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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:image004.png@01D752FB.04011E10] [cid:image005.jpg@01D752FB.04011E10] [cid:image001.png@01D752F8.E6507AC0] [cid:image002.png@01D752F8.E6507AC0] [cid:image006.png@01D752FB.04011E10][cid:image007.jpg@01D752FB.04011E10]
________________________________ 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.
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
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://secure-web.cisco.com/1YPN3hs4SyjZclyss7RMMOissR1aZ8Uwn4a_0Jq5vYrfci6...
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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
* 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.
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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________________________________ 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.
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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.
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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________________________________ 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.
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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto: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 mailto: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 &nb sp; ------------------------------------------------------------------------ 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 <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>
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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.
[cid:image007.jpg@01D75A0D.AF8124B0][cid:image008.jpg@01D75A0D.AF8124B0][cid:image012.jpg@01D75A0D.AF8124B0]
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
* External Email - Caution *
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:
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@01D75A09.597256B0] [cid:image002.jpg@01D75A09.597256B0] [cid:image003.png@01D75A09.597256B0] [cid:image004.png@01D75A09.597256B0] &nb sp; [cid:image005.png@01D75A09.597256B0][cid:image006.jpg@01D75A09.597256B0]
________________________________ 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.
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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________________________________ 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.
________________________________ 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.
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.edu 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.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:image007.jpg@01D75ACA.63BAD040][cid:image008.jpg@01D75ACA.63BAD040][cid:image009.jpg@01D75ACA.63BAD040]
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
* External Email - Caution *
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:
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:image010.png@01D75ACA.63BAD040] [cid:image011.jpg@01D75ACA.63BAD040] [cid:image012.png@01D75ACA.63BAD040] [cid:image013.png@01D75ACA.63BAD040] &nb sp; [cid:image014.png@01D75ACA.63BAD040][cid:image015.jpg@01D75ACA.63BAD040]
________________________________ 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.
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
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________________________________ 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.
________________________________ 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.
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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:image001.png@01D75AD3.6D815230] [cid:image002.png@01D75AD3.6D815230] [cid:image003.jpg@01D75AD3.93DFDC80]
From: freesurfer-bounces@nmr.mgh.harvard.edu 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.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
External Email - Use Caution
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:image004.jpg@01D75AD3.6D815230][cid:image005.jpg@01D75AD3.6D815230][cid:image006.jpg@01D75AD3.6D815230]
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
* External Email - Caution *
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:
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:image007.png@01D75AD3.6D815230] [cid:image008.jpg@01D75AD3.6D815230] [cid:image009.png@01D75AD3.6D815230] [cid:image010.png@01D75AD3.6D815230] &nb sp; [cid:image011.png@01D75AD3.6D815230][cid:image012.jpg@01D75AD3.6D815230]
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________________________________ 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.
________________________________ 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.
________________________________ 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.
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.edu 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.edu Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
External Email - Use Caution
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:image001.png@01D75ADC.26702E30][cid:image002.png@01D75ADC.26702E30] [cid:image003.jpg@01D75ADC.26702E30]
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
External Email - Use Caution
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:image004.jpg@01D75ADC.26702E30][cid:image005.jpg@01D75ADC.26702E30][cid:image006.jpg@01D75ADC.26702E30]
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
* External Email - Caution *
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:
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:image007.png@01D75ADC.26702E30] [cid:image008.jpg@01D75ADC.26702E30] [cid:image009.png@01D75ADC.26702E30] [cid:image010.png@01D75ADC.26702E30] &nb sp; [cid:image011.png@01D75ADC.26702E30][cid:image012.jpg@01D75ADC.26702E30]
________________________________ 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.
________________________________ 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.
________________________________ 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.
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:image002.jpg@01D75BB1.868A5270][cid:image004.jpg@01D75BB1.868A5270]
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:image013.png@01D75BAC.68A6BFA0][cid:image006.jpg@01D75BB1.868A5270]
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:image007.jpg@01D75BB1.868A5270][cid:image008.jpg@01D75BB1.868A5270]
From: freesurfer-bounces@nmr.mgh.harvard.edu 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.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
External Email - Use Caution
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:image016.png@01D75BAC.68A6BFA0][cid:image017.png@01D75BAC.68A6BFA0] [cid:image018.jpg@01D75BAC.68A6BFA0]
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
External Email - Use Caution
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:image019.jpg@01D75BAC.68A6BFA0][cid:image020.jpg@01D75BAC.68A6BFA0][cid:image021.jpg@01D75BAC.68A6BFA0]
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
* External Email - Caution *
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:
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:image022.png@01D75BAC.68A6BFA0] [cid:image023.jpg@01D75BAC.68A6BFA0] [cid:image024.png@01D75BAC.68A6BFA0] [cid:image025.png@01D75BAC.68A6BFA0] &nb sp; [cid:image026.png@01D75BAC.68A6BFA0][cid:image027.jpg@01D75BAC.68A6BFA0]
________________________________ 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.
________________________________ 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.
________________________________ 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.
________________________________ 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.
External Email - Use Caution
As a followup to my previous post, here is the aparc+aseg in that same region.
