voila....thanks for your help
On Thu, Aug 16, 2012 at 2:09 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
Can you send me trac-all.log?
On Thu, 16 Aug 2012, Richard Binney wrote:
So looking back at my previous successful attempts, it appears that both
data.nii.gz and nodif_brain_mask.nii.gz should be symbolic links (to dwi and lowb_, presumably). that correct?
So for some reason these symbolic links were not created. I wasn't over-writing. It was a fresh run on a previously non-existent directory (the trac-all script automatically creates a new subject-specific directory in my TRACULA_output directory [specified in dmrirc]).
The control.dat file is an oddity. It appears to be a control points file from the RECON output and has a modification date 2 days after the -prep was run and on the day (but a few hours before) I ran bedpost (wierdly it has a write date of 1969). I have no idea what has happened here. May have been a random copying/saving error I made at some point (???? :s)
Forgetting control.dat, what do you think could be happening here?
Many thanks for your help.
Richard
On Thu, Aug 16, 2012 at 1:24 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
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 xfmsThe 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/**compliancelinehttp://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.