thanks Anastasia for taking the time into this, once again! the logs can be found here https://dl.dropboxusercontent.com/u/8209026/p14ab.zip cheers ds
On Wed, Dec 11, 2013 at 8:11 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Sorry, I can't tell what happened without looking at the log file. Could > you send it along? > > > On Wed, 11 Dec 2013, David Soto wrote: > > hi Anastasia, I tried then to recontruct the remaining tracts of this >> participant for which I could not do the right ILF due to diffusion loss >> >> I set the pathlist like this: set pathlist = ( lh.cst_AS rh.cst_AS \ >> lh.unc_AS rh.unc_AS \ >> fmajor_PP fminor_PP \ >> lh.atr_PP rh.atr_PP \ >> lh.ccg_PP rh.ccg_PP \ >> lh.cab_PP rh.cab_PP \ >> lh.slfp_PP rh.slfp_PP \ >> lh.slft_PP rh.slft_PP ) >> >> and while it generated most the lh.slfp_PP rh.slfp_PP \ >> lh.slft_PP rh.slft_PP are missing >> >> is this expected given that the issues with the ILF? >> >> I could not find any errors in the logs relative to the SLFTs >> >> 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/dif >> f >> /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/ >> >> -- http://www1.imperial.ac.uk/medicine/people/d.soto/
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