[cid:image005.jpg@01D75BB4.4E06FA40] [cid:image003.png@01D75BB4.4E0091A0]
From: freesurfer-bounces@nmr.mgh.harvard.edu 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.edu Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
* External Email - Caution *
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:image002.jpg@01D75BB1.868A5270][cid:image004.jpg@01D75BB1.868A5270]
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:image013.png@01D75BAC.68A6BFA0][cid:image006.jpg@01D75BB1.868A5270]
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:image007.jpg@01D75BB1.868A5270][cid:image008.jpg@01D75BB1.868A5270]
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
External Email - Use Caution
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:image016.png@01D75BAC.68A6BFA0][cid:image017.png@01D75BAC.68A6BFA0] [cid:image018.jpg@01D75BAC.68A6BFA0]
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
External Email - Use Caution
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:image019.jpg@01D75BAC.68A6BFA0][cid:image020.jpg@01D75BAC.68A6BFA0][cid:image021.jpg@01D75BAC.68A6BFA0]
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
* External Email - Caution *
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:
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:image022.png@01D75BAC.68A6BFA0] [cid:image023.jpg@01D75BAC.68A6BFA0] [cid:image024.png@01D75BAC.68A6BFA0] [cid:image025.png@01D75BAC.68A6BFA0] &nb sp; [cid:image026.png@01D75BAC.68A6BFA0][cid:image027.jpg@01D75BAC.68A6BFA0]
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________________________________ 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.
________________________________ 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.
________________________________ 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.
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
External Email - Use Caution
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
* External Email - Caution *
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
External Email - Use Caution
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
External Email - Use Caution
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
* External Email - Caution *
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:
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: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]
________________________________ 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.
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________________________________ 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.
________________________________ 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.
________________________________ 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.
________________________________ 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.
________________________________ 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.
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Thx Bruce, I'll edit the CPs as you suggest.
How do you explain brain in the updated brainmask being removed in the occipital region? I made no edits or changes in that area?. Do I need to edit the brainmask by cloning to the T1?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: Monday, June 07, 2021 3:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * 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.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 7, 2021 4:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FW: WM or Pial edits to correct surfaces
External Email - Use Caution
External Email - Use Caution As a followup to my previous post, here is the aparc+aseg in that same region.
[cid:image001.jpg@01D75BC2.05217220][cid:image002.png@01D75BC2.05217220]
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
* External Email - Caution *
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:image003.jpg@01D75BC2.05217220][cid:image004.jpg@01D75BC2.05217220]
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:image005.png@01D75BC2.05217220][cid:image006.jpg@01D75BC2.05217220]
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:image007.jpg@01D75BC2.05217220][cid:image008.jpg@01D75BC2.05217220]
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
External Email - Use Caution
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:image009.png@01D75BC2.05217220][cid:image010.png@01D75BC2.05217220] [cid:image011.jpg@01D75BC2.05217220]
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
External Email - Use Caution
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:image012.jpg@01D75BC2.05217220][cid:image013.jpg@01D75BC2.05217220][cid:image014.jpg@01D75BC2.05217220]
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
* External Email - Caution *
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:
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:image015.png@01D75BC2.05217220] [cid:image016.jpg@01D75BC2.05217220] [cid:image017.png@01D75BC2.05217220] [cid:image018.png@01D75BC2.05217220] &nb sp; [cid:image019.png@01D75BC2.05217220][cid:image020.jpg@01D75BC2.05217220]
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________________________________ 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.
It's really hard to say without looking at your data. You have to be careful not to accidentally add CPs outside of brain though as that can mess everything up Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Monday, June 7, 2021 6:24 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
External Email - Use Caution
External Email - Use Caution Thx Bruce, I'll edit the CPs as you suggest.
How do you explain brain in the updated brainmask being removed in the occipital region? I made no edits or changes in that area?. Do I need to edit the brainmask by cloning to the T1?
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: Monday, June 07, 2021 3:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * 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.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 7, 2021 4:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FW: WM or Pial edits to correct surfaces
External Email - Use Caution
External Email - Use Caution As a followup to my previous post, here is the aparc+aseg in that same region.
