candidate, Queensland Brain Institute*

*The University of Queensland*
*Building 79, St Lucia QLD 4072*
*https://qbi.uq.edu.au/profile/877/md-mamun-al-amin
*
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Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

2018-09-21 Thread Yendiki, Anastasia

Thank you. Can you also send screenshots of your original DWIs, if they don't 
look like this?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Matthew Grecsek 

Sent: Friday, September 21, 2018 10:27:37 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

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Hi Anastasia,

Please see attached screenshots from dwi.nii.gz. The first 4 are rotated 90 
degrees around y axis and the last 2 are top and bottom.

Thanks,

-Matt

On Thu, Sep 20, 2018 at 7:19 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Matt - I am asking about the raw diffusion images. You sent a screenshot of 
an FA map that looked truncated, with slices missing from the bottom of the 
brain (which explains why the error happened for the ILF, which would go 
through that missing part of the brain). Does dmri/dwi.nii.gz look like that?

Best,

a.y

From: 
freesurfer-boun...@nmr.mgh.harvard.edu

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek mailto:m...@grecsek.com>>
Sent: Thursday, September 20, 2018 2:00:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

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If you are referring to the T1 raw images, no they appear normal and the 
standard Freesurfer pipeline generates correct volumes.

If you are referring to the DTI raw images off the scanner, they also don't 
appear to have brain parts missing, although some appear more noisy and 
pixelated than others.

This is a mTBI subject with no other anatomical brain anomalies scanned with a 
Siemens 3T.

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700

Do the raw images look like that too?

From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Matthew Grecsek 
mailto:m...@grecsek.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, September 19, 2018 at 4:07 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

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Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and kicked
off the process with -s and -i flags.

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain that
is cut off from any of the images? Also, can you attach your config file?
Thanks!

a.y

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[Freesurfer] mri_glmfit-sim error

2018-09-21 Thread C.P.E. Rollins

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Hello Freesurfer Developpers,

I'm trying to use mri_glmfit-sim to make clusterwise corrections but am 
running into the following error:

- XFM matrix (RAS2RAS) ---
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/mri/transforms/talairach.xfm
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;
MRISread('\ufffd\ufffd): could not open file
No such file or directory

Reading source surface 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white
mri_surfcluster.bin: could not read surface 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white

No such file or directory

I've attached here the log file. I was wondering if you had any insights 
into the error?


Thanks a lot for your help.

Colleen
cd /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
/applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim
--glmdir rh.10.thickness.glmdir --cache 2 abs --cwp 0.05 --2spaces

$Id: mri_glmfit-sim,v 1.60.2.4 2016/11/17 18:01:28 zkaufman Exp $
Fri Sep 21 16:21:47 BST 2018
Linux wbic-gate-1 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 
GNU/Linux
cper2
setenv SUBJECTS_DIR /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0

Original mri_glmfit command line:
cmdline mri_glmfit.bin --y rh.10.thickness.post.mgh --fsgd FSGD.txt doss --C 
contrast_doss.txt --surf fsaverage rh --cortex --glmdir rh.10.thickness.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = doss
fwhm = 14.003044
CSD 
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/rh/cortex/fwhm14/abs/th20/mc-z.csd
mri_surfcluster --in rh.10.thickness.glmdir/contrast_doss.txt/sig.mgh --mask 
rh.10.thickness.glmdir/mask.mgh --cwsig 
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.cluster.mgh --sum 
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.cluster.summary 
--ocn rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.ocn.mgh 
--annot aparc --cwpvalthresh 0.05 --o 
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.masked.mgh 
--no-fixmni --csd 
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/rh/cortex/fwhm14/abs/th20/mc-z.csd
 --csdpdf rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.pdf.dat 
--vwsig rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.voxel.mgh 
--vwsigmax 
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.voxel.max.dat 
--oannot rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.ocn.annot 
--bonferroni 2 --surf white
Creating CDFs from CSD files
csd->threshsign = 0
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $
hemi   = rh
srcid  = rh.10.thickness.glmdir/contrast_doss.txt/sig.mgh 
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = abs
thmin  = 2
thmax  = -1
fdr= -1
minarea= 0
Bonferroni  = 2
xfmfile= talairach.xfm
nth = -1
outid= 
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.masked.mgh MGH
ocnid= rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.ocn.mgh 
MGH
sumfile  = 
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.cluster.summary
subjectsdir= /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
FixMNI = 0
Found 148285 vertices in mask
Found 148285 vertices in mask
Found 148285 points in clabel.
- XFM matrix (RAS2RAS) ---
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/mri/transforms/talairach.xfm
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;

