Hi David - Based on the error message in your log file, the right angular bundle (rh.cab) is also failing. Looks like a similar problem with the right ILF, probably that tract is also affected by the blank slices in your volume. Nothing on the list after rh.cab gets reconstructed because of this error.
I'd try removing the rh.cab from the list too. Hope this helps, a.y On Thu, 12 Dec 2013, David Soto wrote:
thanks Anastasia for taking the timeinto 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/di f 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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