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Greg,

 

I tried what you recommended. I ran several iterations with

PlaceT1PialSurf --max-cbv-dist 6 (8 and 10), with and without controls points. No meaningful changes occur with pulling out the pial and adding CPs. In fact the CPS may cause more harm since the intensities are around 60-70.

 

The issue  appears  to be intensity-gradient related. The  raw T1 has a  mild intensity inhomogeneity where the anterior is darker than posterior

regions, including darker cortex especially  in frontal pole cortex. The N3 gain field correction does not appear to have had much on an effect. This is illustrated in the images  below. Raw T1 (left), brainmask, brainmask/pial surface.

 

 

 

Are there other options with the N3 correction in freesurfer?

 

Can we input another T1 which has been pre-processed using another method, perhaps using  ANTS N4, which appears to do better with the gain field correction.

 

Jim

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of 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

 

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Thanks Doug. Will try with difference distances. Where is the expert file placed?

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <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.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

 

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