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
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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
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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