hi - thanks , not sure though...the no_dif brain mask seems ok, if that is what you meant...
I did re-run the processing and in the last run I can not see the WARN you mentioned the latest preprocessing output from the preprocessing can be found here: https://dl.dropboxusercontent.com/u/8209026/prepro.txt the dlabel/diff output got stuck with the rh.ilf_AS_avg33 which only contains thee _mni_bbr_cpts_5.txt but nothing else thanks so much ds On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi David - Sorry for the delayed response due to traveling. > > There's a warning about the right ILF in the log file that may offer a > clue: > > WARN: Initial control point 37 56 -6 is not in DWI volume - is DWI cropped? > WARN: Replacing with closest point in volume (37 56 0) > WARN: Initial control point 38 45 -1 is not in DWI volume - is DWI cropped? > WARN: Replacing with closest point in volume (38 45 0) > WARN: Initial start point 37 56 0 is not in start ROI > WARN: Replacing with closest point in start ROI (31 56 0) > > Is the brain mask cropped on either end of the right ILF? You mentioned > that you already checked the registration of the FA map to the template > space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's nothing > wrong there. > > a.y > > On Sat, 16 Nov 2013, David Soto 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 > notopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_avg > > 33_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/
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