External Email - Use Caution
Greg,
Additional clarification.
Are these 2 options runs independently - i.e. separate tests?
For example, add CPs to brain.mgz and then rerun entire recon-all -all command?
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
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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Thursday, May 27, 2021 5:25 PM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1YPN3hs4SyjZclyss7RMMOissR1aZ8Uwn4a_0Jq5vYrfci6...
________________________________ 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.
