Re: [Freesurfer] Trakula

Hi Anastasia, Thank you very much for your help and recommendations. I will try to fix These Problems. I would like to ask you one more question. Is there any command which could help me to invert the gradient vectors for my DWI scan in the z direction? Best Bahram 2015-08-24 17:57 GMT+02:00

Re: [Freesurfer] Trakula

Hi Bahram - The gradient table is a text file with 3 columns. You need to multiply the 3rd column by -1. You can do this in matlab, awk, perl, or any scripting language that handles text files. Best, a.y On Wed, 26 Aug 2015, B M wrote: Hi Anastasia, Thank you very much for your help and

Re: [Freesurfer] Trakula

Hi Anastasia, please find the files in attachment. Best regards Bahram 2015-08-19 21:55 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - There are some errors in there related to registration files. Can you please send these files?

Re: [Freesurfer] Trakula

Hi Bahram - The anatomical-to-diffusion registration matrix is all zeros, so something went wrong there. I'll need to see all the output files to investigate. Can you please zip up this subject's tracula output directories (dmri, dmri.bedpostX, dpath, dlabel, scripts) and upload everything

Re: [Freesurfer] Trakula

Hi Bahram - There are some errors in there related to registration files. Can you please send these files? bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat Thanks, a.y On Tue, 18 Aug 2015, B M wrote:

Re: [Freesurfer] Trakula

Hi Anastasia, Please find attached the trac-all.log file. Thank you very much for your help. Bahram 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote:

Re: [Freesurfer] Trakula

Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote: Dear experts, I have the last version of tTrakula. i did the first step with   trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown

[Freesurfer] Trakula

Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found

Re: [Freesurfer] trakula segmentation fault

Hi Anastasia, I ran: - bedpostx /media/vivi/images/freesurfer/00112288Proc/dmri and got the following output: subjectdir is /media/vivi/images/freesurfer/00112288Proc/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage But before it

Re: [Freesurfer] trakula segmentation fault

Hi Viviana - Does it die at that point or does it keep running? If it's the latter it doesn't look wrong. For your first problem you should make sure that your path includes the bin/ directory under the FSL distribution. a.y On Wed, 25 Apr 2012, Viviana Siless wrote: Hi Anastasia, I ran:

Re: [Freesurfer] trakula segmentation fault

Hi Viviana - I cannot replicate this on our systems but I think I know what your system may be fussy about and I'll amend it. For now, if you don't get any outputs can you please try running bedpostx directly on /media/vivi/images/freesurfer/00112288Proc/dmri and see if that works?

Re: [Freesurfer] trakula segmentation fault

Hello Anastasia, It fixed the bug. Thank you so much! Now Im running trac-all -bedp -c But it's been running for already 3 days, and it just printed that: trac-all -bedp -c /media/vivi/images/freesurfer/dmrirc.example INFO: SUBJECTS_DIR is /media/vivi/images/freesurfer INFO: Diffusion root is

Re: [Freesurfer] trakula segmentation fault

Hi Anastasia, My mistake with the expiration date. Please try with this link: https://transfert.inria.fr/fichiers/0b1013b5de0fc0cc9e8dd2d6101a054b/testData.tar.gz Thanks! Viviana Siless -- Parietal Team, INRIA Saclay Neurospin, Centre CEA de Saclay 91191 Gif sur Yvette – FRANCE On Tue, Apr 17,

Re: [Freesurfer] trakula segmentation fault

Hi Viviana - I suspect it may be b/c you're using the 2mm-resolution MNI template brain, and our atlas was built using the 1mm one. From your dmrirc file: # MNI template (the only option for inter-subject registration in this version) # Default:

Re: [Freesurfer] trakula segmentation fault

Hi Anastasia, Here is the data: https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gzLet me know if you have any trouble. I changed to the other track-all, and the error is the same. Please let me know if I'm doing anything wrong! Thank you! Viviana Siless --

Re: [Freesurfer] trakula segmentation fault

Hi Viviana - If you upload this data set I'm happy to look at it. Also, I strongly recommend getting the updated version of trac-all from the wiki (I'm guessing from the log file that you're probably not using that?) See 2012/01/09 update here: