Hi David - I am not convinced that all the regisrtrations have worked well for this subject. The fact that some of the coordinates of the control points, which are mapped from template to individual space, are negative in individual space (see INFO messages in log file), means that some part of the brain in templated space is mapped outside the field of view in individual DWI space. Can you send any screenshots that show the quality of the DWI to anatomical and DWI to MNI registrations?
Thanks, a.y On Mon, 2 Dec 2013, David Soto wrote:
hi - thanks , not sure though...the no_dif brain maskseems 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: Couldnotopen/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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