Hi Stefano - All is well here, thank you. Yes, you can run bedpostx directly on the dmri directory. If you search for bedpostx in the freesurfer email list archives, you'll find the info you need since other people have done this before.
a.y
On Tue, 12 Feb 2013, stdp82@virgilio.it wrote:
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
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.