The symlinks are actually created in the -bedp step, not the -prep step. If you're running bedpostx outside of trac-all, you need to create them yourself.
On Thu, 16 Aug 2012, Watson, Christopher wrote: > I've just taken to making the sym links myself after running trac-prep and > before running bedpostx. Then everything should run normally. > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Thursday, August 16, 2012 4:24 PM > To: Richard Binney > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] TRACULA -prep error > > Hi Richard - In the listing you sent below I do see the a > nodif_brain_mask.nii.gz and a control.dat, although I have no idea what > control.dat is. As for data.nii.gz, it should be created as a symbolic > link to dwi.nii.gz, since bedpostx indeed expects it to be called "data". > I have not seen this problem before, but does it occur only when you rerun > and overwrite things in the same directory, or also when you start a fresh > run on a previously non-existent directory? > > a.y > > On Thu, 16 Aug 2012, Richard Binney wrote: > >> Hi Anastasia et al., >> >> I previously had TRACULA running wonderfully on a test dataset. I was tasked >> with writing an in-house step-by-step manual for dummies. Since then, a >> colleague has followed my manual with a new dataset and had problems. After >> trying to determine whether it was her install or something about her data >> and failing to find anything, I returned to re-run the subject I had already >> successfully processed. Nothing has changed in my install (TRAC-all version >> etc) ODDLY, this re-run is suffering from the same problem as my colleague. >> >> We ran trac-all -prep -dmrirc and it exited without any errors. However, >> there seem to be some files missing from the output: >> >> control.dat >> >> data.nii.gz >> >> nodif_brain_mask.nii.gz >> >> >> >> Bedpostx will not run due to the data file being missing and I'm sure the >> other missing files will cause problems. >> >> What is going on? >> >> I knew to look for these files as at some point I found the following list >> for the \dmri\. I can not re-find a post with this list so I'm sorry if it >> related to a solution to our current problem. >> >> Please help >> >> Richard >> >> brain_anat_mni.nii.gz >> >> dtifit_L2.nii.gz dwi_orig_flip.nii.gz >> >> brain_anat.nii.gz >> >> dtifit_L3.nii.gz >> >> dwi_orig.mghdti.bvals >> >> brain_anat_orig.nii.gz dtifit_MD.nii.gz >> >> dwi_orig.mghdti.bvecs >> >> bvals >> >> dtifit_MO.nii.gz dwi_orig.nii.gz >> >> bvecs >> >> dtifit_S0.nii.gz dwi_snr.txt >> >> bvecs.norot >> >> dtifit_V1.nii.gz lowb_brain.nii.gz >> >> control.dat >> >> dtifit_V2.nii.gz >> >> lowb.nii.gz >> >> data.nii.gz >> >> dtifit_V3.nii.gz >> >> mni >> >> dtifit_FA.nii.gz >> >> dwi.ecclog >> >> nodif_brain_mask.nii.gz >> >> dtifit_L1.nii.gz >> >> dwi.nii.gz >> >> xfms >> >> >> >> > > > _______________________________________________ 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.
