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/
> > >
> > >
> > >
> > >
> > >
> >
> >
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> >
> >
> >
>
>
>
>
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>
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