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
thanks Anastasia for taking the time
into 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
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 \
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
Hi, just a though, would it be possible to skip the
reconstruction 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
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
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
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
thanks Anastasia, see the link below pls
https://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
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
thanks for that, it is not so clear the missing slices from the FA scan
in subject space but guess that is the issue!
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
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
hi - thanks , not sure though...the no_dif brain mask
seems 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:
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
hi , I have run this subject again, checking all the processing
stages, and still get the same issues. I have placed the
new output from the preprocessing stage (this is only
1.4 megabytes as the previous one had 2 preprocessing jobs
appended)
you can find it here:
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
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
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
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
Hi Anastasia:
I wish to echo David's sentiments. Thanks for this great software. I was
able to process and extract data for all brains without losing any of the
brains. Thanks so much.
best,
Alan
On Fri, Aug 16, 2013 at 12:14 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Ok,
hi - yes it as 65 -output pasted below, cheers
dsoto@wmen-dsoto3:~/Documents/fmri/rsdtianawmgui/14AB/dmri$ mri_info
dwi.nii.gz Volume information for dwi.nii.gz
type: nii
dimensions: 96 x 96 x 46 x 65
voxel sizes: 2., 2., 2.2999
type: FLOAT (3)
Ok, actually the error about the data and bvals/bvecs not having the same
size occured the first time you ran trac-all, but it seems to have been
fixed the second time you ran it, based on the log file.
I suspect the current problem is caused by poor registration. Have you
checked the
/
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 09 August 2013 22:44
To: Soto, David
Subject: Re: [Freesurfer] trac-all inquiry
Are you rotating the gradient vectors accordingly? This is done in
trac-all after running eddy_correct.
On Fri, 9 Aug 2013
August 2013 23:15
To: Soto, David
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] trac-all inquiry
When you apply a rotation to the DWIs (as eddy_correct does), you need to
apply the same rotation to the corresponding gradient vectors. See for
example: Leemans, A., Jones, D. K., Jun 2009
@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] trac-all inquiry
When you apply a rotation to the DWIs (as eddy_correct does), you need to
apply the same rotation to the corresponding gradient vectors. See for
example: Leemans, A., Jones, D. K., Jun 2009. The B-matrix must be rotated
when correcting
/medicine/people/d.soto/
From: Soto, David
Sent: 07 August 2013 23:47
To: Anastasia Yendiki
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] trac-all inquiry
Hi Anastasia, I checked the becs and bvals files,
there was a bug in the transposition
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] trac-all inquiry
Hi David - Every time you run trac-all, the results get appended to this
file, so you need to look for error messages only in the more recent
invocation of trac-all. The first error there seems to be:
Error
: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] trac-all inquiry
I see, you're using the old version of tracula (from freesurfer 5.1). In
that version, you had to define the number of low-b images in the
configuration file. I strongly recommend updating to freesurfer 5.3. A lot
of things have
I see, you're using the old version of tracula (from freesurfer 5.1). In
that version, you had to define the number of low-b images in the
configuration file. I strongly recommend updating to freesurfer 5.3. A lot
of things have improved in tracula since then.
Also, in the future please
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of David Soto
[d.s...@imperial.ac.uk]
Sent: Friday, August 02, 2013 5:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] trac-all inquiry
Hi,
I have successfully run recon-all in my dataset
and now am attempting to use trac-all on my diffusion
...@nmr.mgh.harvard.edu] on behalf of David Soto
[d.s...@imperial.ac.uk]
Sent: Friday, August 02, 2013 5:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] trac-all inquiry
Hi,
I have successfully run recon-all in my dataset
and now am attempting to use trac-all on my diffusion data
Hi David - You need to run each of the steps (-prep, -bedp, -path)
separately. You can't run them all at the same time. See tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula
Hope this helps,
a.y
On Fri, 2 Aug 2013, David Soto wrote:
Hi,
I have
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