Hi Stefano - The order of the 3 trac-all steps is not inter-changeable. You need to run bedpostx *before* you can run the path reconstruction.
a.y
On Wed, 13 Feb 2013, stdp82@virgilio.it wrote:
Thank you Anastasia. But I do not understand why I have the error in trac-all -path. The configuration file that I have attached is good? Stefano
----Messaggio originale---- Da: stdp82@virgilio.it Data: 12-feb-2013 23.27 A: ayendiki@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: R: trac-all -path error
Hi Anastasia, thanks! I hope that is all ok in Boston.
I'm attaching the configuration file that I'm using.
I'd like ask you if/how I can also run the second step of trac-all (bedpostx) using FSL on other pc? May I directly run in FSL dmri folder? Do you think that I should rename some files?
An additional question. For some subjects (no for subject that I'm running with the config file that I have attached) I have 16 direction and b=0 is the last of these. Is the nb0=16?
Thank you very much.
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 12-feb-2013 17.45 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: trac-all -path error
Hi Stefano - There is no need to attach the trac-all script, I am quite familiar with it. Perhaps you could attach the configuration file that you set up?
Thanks, a.y
On Mon, 11 Feb 2013, stdp82@virgilio.it wrote:
I'm attaching my trac-all file for check.Thanks,
Stefano
----Messaggio originale---- Da: stdp82@virgilio.it Data: 11-feb-2013 14.42 A: freesurfer@nmr.mgh.harvard.edu Cc: ayendiki@nmr.mgh.harvard.edu Ogg: [Freesurfer] trac-all -path error
Hi list, I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this error:
Loading mask from /Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX niiRead(): error opening file /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz
From http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22066.html%C2%... I'm deducing that the error may be related trace-all upload.
I have doing this upload but I visualize always the same error.
I attached tract-all uploades file that live in /Applications/freesurfer/bin.
Please, could you check it?
I have also other question. May I run the second step of trac-all (bedpostx) using FSL on other pc? In
this
way, could I directly run in FSL dmri folder? Do you think that I should rename some files?
Thanks,
Stefano
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