[cid:image001.jpg@01D75BCB.22DFCCE0][cid:image002.png@01D75BCB.22DFCCE0]
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
* External Email - Caution *
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:image003.jpg@01D75BCB.22DFCCE0][cid:image004.jpg@01D75BCB.22DFCCE0]
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:image005.png@01D75BCB.22DFCCE0][cid:image006.jpg@01D75BCB.22DFCCE0]
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:image007.jpg@01D75BCB.22DFCCE0][cid:image008.jpg@01D75BCB.22DFCCE0]
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
External Email - Use Caution
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:image009.png@01D75BCB.22DFCCE0][cid:image010.png@01D75BCB.22DFCCE0] [cid:image011.jpg@01D75BCB.22DFCCE0]
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
External Email - Use Caution
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:image012.jpg@01D75BCB.22DFCCE0][cid:image013.jpg@01D75BCB.22DFCCE0][cid:image014.jpg@01D75BCB.22DFCCE0]
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
* External Email - Caution *
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:
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:image015.png@01D75BCB.22DFCCE0] [cid:image016.jpg@01D75BCB.22DFCCE0] [cid:image017.png@01D75BCB.22DFCCE0] [cid:image018.png@01D75BCB.22DFCCE0] &nb sp; [cid:image019.png@01D75BCB.22DFCCE0][cid:image020.jpg@01D75BCB.22DFCCE0]
________________________________ 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.
_______________________________________________
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________________________________ 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.
________________________________ 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.
________________________________ 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.
________________________________ 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.
________________________________ 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.
________________________________ 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.
External Email - Use Caution
Bruce, that did the trick, with additional CPs to the WM. See below. I'm still not sure why some occipital brain was removed in the brainmask.
[cid:image001.jpg@01D75C78.32476690][cid:image001.jpg@01D75BCB.22DFCCE0]
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: Monday, June 07, 2021 5:30 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * It's really hard to say without looking at your data. You have to be careful not to accidentally add CPs outside of brain though as that can mess everything up 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: Monday, June 7, 2021 6:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
External Email - Use Caution
External Email - Use Caution Thx Bruce, I'll edit the CPs as you suggest.
How do you explain brain in the updated brainmask being removed in the occipital region? I made no edits or changes in that area?. Do I need to edit the brainmask by cloning to the T1?
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: Monday, June 07, 2021 3:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * 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.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 7, 2021 4:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FW: WM or Pial edits to correct surfaces
External Email - Use Caution
External Email - Use Caution As a followup to my previous post, here is the aparc+aseg in that same region.
[cid:image022.jpg@01D75C78.323E17C0][cid:image023.png@01D75C78.323E17C0]
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
* External Email - Caution *
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:image024.jpg@01D75C78.323E17C0][cid:image025.jpg@01D75C78.323E17C0]
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:image026.png@01D75C78.323E17C0][cid:image027.jpg@01D75C78.323E17C0]
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:image028.jpg@01D75C78.323E17C0][cid:image029.jpg@01D75C78.323E17C0]
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:image030.png@01D75C78.323E17C0][cid:image031.png@01D75C78.323E17C0] [cid:image032.jpg@01D75C78.323E17C0]
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:image033.jpg@01D75C78.323E17C0][cid:image034.jpg@01D75C78.323E17C0][cid:image035.jpg@01D75C78.323E17C0]
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
* External Email - Caution *
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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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:image036.png@01D75C78.323E17C0] [cid:image037.jpg@01D75C78.323E17C0] [cid:image038.png@01D75C78.323E17C0] [cid:image039.png@01D75C78.323E17C0] &nb sp; [cid:image040.png@01D75C78.323E17C0][cid:image041.jpg@01D75C78.323E17C0]
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You mean before? It was because the normalization was making some of the WM intensities so bright that they no longer looked like white matter (more like fat or something)
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Tuesday, June 8, 2021 4:08 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Bruce, that did the trick, with additional CPs to the WM. See below. I'm still not sure why some occipital brain was removed in the brainmask.
[cid:image001.jpg@01D75C81.08F9E390][cid:image002.jpg@01D75C81.08F9E390]
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: Monday, June 07, 2021 5:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * It's really hard to say without looking at your data. You have to be careful not to accidentally add CPs outside of brain though as that can mess everything up 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: Monday, June 7, 2021 6:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, I'll edit the CPs as you suggest.
How do you explain brain in the updated brainmask being removed in the occipital region? I made no edits or changes in that area?. Do I need to edit the brainmask by cloning to the T1?
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: Monday, June 07, 2021 3:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * 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.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 7, 2021 4:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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:image002.jpg@01D75C81.08F9E390][cid:image003.png@01D75C81.08F9E390]
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
* External Email - Caution *
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:image004.jpg@01D75C81.08F9E390][cid:image005.jpg@01D75C81.08F9E390]
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:image006.png@01D75C81.08F9E390][cid:image007.jpg@01D75C81.08F9E390]
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:image008.jpg@01D75C81.08F9E390][cid:image009.jpg@01D75C81.08F9E390]
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:image010.png@01D75C81.08F9E390][cid:image011.png@01D75C81.08F9E390] [cid:image012.jpg@01D75C81.08F9E390]
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:image013.jpg@01D75C81.08F9E390][cid:image014.jpg@01D75C81.08F9E390][cid:image015.jpg@01D75C81.08F9E390]
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
* External Email - Caution *
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:
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:image016.png@01D75C81.08F9E390] [cid:image017.jpg@01D75C81.08F9E390] [cid:image018.png@01D75C81.08F9E390] [cid:image019.png@01D75C81.08F9E390] &nb sp; [cid:image020.png@01D75C81.08F9E390][cid:image021.jpg@01D75C81.08F9E390]
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________________________________ 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.
