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
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If the
> > e-mail was sent to you
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> > but does not contain patient information,
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> >
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> >
> >
> > --
> >
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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