Reading source surface 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white
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[Freesurfer] calculated cortical thickness from segmented binary gray matter and white matter images from other software

2018-09-21 Thread yuanchao.zha...@gmail.com

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Dear experts,

Is there any way I can calculate the cortical thickness based on gray matter 
and white matter binary images from other software. 
I mean I have a image in native space with white matter voxels labelled as 10 
and gray matter voxels labelled as 5.
Is there any way I can manage to calculate the cortical maps from this image 
using freesurfer?

Thanks a lot!

Best,

Yuanchao Zhang



yuanchao.zha...@gmail.com
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Re: [Freesurfer] Ynt: Ynt: linux data and macbook

2018-09-21 Thread Bruce Fischl

Hi Emre

we have worked hard to reduce the differences in the results across 
platform, but in general you should analyze all your subjects on the same 
hardware/software. You can certainly run higher level analysis on the mac 
if all your subjects have been run through recon-all on a linux box, but 
don't run some recons on mac and some on linux

cheers
Bruce

On Fri, 21 Sep 2018, emre wrote:

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Different in the workplace with the computer at home. linux at work, macbook at 
home. 
Is it a problem if I work two?

macbook recon -all -all =(?) linux recon - all -all

Gönderen Outlook

Gönderen: Greve, Douglas N.,Ph.D. 
Gönderildi: 21 Eylül 2018 Cuma 07:31
Kime: emre; Freesurfer support list
Konu: Re: Ynt: [Freesurfer] linux data and macbook  
sorry, we need way more detail

On 9/20/18 11:59 PM, emre wrote:

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  thalamus and hippocampus

Gönderen Outlook

Gönderen: Greve, Douglas N.,Ph.D.  adına
freesurfer-boun...@nmr.mgh.harvard.edu 
Gönderildi: 21 Eylül 2018 Cuma 00:15
Kime: freesurfer@nmr.mgh.harvard.edu
Konu: Re: [Freesurfer] linux data and macbook  
what segmentation?

On 09/20/2018 12:53 PM, emre wrote:
>
> External Email - Use Caution
>
>
> hi freesurfer team,
>
> I analyzed the data at linux, this data i can use in macbook for
> segmantation?
> (linux only reconall -all, other analyze in macbook)
>
> Is it possible without problems?
>
>
> thanks, good luck
>
> Gönderen Outlook 
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Best way to update Freeview

2018-09-21 Thread Maksimovskiy, Arkadiy

Dear Experts,

Updating Freeview came up as a potential solution for a problem in a different 
thread, so I posting this as a separate issue, since the question stands on its 
own.

I am currently using “Freeview Version 2.0” – Build Jan 19 2017. This version 
came with the Freesurfer 6.0 package, but from browsing the wiki, it seems that 
this version is out of date and requires a separate update.

When I attempted to update Freeview, by clicking on “freeview_osx.tar.gz” using 
the link at Step 2 for Mac (located at this page: 
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview), I get the following 
error message: “The requested URL 
/pub/dist/freesurfer/freeview/freeview_osx.tar.gz was not found on this server.”

I was wondering if there might a different way to obtain the latest Freeview 
version.

Thank you for your help,
arkadiy

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Re: [Freesurfer] Dead Links to 3rd Party Libraries

2018-09-21 Thread Dicamillo, Robert

Hello Joseph,

Try this link for the 3rd party libs (to use with the cmake build)

http://surfer.nmr.mgh.harvard.edu/pub/data/fspackages/prebuilt/

- rob

On Sep 20, 2018, at 8:39 PM, Moon, Joseph Young-Joon 
mailto:moo...@llnl.gov>> wrote:


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Hi,

I’m trying to build Freesurfer according to the instructions 
athttp://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page

However, the FTP link to prebuilt 3rd party libraries seems to be down. The 
directory “ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt” 
is no longer being hosted.