________________________________ 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.
________________________________ 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.
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I simply added additional CPs to the original ones (on the left) .
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: Tuesday, June 08, 2021 3:12 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * You mean before? It was because the normalization was making some of the WM intensities so bright that they no longer looked like white matter (more like fat or something)
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: Tuesday, June 8, 2021 4:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Bruce, that did the trick, with additional CPs to the WM. See below. I'm still not sure why some occipital brain was removed in the brainmask.
[cid:image001.jpg@01D75CAF.AA77A940][cid:image022.jpg@01D75CAF.AA77A940]
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: Monday, June 07, 2021 5:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * It's really hard to say without looking at your data. You have to be careful not to accidentally add CPs outside of brain though as that can mess everything up 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: Monday, June 7, 2021 6:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, I'll edit the CPs as you suggest.
How do you explain brain in the updated brainmask being removed in the occipital region? I made no edits or changes in that area?. Do I need to edit the brainmask by cloning to the T1?
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: Monday, June 07, 2021 3:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * 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.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 7, 2021 4:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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:image022.jpg@01D75CAF.AA77A940][cid:image023.png@01D75CAF.AA77A940]
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:image024.jpg@01D75CAF.AA77A940][cid:image025.jpg@01D75CAF.AA77A940]
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:image026.png@01D75CAF.AA77A940][cid:image027.jpg@01D75CAF.AA77A940]
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:image028.jpg@01D75CAF.AA77A940][cid:image029.jpg@01D75CAF.AA77A940]
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:image030.png@01D75CAF.AA77A940][cid:image031.png@01D75CAF.AA77A940] [cid:image032.jpg@01D75CAF.AA77A940]
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:image033.jpg@01D75CAF.AA77A940][cid:image034.jpg@01D75CAF.AA77A940][cid:image035.jpg@01D75CAF.AA77A940]
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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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:image036.png@01D75CAF.AA77A940] [cid:image037.jpg@01D75CAF.AA77A940] [cid:image038.png@01D75CAF.AA77A940] [cid:image039.png@01D75CAF.AA77A940] &nb sp; [cid:image040.png@01D75CAF.AA77A940][cid:image041.jpg@01D75CAF.AA77A940]
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Great, so you are all set then?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Tuesday, June 8, 2021 10:45 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution I simply added additional CPs to the original ones (on the left) .
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: Tuesday, June 08, 2021 3:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * You mean before? It was because the normalization was making some of the WM intensities so bright that they no longer looked like white matter (more like fat or something)
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: Tuesday, June 8, 2021 4:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Bruce, that did the trick, with additional CPs to the WM. See below. I'm still not sure why some occipital brain was removed in the brainmask.
[cid:image001.jpg@01D75D1D.5C3FD180][cid:image002.jpg@01D75D1D.5C3FD180]
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: Monday, June 07, 2021 5:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * It's really hard to say without looking at your data. You have to be careful not to accidentally add CPs outside of brain though as that can mess everything up 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: Monday, June 7, 2021 6:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, I'll edit the CPs as you suggest.
How do you explain brain in the updated brainmask being removed in the occipital region? I made no edits or changes in that area?. Do I need to edit the brainmask by cloning to the T1?
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: Monday, June 07, 2021 3:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * 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.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 7, 2021 4:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] FW: WM or Pial edits to correct surfaces
External Email - Use Caution
External Email - Use Caution As a followup to my previous post, here is the aparc+aseg in that same region.
[cid:image002.jpg@01D75D1D.5C3FD180][cid:image003.png@01D75D1D.5C3FD180]
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
* External Email - Caution *
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:image004.jpg@01D75D1D.5C3FD180][cid:image005.jpg@01D75D1D.5C3FD180]
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:image006.png@01D75D1D.5C3FD180][cid:image007.jpg@01D75D1D.5C3FD180]
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:image008.jpg@01D75D1D.5C3FD180][cid:image009.jpg@01D75D1D.5C3FD180]
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:image010.png@01D75D1D.5C3FD180][cid:image011.png@01D75D1D.5C3FD180] [cid:image012.jpg@01D75D1D.5C3FD180]
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:image013.jpg@01D75D1D.5C3FD180][cid:image014.jpg@01D75D1D.5C3FD180][cid:image015.jpg@01D75D1D.5C3FD180]
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:image016.png@01D75D1D.5C3FD180] [cid:image017.jpg@01D75D1D.5C3FD180] [cid:image018.png@01D75D1D.5C3FD180] [cid:image019.png@01D75D1D.5C3FD180] &nb sp; [cid:image020.png@01D75D1D.5C3FD180][cid:image021.jpg@01D75D1D.5C3FD180]
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Thx Bruce, CPs did the trick.
