thanks for that, it is not so clear the missing slices from the FA scan in subject space but guess that is the issue! cheers ds
On Wed, Dec 4, 2013 at 2:32 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > Hi David - The screeenshots show that several slices are blank in the > diffusion data, and these indeed go through the right ILF. I'd check your > original diffusion dicoms for this subject and see if that's indeed the > case. > > a.y > > > On Wed, 4 Dec 2013, David Soto wrote: > > thanks Anastasia, see the link below >> plshttps://dl.dropboxusercontent.com/u/8209026/regs.zip >> >> >> you will find 2 pairs of images >> pair one: there are 2 files starting by ind2anat, one showing >> the T1 and the other the FA in the same coordinates, you will see that >> align >> well >> >> pair two: here are 2 files starting by MNI, one showing the FA in mni >> space >> and the other the mni T1_1mm template..seem fine to me, though there seem >> to >> be some coverage deficit in the FA map in the bottom right of the image >> >> cheers >> ds >> >> >> On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu> wrote: >> >> 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.il >> f_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/ >> > >> > >> >> >> >> >> -- >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> >> -- http://www1.imperial.ac.uk/medicine/people/d.soto/
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