On 5/28/2021 2:17 PM, Alexopoulos, Dimitrios wrote:
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Greg,
Additional clarification.
Are these 2 options runs independently - i.e. separate tests?
Not sure what you mean here
For example, add CPs to brain.mgz and then rerun entire recon-all -all
command?
You don't need to run with -all (you can but inefficient). You can start
at the appropriate -autorecon2-X
Is the experts options file used with the CPs above in one run or
separate run using
recon-all -s subject -expert yourexpertoptions.txt -pial -lh
Once you run it once with an expert option, it will copy the expert
options file into the output folder, then you just need to specify
-xopts-use on subsequent runs
Jim
*From:*Alexopoulos, Dimitrios
*Sent:* Friday, May 28, 2021 1:08 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* RE: [Freesurfer] WM or Pial edits to correct surfaces
Thanks Doug. Will try with difference distances. Where is the expert
file placed?
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of
*Douglas N. Greve
*Sent:* Thursday, May 27, 2021 5:25 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] WM or Pial edits to correct surfaces
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There might be a couple things happening. First, I would try adding a
few control points in that area; make sure they are in true WM in
voxels that have a value less than 110 on the brain.mgz file. This
might help push the white surface further out (the WM in that gyrus is
very thin). It might also help push the pial surface out. The next
thing you can try is to increase the maximum distance over which the
edge is searched for. These young subjects have very plump/thick
cortices. You can do that with an expert options file. Create a text
file with the following content:
PlaceT1PialSurf --max-cbv-dist 6
Where "6" tells it to search 6 mm rather than the default 5. You may
need to play with the number
You can then run recon-all with
recon-all -s subject -expert yourexpertoptions.txt -pial -lh
The above command will run just the pial of just the lh hemi, so you
should have your answer in a few minutes
On 5/27/2021 2:19 PM, Alexopoulos, Dimitrios wrote:
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Hi users,
We’re having some issues with running some of our 2-3yo data
(0.8mm isotropic) through FS7 with and without the -hires flag.
There are persistent issues with the frontal lobe regions where
the pial has not extended to outer surface as illustrated below.
The WM surface contour look reasonable but the pial has
underestimated the outer cortex resulting in an incorrect surface
(below).
I don’t think control points will work (low intensity values in
the 50-60s), and no WM to add to the WM.mgz.
Any suggestion on how to push the pial surface out to capture the
cortical surface??
Thx.
Jim
&nb
sp;
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