The issue with voxels in the occipital region being removed in the brainmask after rerunning with CPs is still occurring and causing surface issues. No CPs have been placed in that region or outside the brain so I'm not sure why with would be occurring. I run recon-all -s subject -hires -autorecon2-cp -autorecon3 after adding CPs only.
Below are the brainmask.mgz after the first run and then after adding CPs on the right with aparc.
[cid:image002.jpg@01D75D67.D6474A90][cid:image003.jpg@01D75D67.D6474A90][cid:image007.jpg@01D75D67.D6474A90]
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: Wednesday, June 09, 2021 9:51 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * Great, so you are all set then?
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: Tuesday, June 8, 2021 10:45 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution I simply added additional CPs to the original ones (on the left) .
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: Tuesday, June 08, 2021 3:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * You mean before? It was because the normalization was making some of the WM intensities so bright that they no longer looked like white matter (more like fat or something)
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: Tuesday, June 8, 2021 4:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Bruce, that did the trick, with additional CPs to the WM. See below. I'm still not sure why some occipital brain was removed in the brainmask.
[cid:image001.jpg@01D75D66.4FB1D1E0][cid:image022.jpg@01D75D66.4FB1D1E0]
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: Monday, June 07, 2021 5:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * It's really hard to say without looking at your data. You have to be careful not to accidentally add CPs outside of brain though as that can mess everything up 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: Monday, June 7, 2021 6:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, I'll edit the CPs as you suggest.
How do you explain brain in the updated brainmask being removed in the occipital region? I made no edits or changes in that area?. Do I need to edit the brainmask by cloning to the T1?
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: Monday, June 07, 2021 3:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * 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.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 7, 2021 4:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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:image022.jpg@01D75D66.4FB1D1E0][cid:image023.png@01D75D66.4FB1D1E0]
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:image024.jpg@01D75D66.4FB1D1E0][cid:image025.jpg@01D75D66.4FB1D1E0]
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:image026.png@01D75D66.4FB1D1E0][cid:image027.jpg@01D75D66.4FB1D1E0]
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:image028.jpg@01D75D66.4FB1D1E0][cid:image029.jpg@01D75D66.4FB1D1E0]
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:image030.png@01D75D66.4FB1D1E0][cid:image031.png@01D75D66.4FB1D1E0] [cid:image032.jpg@01D75D66.4FB1D1E0]
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:image033.jpg@01D75D66.4FB1D1E0][cid:image034.jpg@01D75D66.4FB1D1E0][cid:image035.jpg@01D75D66.4FB1D1E0]
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:image036.png@01D75D66.4FB1D1E0] [cid:image037.jpg@01D75D66.4FB1D1E0] [cid:image038.png@01D75D66.4FB1D1E0] [cid:image039.png@01D75D66.4FB1D1E0] &nb sp; [cid:image040.png@01D75D66.4FB1D1E0][cid:image041.jpg@01D75D66.4FB1D1E0]
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That's odd and does seem like a bug. Can you tar/gzip this subject and upload it? What volume are you showing the aparc over?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Wednesday, June 9, 2021 8:42 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, CPs did the trick.
The issue with voxels in the occipital region being removed in the brainmask after rerunning with CPs is still occurring and causing surface issues. No CPs have been placed in that region or outside the brain so I'm not sure why with would be occurring. I run recon-all -s subject -hires -autorecon2-cp -autorecon3 after adding CPs only.
Below are the brainmask.mgz after the first run and then after adding CPs on the right with aparc.
[cid:image002.jpg@01D75D73.93A16890][cid:image003.jpg@01D75D73.93A16890][cid:image004.jpg@01D75D73.93A16890]
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: Wednesday, June 09, 2021 9:51 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * Great, so you are all set then?
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: Tuesday, June 8, 2021 10:45 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution I simply added additional CPs to the original ones (on the left) .
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: Tuesday, June 08, 2021 3:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * You mean before? It was because the normalization was making some of the WM intensities so bright that they no longer looked like white matter (more like fat or something)
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: Tuesday, June 8, 2021 4:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Bruce, that did the trick, with additional CPs to the WM. See below. I'm still not sure why some occipital brain was removed in the brainmask.
[cid:image005.jpg@01D75D73.93A16890][cid:image006.jpg@01D75D73.93A16890]
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: Monday, June 07, 2021 5:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * It's really hard to say without looking at your data. You have to be careful not to accidentally add CPs outside of brain though as that can mess everything up 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: Monday, June 7, 2021 6:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, I'll edit the CPs as you suggest.
