Making a new folding atlas is not an easy task. I wrote a script to help
called "make_folding_atlas". It is a very time consuming process, and
the script assumes that you have access to a cluster running PBS/Torque
through the pbsubmit command. If you don't have that, you could either
write a script called pbsubmit that does something else or you could
look at the script and pull out the elements you need.
On 2/27/17 5:27 AM, Marco Martinolli wrote:
Dear all,
I am new to FreeSurfer and I want to reproduce on 20 subjects the
registration strategy as explained in Fischl paper:
High-resolution inter-subject averaging and a coordinate system for
the cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and
Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999)
I found the page SurfaceRegAndTemplates - Free Surfer Wiki
<https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates> which
is about the creation of a template for between-subject analysis but I
am not sure if I have simply to use mris_make_template (in fact I do
have the files spere.reg from the reconstruction step) or if I have to
follow the 2-rounds procedure described in the page calling twice the
make_average_subject. Which is the more correct one for my purpose?
Right now, I tried with the second option but I encountered two
different problems:
1. calling make_average_subject it works for 1 hour but at a certain
moment it exit with errors saying that it does not find the file
norm.mgz for the volume
--> since I thought I was not interested in the volume registration, I
tried to run the command with the --no-vol flag and in this way it
works, but I am not sure this does not lead to any unpleasant
consequence in the next steps
So the command I used is:
make_average_subject --out NEW_TEMPLATE_SURFACE --subjects s1 s2 s3
... --no-vol
2. the mris_preprocess step (after having registered the subjects
obtaining sphere.reg.newtemplate files) does not work as described in
the page in the link. I have to use the input --meas thickness, the
hemisphere --hemi lh/rh, the output file --out
preproc-lh-thicknesss-mgh and especially the target flag --target
NEW_TEMPLATE SURFACE. So the whole command line is:
mris_preproc --surfreg sphere.reg.newtemplate --s s1 --s s2 --s s3...
--meas thickness --hemi lh --out preproc-lh-thicknesss-mgh --target
NEW_TEMPLATE_SURFACE
Is it correct?
I get the error that it does not find the target file. For instance
when it takes subject 50002_recon it says that
50002_recon/surf/lh.NEW_TEMPLATE_SURFACE.sphere.reg does not exist.
And it's true because it is in the subject folder NEW_TEMPLATE_SURFACE
indeed and in the subjects folder I just have lh.sphere.reg.newtemplate.
-------------------------------------------------------------------------------
sysname Linux
hostname marco-Lenovo-Yoga-2-Pro
machine x86_64
user marco
srcsubject = 50002_recon
srcval =
/home/marco/Desktop/SUBJECTS_freeSurfer/50002_recon/surf/lh.thickness
srctype = curv
trgsubject = NEW_TEMPLATE_SURFACE
trgval = ./tmp.mris_preproc.9144/50002_recon.1.mgh
trgtype =
srcsurfreg = NEW_TEMPLATE_SURFACE.sphere.reg
trgsurfreg = sphere.reg.newtemplate
srchemi = lh
trghemi = lh
frame = 0
fwhm-in = 0
fwhm-out = 0
label-src = lh.cortex.label
label-trg = lh.cortex.label
OKToRevFaceOrder = 1
UseDualHemi = 0
Reading source surface reg
/home/marco/Desktop/SUBJECTS_freeSurfer/50002_recon/surf/lh.NEW_TEMPLATE_SURFACE.sphere.reg
No such file or directory
mri_surf2surf: could not read surface
/home/marco/Desktop/SUBJECTS_freeSurfer/50002_recon/surf/lh.NEW_TEMPLATE_SURFACE.sphere.reg
No such file or directory
----------------------------------------------------------------------------------------------
I decided to skip the mris_preproc phase and end the procedure of the
online documentation. So I run again make_average_subject with
--no-vol and with the additional option --surf-reg sphere.reg.newtemplate.
The result is the FINAL_TEMPLATE folder.
Now, observing the mgh file in the mri subfolder called
"mni305.cor.mgz", the template appears to be quite blurred. Is it the
template or something else?
In order to have all the subjects aligned with this final template I
have to run again the registrations as in the second step, right?
I apologize for the huge amount of questions, but I am a lot confused
and I spent a lot of time thinking what I should do.
Please, any help you could give me would be highly appreciated, even
more if you are clear in the explanation.
Best regards,
Marco
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