Hi Michael - There is no bvec file associated with the base template. The
base template is a structural (the median of a subject's structural time
points) and not a diffusion scan.
The way you'd want to account for different amounts of motion across
subjects in a cross-sectional analysis, you'd probably want to account for
different changes in motion in a longitudinal study. Whether you'd also
want to discard data is an open question.
a.y
On Mon, 4 Jul 2016, Harms, Michael wrote:
So, what bvec/bvec file should be associated with the BASE scan? It isn’t
clear to me how the bvec/bval in the BASE scan get used in trac-paths.
I see the point of your note of caution, but unless someone moved the same
amount (and for the same frames) for their sessions in a longitudinal
study, the same issue applies, even if you use all frames “as is”. In
that case, the potential bias would be due to using data of differing
quality across sessions. In a sense, we are just making the issue
explicit by discarding bad frames as part of a QC step.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
On 7/4/16, 2:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:
Hi Michael - Indeed it should not be too difficult to add the feature of
specifying the b-value table for each scan and I can add this in the next
version.
However, I would be a bit careful with removing different DWI volumes for
different time points. The acquisition should be as consistent as possible
across time points. If you find that there's a longitudinal change, would
this be because there were different directions/b-values in each time
point or because of an actual change in the brain? I suppose that, unless
there's a systematic bias, you might expect that these changes will be in
different directions for different subjects and would then average out.
But it's a tricky issue.
Best,
a.y
On Fri, 1 Jul 2016, Harms, Michael wrote:
Hi Anastasia,
Looking through the trac-preproc and trac-paths scripts, it is now clear
to me that all the time points for a given subject have to be
contained/specified
within the same dmrirc configuration file in order to implement a
longitudinal TRACULA analysis. So, I've answered my previous question in
that regard.
The challenge in our case is that we have separately pre-processed the
dMRI data for each subject and time point, removing bad frames/volumes
(using the
DTIPrep QA tool). Thus, the bvecs/bvals are not identical for all the
time points of a given subject. We can specify the bvec file for each
subject/time
point using the bveclist configuration parameter. But there is no
analog available for bvals, since only a single bvalfile can be
specified.
I see that this issue has been raised in a couple other posts relatively
recently (2015):
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html
but no working solution was provided at that time.
I’m wondering if there is perhaps now a development version of TRACULA
that supports a “bvallist” capability? If not, it doesn’t look like it
would be too
difficult to modify trac-all to include that capability (modeling after
what is already in trac-all for the bveclist/bvecfile stuff). But, in
that case,
it isn’t immediately clear to me if there are other downstream “gotchas”
in the preproc, paths, or stats stage specific scripts/binaries that
would need
modifications as well. [I don’t see anything in the sections related to
the BASE-specific processing in trac-preproc involving bvals/bvecs, so
think we are
fine there. But it is harder for me to tell what is going on in
trac-paths].
thanks,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Harms,
Michael" <mha...@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, June 29, 2016 at 5:00 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula
Hi,
When running TRACULA with longitudinal data, is it necessary for all
scan waves of a given subject to be included in a single dmrirc file? My
initial
thought was “no”, that it would be fine to run one scan wave per subject
per dmrirc file (as long as the “baselist” variable is set appropriately
for each
scan wave and subject).
But looking at the ‘trac-all’ script, I see
if ($#baselist == 0) then#--->>> A single time point for each subject
…
else#--->>> Multiple time points for each subject
…
So, I’m wondering why different sections in the code would be necessary
if in fact it is ok to process a single scan wave per dmrirc file.
thanks,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
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