How do you explain brain in the updated brainmask being removed in the occipital region? I made no edits or changes in that area?. Do I need to edit the brainmask by cloning to the T1?
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: Monday, June 07, 2021 3:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * 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.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 7, 2021 4:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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:image006.jpg@01D75D73.93A16890][cid:image007.png@01D75D73.93A16890]
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:image008.jpg@01D75D73.93A16890][cid:image009.jpg@01D75D73.93A16890]
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@01D75D73.93A16890][cid:image011.jpg@01D75D73.93A16890]
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@01D75D73.93A16890][cid:image013.jpg@01D75D73.93A16890]
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@01D75D73.93A16890][cid:image015.png@01D75D73.93A16890] [cid:image016.jpg@01D75D73.93A16890]
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@01D75D73.93A16890][cid:image018.jpg@01D75D73.93A16890][cid:image019.jpg@01D75D73.93A16890]
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@01D75D73.93A16890] [cid:image021.jpg@01D75D73.93A16890] [cid:image023.png@01D75D73.93A16890] [cid:image024.png@01D75D73.93A16890] &nb sp; [cid:image025.png@01D75D73.93A16890][cid:image026.jpg@01D75D73.93A16890]
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The aparc is overlain on the braimask after the rerun wih CPs utilized.
Where csn I can upload the 2 datasets (First run and rerun with CPs)?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: Wednesday, June 09, 2021 8:08 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * That's odd and does seem like a bug. Can you tar/gzip this subject and upload it? What volume are you showing the aparc over?
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: Wednesday, June 9, 2021 8:42 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, CPs did the trick.
The issue with voxels in the occipital region being removed in the brainmask after rerunning with CPs is still occurring and causing surface issues. No CPs have been placed in that region or outside the brain so I'm not sure why with would be occurring. I run recon-all -s subject -hires -autorecon2-cp -autorecon3 after adding CPs only.
Below are the brainmask.mgz after the first run and then after adding CPs on the right with aparc.
[cid:image001.jpg@01D75E0C.7550FF60][cid:image002.jpg@01D75E0C.7550FF60][cid:image003.jpg@01D75E0C.7550FF60]
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: Wednesday, June 09, 2021 9:51 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * Great, so you are all set then?
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: Tuesday, June 8, 2021 10:45 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution I simply added additional CPs to the original ones (on the left) .
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: Tuesday, June 08, 2021 3:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * You mean before? It was because the normalization was making some of the WM intensities so bright that they no longer looked like white matter (more like fat or something)
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: Tuesday, June 8, 2021 4:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Bruce, that did the trick, with additional CPs to the WM. See below. I'm still not sure why some occipital brain was removed in the brainmask.
[cid:image004.jpg@01D75E0C.7550FF60][cid:image005.jpg@01D75E0C.7550FF60]
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: Monday, June 07, 2021 5:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * It's really hard to say without looking at your data. You have to be careful not to accidentally add CPs outside of brain though as that can mess everything up 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: Monday, June 7, 2021 6:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, I'll edit the CPs as you suggest.
How do you explain brain in the updated brainmask being removed in the occipital region? I made no edits or changes in that area?. Do I need to edit the brainmask by cloning to the T1?
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: Monday, June 07, 2021 3:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * 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.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 7, 2021 4:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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:image005.jpg@01D75E0C.7550FF60][cid:image007.png@01D75E0C.7550FF60]
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:image008.jpg@01D75E0C.7550FF60][cid:image009.jpg@01D75E0C.7550FF60]
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@01D75E0C.7550FF60][cid:image011.jpg@01D75E0C.7550FF60]
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@01D75E0C.7550FF60][cid:image013.jpg@01D75E0C.7550FF60]
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@01D75E0C.7550FF60][cid:image015.png@01D75E0C.7550FF60] [cid:image016.jpg@01D75E0C.7550FF60]
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@01D75E0C.7550FF60][cid:image018.jpg@01D75E0C.7550FF60][cid:image019.jpg@01D75E0C.7550FF60]
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@01D75E0C.7550FF60] [cid:image021.jpg@01D75E0C.7550FF60] [cid:image022.png@01D75E0C.7550FF60] [cid:image023.png@01D75E0C.7550FF60] &nb sp; [cid:image024.png@01D75E0C.7550FF60][cid:image025.jpg@01D75E0C.7550FF60]
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Bruce ,
I have uploaded a subject for which this voxel removal in the brainmask.mgz is present after re-running with CPs. Two studies were uploaded to transfer/incoming:
1. MOD2065_Y2_a_fs7.zip - first FS7.1 run using recon-all -hires -all
2. MOD2065_Y2_a_fs7_cp.zip - FS7.1 rerun with Control Points using recon-all -hires -all
Your feedback would be appreciated. FS7.1 run on linux ubuntu 18.04.
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: Wednesday, June 09, 2021 8:08 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * That's odd and does seem like a bug. Can you tar/gzip this subject and upload it? What volume are you showing the aparc over?