Please let me know if I misunderstood something!

Thanks,
Joseph Moon

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[Freesurfer] make_average_subject error

2018-09-21 Thread C.P.E. Rollins

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Hello Freesurfer Developpers,

I'm attempting to make a study specific template using all of my 
subjects as input using the make_average_subject command, but am 
receiving the following error:

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/mri/aseg.presurf.hypos.mgz

ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
Segmentation fault (core dumped)
Linux wbic-cs-5 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) 
x86_64 GNU/Linux


recon-all -s average_v2 exited with ERRORS at Fri Sep 21 11:11:25 BST 
2018


I've attached here the full log file.

I read in this forum: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57030.html 
to try installing the following patch: 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
and had asked our computing support team to install it before the 
current run of make_average_subject, so the error seems to be happening 
despite the patch. I would greatly appreciate your suggestions for 
resolving the error.


Thanks very much,

ColleenFri Sep 21 11:06:50 BST 2018
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2
/applications/freesurfer/freesurfer_6.0.0/bin/recon-all
-s average_v2 -cortribbon -aparc2aseg
subjid average_v2
setenv SUBJECTS_DIR /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0
Actual FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux wbic-cs-5 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksizeunlimited
coredumpsize unlimited
memoryuse37748736 kbytes
vmemoryuse   unlimited
descriptors  65536 
memorylocked unlimited
maxproc  193538 
maxlocks unlimited
maxsignal193538 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:  49564564   10631376   38933188  64716 1772526734152
-/+ buffers/cache:3719972   45844592
Swap: 16200696 133356   16067340


program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/21-10:06:50-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: cper2  Machine: wbic-cs-5  Platform: Linux  PlatformVersion: 3.16.0-6-amd64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/21-10:06:50-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: cper2  Machine: wbic-cs-5  Platform: Linux  PlatformVersion: 3.16.0-6-amd64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/21-10:06:50-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: cper2  Machine: wbic-cs-5  Platform: Linux  PlatformVersion: 3.16.0-6-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/09/21-10:06:50-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: cper2  Machine: wbic-cs-5  Platform: Linux  PlatformVersion: 3.16.0-6-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/21-10:06:50-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: cper2  Machine: wbic-cs-5  Platform: Linux  PlatformVersion: 3.16.0-6-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $

Re: [Freesurfer] matlab MEXFile error in thalamic nuclei segmentation script

2018-09-21 Thread Iglesias Gonzalez, Eugenio

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Hi Carme,
This has to do with the CentOS version.
Please try the version compiled on CentOS6 (that should fix the problem).
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Carme Uribe Codesal 

Reply-To: Freesurfer support list 
Date: Friday, 21 September 2018 at 10:03
To: Freesurfer support list 
Subject: [Freesurfer] matlab MEXFile error in thalamic nuclei segmentation 
script


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Dear FreeSurfer users,

I am trying to run the Thalamic nuclei and the hippocampal/amygdala 
segmentation scripts but there is an error with the matlab license.
The error message is:

LD_LIBRARY_PATH is 
.:/nas01/users/carme/freesurfer/MCRv84//runtime/glnxa64:/nas01/users/carme/freesurfer/MCRv84//bin/glnxa64:/nas01/users/carme/freesurfer/MCRv84//sys/os/glnxa64:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/libexec/NX3/lib64/Xinerama:/usr/lib/nx/X11
Invalid MEX-file 
'/tmp/MCR_714808722/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64':
 /lib64/libc.so.6: version `GLIBC_2.14' not found (required by 
/tmp/MCR_714808722/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64)

Error in kvlClear (line 11)

Error in SegmentThalamicNuclei (line 203)

MATLAB:invalidMEXFile

Thanks!

