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.
----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
> 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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