Hi Jon,
Usually you would select a specific subject to be the target, sometimes
that subject is in the mid age range, etc. Also sometimes people remove
that subject from the study to not introduce a bias.
In most cases, however, people simply use fsaverage unless they have a
reason to switch.
I don't know how you create your own 'average' surface. Maybe someone
else can answer that.
Best, Martin
On 11/06/2013 02:57 PM, Jonathan Holt wrote:
OH,
I see, then how would I generate my own study average, if I wanted to
do so?
On Nov 6, 2013, at 2:48 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu
<mailto:mreu...@nmr.mgh.harvard.edu>> wrote:
Hi Jon,
that is just a placeholder, indicating that this can be your own
average in a real study. You can simply use 'fsaverage' for it, now.
Best, Martin
On Nov 6, 2013, at 2:22 PM, Jonathan Holt <whats...@umich.edu
<mailto:whats...@umich.edu>> wrote:
Thanks a ton Martin,
can you possibly clue me into where I could find study_average?
best,
jon
On Nov 6, 2013, at 2:16 PM, Martin Reuter
<mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>>
wrote:
Hi Jon,
passing the --qdec-long flag to mris_preproc will automatically
generate the right names (e.g. the .long. directories) and take the
data from there. You can pass the study_average vie the --target
flag. The default is to use fsaverage which is distributed with
FreeSurfer.
So mris_preproc maps the thickness maps to the subject average,
while the mris_surf2surf command is for smoothing the stack of
thickness maps and generates the …_sm10.mgh file.
Best, Martin
On Nov 6, 2013, at 2:07 PM, Jonathan Holt <whats...@umich.edu
<mailto:whats...@umich.edu>> wrote:
FS experts,
I have two questions, when running mris_preproc and mri_surf2surf
should I be passing these any of the .long directories created
with recon-all -long? As I read through the tutorial I’m missing
their significance in the analysis section of the longitudinal
stream. It seems like fsaverage is being used (I’m not sure when
that was even generated)
Secondly, I see that mris_preproc outputs a thickness.mgh file,
but I’m wondering where, in your tutorial examples
lh.thickness_sm10.mgh comes from/is located. Found in
*mri_surf2surf* --hemi lh --s fsaverage --sval lh.thickness.mgh
--tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape
best,
jon
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---------------------------------
Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>
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Web : http://reuter.mit.edu <http://reuter.mit.edu/>
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---------------------------------
Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>
reu...@mit.edu <mailto:reu...@mit.edu>
Web : http://reuter.mit.edu <http://reuter.mit.edu/>
--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
_______________________________________________
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