Carme Uribe
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Re: [Freesurfer] matlab MEXFile error in thalamic nuclei segmentation script

2018-09-21 Thread Fereshte

External Email - Use Caution

Hi Carme,
In case of MEX file errors,  I think you need to have the compilers
(Fortran and C). Check what suits your version the most.
Cheers,
Fereshte

On Fri, Sep 21, 2018 at 12:33 PM Carme Uribe Codesal 
wrote:

> External Email - Use Caution
>
> Dear FreeSurfer users,
>
> I am trying to run the Thalamic nuclei and the hippocampal/amygdala
> segmentation scripts but there is an error with the matlab license.
> The error message is:
>
> LD_LIBRARY_PATH is
> .:/nas01/users/carme/freesurfer/MCRv84//runtime/glnxa64:/nas01/users/carme/freesurfer/MCRv84//bin/glnxa64:/nas01/users/carme/freesurfer/MCRv84//sys/os/glnxa64:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/libexec/NX3/lib64/Xinerama:/usr/lib/nx/X11
> Invalid MEX-file
> '/tmp/MCR_714808722/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64':
> /lib64/libc.so.6: version `GLIBC_2.14' not found (required by
> /tmp/MCR_714808722/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64)
>
> Error in kvlClear (line 11)
>
> Error in SegmentThalamicNuclei (line 203)
>
> MATLAB:invalidMEXFile
>
> Thanks!
>
> Carme Uribe
> ___
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[Freesurfer] Ynt: Ynt: linux data and macbook

2018-09-21 Thread emre

External Email - Use Caution

Different in the workplace with the computer at home. linux at work, macbook at 
home.
Is it a problem if I work two?

macbook recon -all -all =(?) linux recon - all -all

Gönderen Outlook

Gönderen: Greve, Douglas N.,Ph.D. 
Gönderildi: 21 Eylül 2018 Cuma 07:31
Kime: emre; Freesurfer support list
Konu: Re: Ynt: [Freesurfer] linux data and macbook

sorry, we need way more detail

On 9/20/18 11:59 PM, emre wrote:

External Email - Use Caution

thalamus and hippocampus

Gönderen Outlook

Gönderen: Greve, Douglas N.,Ph.D. 
 adına 
freesurfer-boun...@nmr.mgh.harvard.edu

Gönderildi: 21 Eylül 2018 Cuma 00:15
Kime: freesurfer@nmr.mgh.harvard.edu
Konu: Re: [Freesurfer] linux data and macbook

what segmentation?

On 09/20/2018 12:53 PM, emre wrote:
>
> External Email - Use Caution
>
>
> hi freesurfer team,
>
> I analyzed the data at linux, this data i can use in macbook for
> segmantation?
> (linux only reconall -all, other analyze in macbook)
>
> Is it possible without problems?
>
>
> thanks, good luck
>
> Gönderen Outlook 
>
>
> ___
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[Freesurfer] matlab MEXFile error in thalamic nuclei segmentation script

2018-09-21 Thread Carme Uribe Codesal

External Email - Use Caution

Dear FreeSurfer users,

I am trying to run the Thalamic nuclei and the hippocampal/amygdala
segmentation scripts but there is an error with the matlab license.
The error message is:

LD_LIBRARY_PATH is
.:/nas01/users/carme/freesurfer/MCRv84//runtime/glnxa64:/nas01/users/carme/freesurfer/MCRv84//bin/glnxa64:/nas01/users/carme/freesurfer/MCRv84//sys/os/glnxa64:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/nas01/users/carme/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/libexec/NX3/lib64/Xinerama:/usr/lib/nx/X11
Invalid MEX-file
'/tmp/MCR_714808722/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64':
/lib64/libc.so.6: version `GLIBC_2.14' not found (required by
/tmp/MCR_714808722/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlGEMSMatlab.mexa64)

Error in kvlClear (line 11)

Error in SegmentThalamicNuclei (line 203)

MATLAB:invalidMEXFile

Thanks!

Carme Uribe
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[Freesurfer] GLM

2018-09-21 Thread 郑凤莲

External Email - Use Caution

Dear experts,


I am using FS 6.0 for some studies. I want to calculate the thickness 
difference between males and females in two group, Young group and Old group. 
In DODS model:


The first step: creat a FSDG file:
GroupDescriptorFile 2
Title Tutorial
Class Young, Female
Class Old, Male
Variables education
Input P01 Young Female 11
Input P02 Old  Male 9
Input P03 Young Male 10


The second step: creat contrast matrix
1 -1 -1 1 0 0 0 0
Is it right? I am not sure if the FSDG file and contrast file are right. 
Waiting for you to solve my problem.
Thanks for your attention and help.


