External Email - Use Caution
Thanks Doug. Will try with difference distances. Where is the expert file
placed?
From: freesurfer-boun...@nmr.mgh.harvard.edu
<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
Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
* External Email - Caution *
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:
External Email - Use Caution
External Email - Use Caution
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
[cid:image001.png@01D753C2.9A297CD0] [cid:image002.jpg@01D753C2.9A297CD0]
[cid:image003.png@01D753C2.9A297CD0] [cid:image004.png@01D753C2.9A297CD0]
&nb sp;
[cid:image005.png@01D753C2.9A297CD0][cid:image006.jpg@01D753C2.9A297CD0]
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/1YPN3hs4SyjZclyss7RMMOissR1aZ8Uwn4a_0Jq5vYrfci6A59120SXSb0sKe_KiChRMyqT03GrtjEpvMXK-ID5_mFZyeiQW6IG4tERBD-TqUOpRAGbH-1tIOXEjrDmjPZYO8KFRoKksLscaqeKhf8kwlTdmb9durYYaCWLRq0NN_oIT4bj7kKl_ewjL6zWkMJu06W9cB4RqOf7el-gq6aPYY2ymbPYfSb4euBdJd-oi8BCKHdsWPI0QIbfan138P5vOHDmVV_iX0y5a0q2olUg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
