Thanks again — it was a huge help!
On 31 Jan 2017, at 18:25, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:
Hi Barbara – Thank you for your kind words. As you’ve read, if the output files are generated, then you’re good to go. Bedpost does not differentiate between longitudinal and cross-sectional data, so it’s run separately on each time point’s …/dmri/ folder.
Best, a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bárbara Avelar Pereira <barbara.avelar.pereira@ki.semailto:barbara.avelar.pereira@ki.se> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, January 30, 2017 at 10:48 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] longitudinal tracula error
Hi Anastasia,
Thanks again for the help! And congrats on tracula — it's a great tool, and the online support is really good :)
I do have a follow-up question, if that’s OK. I’m currently running bedpost, and it gives the following error:
(…) 53 slices processed 54 slices processed 54 slices processed 55 slices processed Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /usr/local/freesurfer/bin/bedpostx_mgh: line 345: kill: (21128) - No such process
I was not running this on a cluster, but I was running a few subjects at the same time so I was wondering if it could be a memory problem? Or a compatibility problem between FSL and freesurfer?
It seems strange that it shows the same slice more than once on the monitor. But from what I read, the monitor is not entirely reliable and the best way to check whether everything ran smoothly is to look at the output. I have all the files that should have been created, but I’m still suspicious that something might be wrong. For example, my merged_xxx files are 50 volumes (should they have the same number of volumes as my original nii file? Because this is not the case...).
I’ve also tried running it directly from the command line and the error is the same (however, since this is longitudinal, when running bedpost from the command line, can I simply run it for each timepoint separately as if it was cross-sectional or is there an extra step?)
Many thanks!
On 26 Jan 2017, at 14:51, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:
Glad to hear it, thanks for checking! If the final 6.0 works, there's no need to dig up the beta.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira [barbara.avelar.pereira@ki.semailto:barbara.avelar.pereira@ki.se] Sent: Thursday, January 26, 2017 3:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] longitudinal tracula error
Hi Anastasia,
Thanks so much for your help! Sorry for the delay in replying -- just wanted to make sure the was problem was indeed solved. Since I'm using a server for which I have no administrative rights, I had to wait before the update was installed. It seems to run perfectly now. I can't find the beta version I was using at the time (just deleted it once I realised I was having the same problem), but if I manage to trace it back, I'll let you know.
Once again, thanks, I'm super grateful!
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia [AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu] Sent: Sunday, January 22, 2017 7:33 PM To: Freesurfer support list Subject: Re: [Freesurfer] longitudinal tracula error
Hi Barbara - If you're using the 5.3 version, then you'll have to download the update from 2014: https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
This should fix the problem. But if there's a version of the 6.0 beta that was having the same problem, please let me know (by sending the trac-all copy of that version) so I can fix that asap.
Thanks!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira [barbara.avelar.pereira@ki.semailto:barbara.avelar.pereira@ki.se] Sent: Friday, January 20, 2017 7:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] longitudinal tracula error
Hi Anastasia,
Thanks so much for your quick reply. I've only tried version 6.0 to determine whether the error was possibly version-related, but that doesn’t seem to be the case… I'm actually working with version 5.3 so I'll send attach the trac-all.local-copy for that if that’s OK. Once again, thank you!
On 20 Jan 2017, at 23:52, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:
Hi Barbara - If you take out the "set baselist" part, you'll run the cross-sectional TRACULA stream, i.e., analyze each time point independently. So you want to leave that in to use the longitudinal TRACULA stream.
The base template itself (i.e., the median of the T1s of the time-points) may not be used, but the files under the base template's directory are used. Longitudinal TRACULA maps between the base space to the space of each DWI time point, as described in the paper.
Can you please attach the file scripts/trac-all.local-copy? Since there's no official 6.0 version yet but multiple beta versions of it, it's hard to know which one you used.
Thanks, a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira [barbara.avelar.pereira@ki.semailto:barbara.avelar.pereira@ki.se] Sent: Friday, January 20, 2017 9:01 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] longitudinal tracula error
Dear FreeSurfer experts,
I’m running tracula on longitudinal data but I’ve encountered the following error at the “trac-all -prep” stage: ERROR: flag ; unrecognized (see below)
trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log /Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd /Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log /Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd /Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c /Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log /Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd /Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ; ERROR: flag ; unrecognized
As an example, I defined the parameters in my dmrirc file as: set subjlist = ( S0001.01_T1 \ S0001.01_T2 \ S0004.00_T1 \ S0004.00_T2 )
set baselist = ( S0001.01 \ S0001.01 \ S0004.00 \ S0004.00 )
set dcmlist = ( S0001.01_T1/DTI.nii \ S0001.01_T2/DTI.nii \ S0004.00_T1/DTI.nii \ S0004.00_T2/DTI.nii )
From the mailing list, it seems a similar issue has been fixed in previous updates but I have tried both version 5.3 and 6.0 and still get this error...
My tracula directory contains 3 directories per participant: 2 with the *.long.* output for timepoint 1 and 2, and a directory with the base. Including the base gives the error above, but if I take it out, it asks for it: ERROR: cannot find /Documents/TRACULA/TEST/S0001.01
From what I understand, the base is not necessary to run any analysis, but it has to be there anyhow (?): https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html Maybe I am understanding this incorrectly?
Since the base is used to create the longitudinal output (*long*), including the aparc+aseg.mgz file, and those are then used in tracula, I thought I could run things without it. I decided to take out the “set baselist” part from the configuration file — this way it seems to run fine (so far). But I assume it’s there for a reason so I’m not sure this is a solution at all...
Any help would be much appreciated!
Details: 1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) platform: CentOS release 6.8 (Final) 3) Operating system details (kernel name, release, version, etc.): Linux 2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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