hi , I have run this subject again, checking all the processing stages, and still get the same issues. I have placed the new output from the preprocessing stage (this is only 1.4 megabytes as the previous one had 2 preprocessing jobs appended) you can find it here: https://dl.dropboxusercontent.com/u/8209026/prepro.txt
as I reminder, one issue I spotted is that the dlabel/diff output does not contain all the files just these anat_brain_mask.bbr.nii.gz anat_brain_mask-vent.bbr.nii.gz aparc+aseg+2mm.bbr.nii.gz aparc+aseg.bbr.nii.gz aparc+aseg_mask.bbr.nii.gz cortex+2mm.bbr.nii.gz cortex+2mm+bs.bbr.nii.gz cortex.bbr.nii.gz lowb_brain_mask.nii.gz notventricles.bbr.nii.gz White-Matter.bbr.nii.gz White-Matter++.bbr.nii.g WHILE FOR THE TRACT RELATED ONES it contains all the relevant file extensions to lh.cst_AS_avg33 lh.ilf_AS_avg33 rh.cst_AS_avg33 but for this one rh.ilf_AS_avg33 (only does he _mni_bbr_cpts_5.txt but does not generate the .nii) any help much appreciated cheers DS On Sat, Nov 16, 2013 at 3:41 PM, David Soto <d.s...@imperial.ac.uk> wrote: > Thanks! > for some weird unknown reason > the log for the preprocessing file of this > subject is unusually big (2.8 megabytes) > please get it from this link > https://dl.dropboxusercontent.com/u/8209026/Archive.zip > cheers > ds > > > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki < > ayend...@nmr.mgh.harvard.edu> wrote: > >> >> Hi David - This log only shows output from the -path step and not from >> the -prep step. The file that's missing should be created during the -prep >> step, so there's no way to figure out what went wrong without seeing the >> output from the pre-processing. >> >> Please cc the freesurfer list on your reply. >> >> Thank you, >> a.y >> >> >> On Sat, 16 Nov 2013, David Soto wrote: >> >> Thanks, please see attachedI only noticed this >>> >>> ERROR: Could not open/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/ >>> dlabel/diff/rh.ilf_AS_avg33_m >>> ni_bbr_cpts_5_std.txt >>> cheers >>> DS >>> >>> >>> On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki >>> <ayend...@nmr.mgh.harvard.edu> wrote: >>> >>> Hi David - Can you please send us the trac-all.log file for this >>> subject? >>> Without seeing where it stopped and what error messages there >>> are it's >>> hard to guess what's going on. >>> >>> Thanks, >>> a.y >>> >>> On Fri, 15 Nov 2013, David Soto wrote: >>> >>> > Hi - >>> > trac-all completed in all my Ps except one >>> > and I noticed that the dlabel/diff output does not contain >>> all the files >>> > >>> > I assessed whether it could be do to poor registration, by >>> checking >>> > the aparc+aseg >>> > file and looks allright >>> > >>> > I also checked the registration of FA maps to standard space >>> by >>> > freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz >>> > dtifit_FA.bbr.nii.gz >>> > and seems fine >>> > >>> > also >>> > >>> > freeview -v brain_anat_orig.nii.gz lowb_brain.nii.gz >>> > >>> > which also seems fine >>> > >>> > any ideas pls? >>> > >>> > thanks! >>> > >>> > ds >>> > >>> > >>> > >>> > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia Yendiki >>> > <ayend...@nmr.mgh.harvard.edu> wrote: >>> > >>> > I suspect the current problem is caused by poor >>> registration. >>> > Have you checked the aparc+aseg and/or the registration >>> from >>> > diffusion to anatomical and from anatomical to MNI? >>> > >>> > On Fri, 16 Aug 2013, David Soto wrote: >>> > >>> > >>> > >>> > -- >>> > http://www1.imperial.ac.uk/medicine/people/d.soto/ >>> > >>> > >>> > >>> > >>> > >>> >>> >>> 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. >>> >>> >>> >>> >>> -- >>> http://www1.imperial.ac.uk/medicine/people/d.soto/ >>> >>> -- >>> <http://www1.imperial.ac.uk/medicine/people/d.soto/> >>> <http://www1.imperial.ac.uk/medicine/people/d.soto/> >>> http://www1.imperial.ac.uk/medicine/people/d.soto/ >>> >>> -- >>> http://www1.imperial.ac.uk/medicine/people/d.soto/ >>> >>>
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