p.s. if you are still struggling with this after trying to be more conservative we can take a look. The other thing you can try if you want to keep your current CP placement is to also add some to the interior of the WM (where things are getting to be in the 130s and 140s). This will limit the spatial extent of the influence of the CPs that are on the thin strands
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Monday, June 7, 2021 4:46 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution As a followup to my previous post, here is the aparc+aseg in that same region.
[cid:image001.jpg@01D75BBE.3CCC3A10][cid:image003.png@01D75BBE.3CCC3A10]
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 Alexopoulos, Dimitrios Sent: Monday, June 07, 2021 3:26 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
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External Email - Use Caution Bruce,
Thanks for the recommenadtion. I editerd several regions by being more aggressive with CPs, whose palcements are shown in The snapshots below. The images on the left of each row below are the original FS ouputs and on the right are the updated outputs with the CPs added and running recon-all -all.
.
Original With CPs
In row 1 the the pial and white surrfaces in the frontal pole region in many cases look much better. The WM has pushed the pial out correctly.
[cid:image005.jpg@01D75BBE.3CCC3A10][cid:image009.jpg@01D75BBE.3CCC3A10]
Row 2:
Not so good a result when adding CPS. The frontal pole pial got pulled out correctly but the WM surface is incorrect. Suggrestions to correct? I aslo noticed that several WM voxels in the updated regions are >110 up to 130-140. Is this expected?
[cid:image010.png@01D75BBE.3CCC3A10][cid:image011.jpg@01D75BBE.3CCC3A10]
Row 3:
CPs appear to have captured more WM and the pial got pushed out correctly in the lateral orbital region. In this example I'm not sure why the occipital pole has data removed in the brainmask. I simply reran recoon-all -all incorporating the updated control,dat. Do I need to add back brain by cloning with the T1?
[cid:image012.jpg@01D75BBE.3CCC3A10][cid:image013.jpg@01D75BBE.3CCC3A10]
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 Fischl, Bruce Sent: Sunday, June 06, 2021 12:59 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
* External Email - Caution * Usually you can do this iteratively. Find some voxels that are clearly wm, but whose intensity is <110 and add some cps there then rerun. In the image below you could put some near the red cursor, which looks darker than the wm more superior
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 Alexopoulos, Dimitrios Sent: Sunday, June 6, 2021 1:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
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External Email - Use Caution Bruce,
Below are snapshots of the brainmask and surfaces in that problematic region. I tried to add some CPs but generally did not because the WM is not visible and/or intensity values are ~70. The cortex is just darker in this region.
[cid:image014.png@01D75BBE.3CCC3A10][cid:image015.png@01D75BBE.3CCC3A10] [cid:image016.jpg@01D75BBE.3CCC3A10]
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 Fischl, Bruce Sent: Sunday, June 06, 2021 10:52 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
* External Email - Caution * Where did you try putting control points? If I understand what you are seeing I would add them to the body of the wm near temporal pole, then check in the brain.mgz to make sure that the intensities have been increased enough (where you put the CPs it should be close to 110, and the WM should be >90 or so most places depending on the details of your acquisition )
Cheers Bruce
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 Alexopoulos, Dimitrios Sent: Saturday, June 5, 2021 2:20 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
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External Email - Use Caution 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.
[cid:image017.jpg@01D75BBE.3CCC3A10][cid:image018.jpg@01D75BBE.3CCC3A10][cid:image019.jpg@01D75BBE.3CCC3A10]
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
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External Email - Use Caution 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:
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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
[cid:image020.png@01D75BBE.3CCC3A10] [cid:image021.jpg@01D75BBE.3CCC3A10] [cid:image022.png@01D75BBE.3CCC3A10] [cid:image023.png@01D75BBE.3CCC3A10] &nb sp; [cid:image024.png@01D75BBE.3CCC3A10][cid:image025.jpg@01D75BBE.3CCC3A10]
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