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: Wednesday, June 9, 2021 8:42 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, CPs did the trick.
The issue with voxels in the occipital region being removed in the brainmask after rerunning with CPs is still occurring and causing surface issues. No CPs have been placed in that region or outside the brain so I'm not sure why with would be occurring. I run recon-all -s subject -hires -autorecon2-cp -autorecon3 after adding CPs only.
Below are the brainmask.mgz after the first run and then after adding CPs on the right with aparc.
[cid:image001.jpg@01D75E43.5C3ED380][cid:image002.jpg@01D75E43.5C3ED380][cid:image003.jpg@01D75E43.5C3ED380]
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: Wednesday, June 09, 2021 9:51 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * Great, so you are all set then?
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: Tuesday, June 8, 2021 10:45 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution I simply added additional CPs to the original ones (on the left) .
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: Tuesday, June 08, 2021 3:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * You mean before? It was because the normalization was making some of the WM intensities so bright that they no longer looked like white matter (more like fat or something)
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: Tuesday, June 8, 2021 4:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
External Email - Use Caution
External Email - Use Caution Bruce, that did the trick, with additional CPs to the WM. See below. I'm still not sure why some occipital brain was removed in the brainmask.
[cid:image004.jpg@01D75E43.5C3ED380][cid:image005.jpg@01D75E43.5C3ED380]
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: Monday, June 07, 2021 5:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * It's really hard to say without looking at your data. You have to be careful not to accidentally add CPs outside of brain though as that can mess everything up 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: Monday, June 7, 2021 6:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, I'll edit the CPs as you suggest.
How do you explain brain in the updated brainmask being removed in the occipital region? I made no edits or changes in that area?. Do I need to edit the brainmask by cloning to the T1?
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: Monday, June 07, 2021 3:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * 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.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 7, 2021 4:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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:image005.jpg@01D75E43.5C3ED380][cid:image007.png@01D75E43.5C3ED380]
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:image008.jpg@01D75E43.5C3ED380][cid:image009.jpg@01D75E43.5C3ED380]
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@01D75E43.5C3ED380][cid:image011.jpg@01D75E43.5C3ED380]
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@01D75E43.5C3ED380][cid:image013.jpg@01D75E43.5C3ED380]
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@01D75E43.5C3ED380][cid:image015.png@01D75E43.5C3ED380] [cid:image016.jpg@01D75E43.5C3ED380]
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@01D75E43.5C3ED380][cid:image018.jpg@01D75E43.5C3ED380][cid:image019.jpg@01D75E43.5C3ED380]
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@01D75E43.5C3ED380] [cid:image021.jpg@01D75E43.5C3ED380] [cid:image022.png@01D75E43.5C3ED380] [cid:image023.png@01D75E43.5C3ED380] &nb sp; [cid:image024.png@01D75E43.5C3ED380][cid:image025.jpg@01D75E43.5C3ED380]
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Hi Bruce,
Was just wondering if anyone was able to have a look at these 2 studies that I uploaded.
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Thursday, June 10, 2021 9:57 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Bruce ,
I have uploaded a subject for which this voxel removal in the brainmask.mgz is present after re-running with CPs. Two studies were uploaded to transfer/incoming:
1. MOD2065_Y2_a_fs7.zip - first FS7.1 run using recon-all -hires -all
2. MOD2065_Y2_a_fs7_cp.zip - FS7.1 rerun with Control Points using recon-all -hires -all
Your feedback would be appreciated. FS7.1 run on linux ubuntu 18.04.
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 Fischl, Bruce Sent: Wednesday, June 09, 2021 8:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * That's odd and does seem like a bug. Can you tar/gzip this subject and upload it? What volume are you showing the aparc over?
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: Wednesday, June 9, 2021 8:42 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, CPs did the trick.
The issue with voxels in the occipital region being removed in the brainmask after rerunning with CPs is still occurring and causing surface issues. No CPs have been placed in that region or outside the brain so I'm not sure why with would be occurring. I run recon-all -s subject -hires -autorecon2-cp -autorecon3 after adding CPs only.
Below are the brainmask.mgz after the first run and then after adding CPs on the right with aparc.
[cid:image001.jpg@01D769C7.C53C22E0][cid:image002.jpg@01D769C7.C53C22E0][cid:image003.jpg@01D769C7.C53C22E0]
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: Wednesday, June 09, 2021 9:51 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * Great, so you are all set then?
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: Tuesday, June 8, 2021 10:45 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution I simply added additional CPs to the original ones (on the left) .
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: Tuesday, June 08, 2021 3:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * You mean before? It was because the normalization was making some of the WM intensities so bright that they no longer looked like white matter (more like fat or something)
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: Tuesday, June 8, 2021 4:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Bruce, that did the trick, with additional CPs to the WM. See below. I'm still not sure why some occipital brain was removed in the brainmask.