Sincerely,
Zheng___
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Re: [Freesurfer] trac-all using nifti

2018-09-21 Thread Heidi Emmanuel Foo

External Email - Use Caution

Hi Anastasia,

Sure, I will try that. Thanks for the advice!

Regards,
Heidi

On Fri, Sep 21, 2018 at 4:49 PM Yendiki, Anastasia 
wrote:

> You need to specify one more option, like -prep, etc. Please follow the
> instructions on the tutorial and, if the problem persists, send the exact
> command line that you ran and the full text of the output that you got.
>
> On Sep 21, 2018 2:42 AM, Heidi Emmanuel Foo  wrote:
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> I think I ran trac-all -c config.txt.
>
> Regards,
> Heidi
>
> On Thu, Sep 20, 2018 at 10:18 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> What is the trac-all command line that you run?
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo <
>> heidifo...@gmail.com>
>> *Sent:* Wednesday, September 19, 2018 11:06:09 PM
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] trac-all using nifti
>>
>>
>> External Email - Use Caution
>>
>> Hi Anastasia,
>>
>> Nope, I don't actually get any output and/or log file.
>>
>> Regards,
>> Heidi Foo
>>
>>
>>
>> On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>> Hi Heidi - The config file that you sent looked fine to me. What is the
>> trac-all command line that you run, and do you get any other output (like a
>> trac-all.log file)?
>>
>>
>> Best,
>>
>> a.y
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo <
>> heidifo...@gmail.com>
>> *Sent:* Monday, September 17, 2018 11:03:47 PM
>> *To:* Freesurfer support list
>> *Subject:* Re: [Freesurfer] trac-all using nifti
>>
>>
>> External Email - Use Caution
>>
>> Hi Anastasia,
>>
>> It seems like I do. Could the problem be the config.txt?
>>
>> Thanks!
>>
>> Best Regards,
>> Heidi Foo
>>
>> On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>> Hi Heidi – Do you have write permission to create the output directory
>> /data_int/heidi/forHeidi/Preprocessed?
>>
>> a.y
>>
>> From:  on behalf of Heidi
>> Emmanuel Foo 
>> Reply-To: Freesurfer support list 
>> Date: Monday, September 17, 2018 at 12:55 AM
>> To: Freesurfer support list 
>> Subject: [Freesurfer] trac-all using nifti
>>
>> External Email - Use Caution
>>
>> Hi Anastasia,
>>
>> I am currently trying to run trac-all with my DWI data. I do not have the
>> DICOM but only the Nifti files and I would like to use the same bval and
>> bvec template for every subject. I created a configiration file as
>> attached. However, I have the following error message:
>>
>> : Command not found.
>> : Command not found.
>> set: Variable name must begin with a letter.
>> does not exist.DIR /data_int/heidi/forHeidi/Preprocessed
>>
>> It would be great if you could advise me on what to do.
>>
>> Thank you!
>>
>> Best Regards,
>> Heidi Foo
>>
>>
>> ___
>> 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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>> 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.
>>
>> ___
>> 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.
>>
>

Re: [Freesurfer] trac-all using nifti

2018-09-21 Thread Yendiki, Anastasia

You need to specify one more option, like -prep, etc. Please follow the 
instructions on the tutorial and, if the problem persists, send the exact 
command line that you ran and the full text of the output that you got.

On Sep 21, 2018 2:42 AM, Heidi Emmanuel Foo  wrote:

External Email - Use Caution

Hi Anastasia,

I think I ran trac-all -c config.txt.

Regards,
Heidi

On Thu, Sep 20, 2018 at 10:18 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

What is the trac-all command line that you run?


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Heidi Emmanuel Foo 
mailto:heidifo...@gmail.com>>
Sent: Wednesday, September 19, 2018 11:06:09 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all using nifti


External Email - Use Caution

Hi Anastasia,

Nope, I don't actually get any output and/or log file.

