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 < ayendiki@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 ayendiki@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 belowplshttps://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 ayendiki@nmr.mgh.harvard.edu wrote:
Hi David - I am not convinced that all the regisrtrationshave 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 ayendiki@nmr.mgh.harvard.edu wrote:
Hi David - Sorry for the delayed response due totraveling.
There's a warning about the right ILF in the log filethat may
offer a clue: WARN: Initial control point 37 56 -6 is not in DWIvolume - is
DWI cropped? WARN: Replacing with closest point in volume (37 56 0) WARN: Initial control point 38 45 -1 is not in DWIvolume - 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
Is the brain mask cropped on either end of the rightILF? You
mentioned that you already checked the registration of the FA mapto the
template space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assumingthere'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 > <ayendiki@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 missingshould
be > created during the -prep step, so there's no wayto
figure out > what went wrong without seeing the output fromthe
> 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 noticedthis
> 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, AnastasiaYendiki
> <ayendiki@nmr.mgh.harvard.edu> wrote: > > Hi David - Can you please send usthe
> trac-all.log file for this > subject? > Without seeing where it stopped andwhat
error > messages there > are it's > hard to guess what's going on. > > Thanks, > a.y > > On Fri, 15 Nov 2013, David Sotowrote:
> > > Hi - > > trac-all completed in all my Psexcept one
> > and I noticed that thedlabel/diff output
> does not contain > all the files > > > > I assessed whether it could be doto poor
> registration, by > checking > > the aparc+aseg > > file and looks allright > > > > I also checked the registration ofFA 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 > > <ayendiki@nmr.mgh.harvard.edu>wrote:
> > > > I suspect the currentproblem is
> caused by poor > registration. > > Have you checked theaparc+aseg
and/or > the registration > from > > diffusion to anatomical andfrom
> anatomical to MNI? > > > > On Fri, 16 Aug 2013, DavidSoto
> wrote: > > > > > > > > -- > > >http://www1.imperial.ac.uk/medicine/people/d.soto/
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