Sorry, trac-all requires freesurfer recons at the moment.
On Thu, 5 Dec 2013, David Soto wrote:
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
<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/
> > >
> > >
> > >
> > >
> > >
> >
> >
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> >
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http://www1.imperial.ac.uk/medicine/people/d.soto/
> >
> >
> >
>
>
>
>
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>
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