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: std...@virgilio.it Data: 12-feb-2013 23.27 A: <ayend...@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: ayend...@nmr.mgh.harvard.edu Data: 12-feb-2013 17.45 A: <std...@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, std...@virgilio.it wrote: > I'm attaching my trac-all file for check.Thanks, > > Stefano > > ----Messaggio originale---- > Da: std...@virgilio.it > Data: 11-feb-2013 14.42 > A: <freesurfer@nmr.mgh.harvard.edu> > Cc: <ayend...@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 > > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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