Regards,
Heidi Foo



On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Heidi - The config file that you sent looked fine to me. What is the 
trac-all command line that you run, and do you get any other output (like a 
trac-all.log file)?


Best,

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Heidi Emmanuel Foo 
mailto:heidifo...@gmail.com>>
Sent: Monday, September 17, 2018 11:03:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all using nifti


External Email - Use Caution

Hi Anastasia,

It seems like I do. Could the problem be the config.txt?

Thanks!

Best Regards,
Heidi Foo

On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Heidi – Do you have write permission to create the output directory 
/data_int/heidi/forHeidi/Preprocessed?

a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Heidi Emmanuel Foo 
mailto:heidifo...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, September 17, 2018 at 12:55 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] trac-all using nifti


External Email - Use Caution

Hi Anastasia,

I am currently trying to run trac-all with my DWI data. I do not have the DICOM 
but only the Nifti files and I would like to use the same bval and bvec 
template for every subject. I created a configiration file as attached. 
However, I have the following error message:

: Command not found.
: Command not found.
set: Variable name must begin with a letter.
does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards,
Heidi Foo


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The information in

Re: [Freesurfer] trac-all using nifti

2018-09-21 Thread Heidi Emmanuel Foo

External Email - Use Caution

Hi Anastasia,

I think I ran trac-all -c config.txt.

Regards,
Heidi

On Thu, Sep 20, 2018 at 10:18 PM Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> What is the trac-all command line that you run?
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo <
> heidifo...@gmail.com>
> *Sent:* Wednesday, September 19, 2018 11:06:09 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] trac-all using nifti
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> Nope, I don't actually get any output and/or log file.
>
> Regards,
> Heidi Foo
>
>
>
> On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Heidi - The config file that you sent looked fine to me. What is the
> trac-all command line that you run, and do you get any other output (like a
> trac-all.log file)?
>
>
> Best,
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo <
> heidifo...@gmail.com>
> *Sent:* Monday, September 17, 2018 11:03:47 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] trac-all using nifti
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> It seems like I do. Could the problem be the config.txt?
>
> Thanks!
>
> Best Regards,
> Heidi Foo
>
> On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Heidi – Do you have write permission to create the output directory
> /data_int/heidi/forHeidi/Preprocessed?
>
> a.y
>
> From:  on behalf of Heidi
> Emmanuel Foo 
> Reply-To: Freesurfer support list 
> Date: Monday, September 17, 2018 at 12:55 AM
> To: Freesurfer support list 
> Subject: [Freesurfer] trac-all using nifti
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> I am currently trying to run trac-all with my DWI data. I do not have the
> DICOM but only the Nifti files and I would like to use the same bval and
> bvec template for every subject. I created a configiration file as
> attached. However, I have the following error message:
>
> : Command not found.
> : Command not found.
> set: Variable name must begin with a letter.
> does not exist.DIR /data_int/heidi/forHeidi/Preprocessed
>
> It would be great if you could advise me on what to do.
>
> Thank you!
>
> Best Regards,
> Heidi Foo
>
>
> ___
> 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
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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
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dispose of the e-mail.

[Freesurfer] Freeview error

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

[Freesurfer] mri_glmfit-sim error

[Freesurfer] calculated cortical thickness from segmented binary gray matter and white matter images from other software

Re: [Freesurfer] Ynt: Ynt: linux data and macbook

[Freesurfer] Best way to update Freeview

Re: [Freesurfer] Dead Links to 3rd Party Libraries

[Freesurfer] make_average_subject error

Re: [Freesurfer] matlab MEXFile error in thalamic nuclei segmentation script

Re: [Freesurfer] matlab MEXFile error in thalamic nuclei segmentation script

[Freesurfer] Ynt: Ynt: linux data and macbook

[Freesurfer] matlab MEXFile error in thalamic nuclei segmentation script

[Freesurfer] GLM

Re: [Freesurfer] trac-all using nifti

Re: [Freesurfer] trac-all using nifti

Re: [Freesurfer] trac-all using nifti

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