ok thanks I did not realise! may I ask something else? 2 of my participants structural scan was distorted and could not be used by recon-all, so can not get the anatomical priors for tracula. It may sound a stupid questio, but is it possible(and worthy) to try to do some registration of the diffusion data into standard space and then use a standard structural template instead to the the anatomical priors?
cheers ds On Thu, Dec 5, 2013 at 2:58 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Of course, you can specify which tracts you want to reconstruct in the > configuration file. Both the sample configuration file in > $FREESURFER_HOME/dmrirc.example and the tracula tutorial have the info on > how to do this. > > On Thu, 5 Dec 2013, David Soto wrote: > > Hi, just a though, would it be possible to skip thereconstruction of the >> >> right ILF, I mean to get the remaining >> tract statistics? >> that would be v/useful >> 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/ >> >> -- http://www1.imperial.ac.uk/medicine/people/d.soto/
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