Re: [Freesurfer] Longitudinal TRACULA: mri_convert
Dear Anastasia,
I emailed with Dr. Knut Jørgen Bjuland because he had a similar issue
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39745.html).
He mentioned that obtaining a new license could solve the issue. It did,
so my problem is resolved.
Best,
Vincent
Dear Anastasia,
I have checked the image and it looks good. I don't think the image is
the problem, especially considering that my issue is also popping up
with standard data. See for example the following code:
$ echo $FREESURFER_HOME
/home/mriuser/privatemodules/freesurfer
$ cksum $(which mri_convert)
1305133180 29171478 /home/mriuser/privatemodules/freesurfer/bin/mri_convert
$ echo $FSLDIR
/home/mriuser/privatemodules/fsl
$ mri_convert ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz test.mgh
mri_convert
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz
test.mgh
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz...
crypt_gkey = (null)
Segmentation fault (core dumped)
The reason I am posting this with 'Longitudinal TRACULA' in the title is
because I only have this issue with the mri_convert that is bundled with
the TRACULA update (see my first post). The original mri_convert bundled
with the centOS6 64bit version of FS 5.3.0 (stable) does let me convert
files. However, this version does not allow multiple frame numbers:
Original frame options of mri_convert (FS v5.3.0 stable centos6 64)
-f, --frame frameno
keep only 0-based frame number
Frame options of the updated mri_convert
(tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz)
-f, --frame frameno [...]
keep only 0-based frame number(s)
Longitudinal TRACULA pushes multiple files as arguments to 'mri_convert
--frame', which is why I need the updated version.
Do you have any suggestions for me?
Thank you!
best,
Vincent
Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA
but
probably something about the format of your input nifti volume. How did you
create that volume? Can you open it in freeview and view it normally?
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert
Hello Freesurfer experts,
I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:
#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux
Some information about my setup:
*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz
*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64
Is there a fix for this problem?
Thanks!
- Vincent
___
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] Longitudinal TRACULA: mri_convert
Dear Anastasia,
I have checked the image and it looks good. I don't think the image is
the problem, especially considering that my issue is also popping up
with standard data. See for example the following code:
$ echo $FREESURFER_HOME
/home/mriuser/privatemodules/freesurfer
$ cksum $(which mri_convert)
1305133180 29171478 /home/mriuser/privatemodules/freesurfer/bin/mri_convert
$ echo $FSLDIR
/home/mriuser/privatemodules/fsl
$ mri_convert ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz test.mgh
mri_convert
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz
test.mgh
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz...
crypt_gkey = (null)
Segmentation fault (core dumped)
The reason I am posting this with 'Longitudinal TRACULA' in the title is
because I only have this issue with the mri_convert that is bundled with
the TRACULA update (see my first post). The original mri_convert bundled
with the centOS6 64bit version of FS 5.3.0 (stable) does let me convert
files. However, this version does not allow multiple frame numbers:
Original frame options of mri_convert (FS v5.3.0 stable centos6 64)
-f, --frame frameno
keep only 0-based frame number
Frame options of the updated mri_convert
(tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz)
-f, --frame frameno [...]
keep only 0-based frame number(s)
Longitudinal TRACULA pushes multiple files as arguments to 'mri_convert
--frame', which is why I need the updated version.
Do you have any suggestions for me?
Thank you!
best,
Vincent
Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA
but
probably something about the format of your input nifti volume. How did you
create that volume? Can you open it in freeview and view it normally?
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert
Hello Freesurfer experts,
I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:
#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux
Some information about my setup:
*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz
*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64
Is there a fix for this problem?
Thanks!
- Vincent
___
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] Longitudinal TRACULA: mri_convert
Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA but probably something about the format of your input nifti volume. How did you create that volume? Can you open it in freeview and view it normally? a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans [vkop...@umich.edu] Sent: Wednesday, November 30, 2016 1:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal TRACULA: mri_convert Hello Freesurfer experts, I am trying to run longitudinal TRACULA but I am getting an error early on in the process that seems to originate from mri_convert: #- /home/mriuser/privatemodules/freesurfer/bin/trac-preproc #- #@# Image corrections Wed Nov 30 09:10:55 EST 2016 mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz /datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz /datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz Segmentation fault (core dumped) Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Some information about my setup: *Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 *Freesurfer TRACULA update installed: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz *Linux version: CentOS Linux release 7.2.1511 (Core) centos-release-7-2.1511.el7.centos.2.10.x86_64 Is there a fix for this problem? Thanks! - Vincent ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
[Freesurfer] Longitudinal TRACULA: mri_convert
Hello Freesurfer experts, I am trying to run longitudinal TRACULA but I am getting an error early on in the process that seems to originate from mri_convert: #- /home/mriuser/privatemodules/freesurfer/bin/trac-preproc #- #@# Image corrections Wed Nov 30 09:10:55 EST 2016 mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz /datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz /datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz Segmentation fault (core dumped) Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Some information about my setup: *Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 *Freesurfer TRACULA update installed: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz *Linux version: CentOS Linux release 7.2.1511 (Core) centos-release-7-2.1511.el7.centos.2.10.x86_64 Is there a fix for this problem? Thanks! - Vincent ___ 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.