[cid:image004.jpg@01D769C7.C53C22E0][cid:image006.jpg@01D769C7.C53C22E0]
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: Monday, June 07, 2021 5:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * It's really hard to say without looking at your data. You have to be careful not to accidentally add CPs outside of brain though as that can mess everything up 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: Monday, June 7, 2021 6:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, I'll edit the CPs as you suggest.
How do you explain brain in the updated brainmask being removed in the occipital region? I made no edits or changes in that area?. Do I need to edit the brainmask by cloning to the T1?
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: Monday, June 07, 2021 3:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * 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.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 7, 2021 4:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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:image006.jpg@01D769C7.C53C22E0][cid:image007.png@01D769C7.C53C22E0]
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:image008.jpg@01D769C7.C53C22E0][cid:image009.jpg@01D769C7.C53C22E0]
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@01D769C7.C53C22E0][cid:image011.jpg@01D769C7.C53C22E0]
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@01D769C7.C53C22E0][cid:image013.jpg@01D769C7.C53C22E0]
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@01D769C7.C53C22E0][cid:image015.png@01D769C7.C53C22E0] [cid:image016.jpg@01D769C7.C53C22E0]
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@01D769C7.C53C22E0][cid:image018.jpg@01D769C7.C53C22E0][cid:image019.jpg@01D769C7.C53C22E0]
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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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:image020.png@01D769C7.C53C22E0] [cid:image021.jpg@01D769C7.C53C22E0] [cid:image022.png@01D769C7.C53C22E0] [cid:image023.png@01D769C7.C53C22E0] &nb sp; [cid:image024.png@01D769C7.C53C22E0][cid:image025.jpg@01D769C7.C53C22E0]
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Just following up. I'm wondering if this is a fs7.1 issue. After adding only CPs and rerunning , voxels in the occipital region of the brainmask.mgz are being removed.
Jim
From: Alexopoulos, Dimitrios Sent: Friday, June 25, 2021 1:39 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FW: WM or Pial edits to correct surfaces
Hi Bruce,
Was just wondering if anyone was able to have a look at these 2 studies that I uploaded.
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: Thursday, June 10, 2021 9:57 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Bruce ,
I have uploaded a subject for which this voxel removal in the brainmask.mgz is present after re-running with CPs. Two studies were uploaded to transfer/incoming:
1. MOD2065_Y2_a_fs7.zip - first FS7.1 run using recon-all -hires -all
2. MOD2065_Y2_a_fs7_cp.zip - FS7.1 rerun with Control Points using recon-all -hires -all
Your feedback would be appreciated. FS7.1 run on linux ubuntu 18.04.
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 Fischl, Bruce Sent: Wednesday, June 09, 2021 8:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * That's odd and does seem like a bug. Can you tar/gzip this subject and upload it? What volume are you showing the aparc over?
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: Wednesday, June 9, 2021 8:42 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, CPs did the trick.
The issue with voxels in the occipital region being removed in the brainmask after rerunning with CPs is still occurring and causing surface issues. No CPs have been placed in that region or outside the brain so I'm not sure why with would be occurring. I run recon-all -s subject -hires -autorecon2-cp -autorecon3 after adding CPs only.
Below are the brainmask.mgz after the first run and then after adding CPs on the right with aparc.
[cid:image001.jpg@01D77649.2DEE96A0][cid:image002.jpg@01D77649.2DEE96A0][cid:image003.jpg@01D77649.2DEE96A0]
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: Wednesday, June 09, 2021 9:51 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * Great, so you are all set then?
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: Tuesday, June 8, 2021 10:45 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution I simply added additional CPs to the original ones (on the left) .
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: Tuesday, June 08, 2021 3:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * You mean before? It was because the normalization was making some of the WM intensities so bright that they no longer looked like white matter (more like fat or something)
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: Tuesday, June 8, 2021 4:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Bruce, that did the trick, with additional CPs to the WM. See below. I'm still not sure why some occipital brain was removed in the brainmask.
[cid:image004.jpg@01D77649.2DEE96A0][cid:image005.jpg@01D77649.2DEE96A0]
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: Monday, June 07, 2021 5:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * It's really hard to say without looking at your data. You have to be careful not to accidentally add CPs outside of brain though as that can mess everything up 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: Monday, June 7, 2021 6:24 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
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External Email - Use Caution Thx Bruce, I'll edit the CPs as you suggest.
How do you explain brain in the updated brainmask being removed in the occipital region? I made no edits or changes in that area?. Do I need to edit the brainmask by cloning to the T1?
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: Monday, June 07, 2021 3:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces
* External Email - Caution * 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.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 7, 2021 4:46 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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:image005.jpg@01D77649.2DEE96A0][cid:image007.png@01D77649.2DEE96A0]
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:image008.jpg@01D77649.2DEE96A0][cid:image009.jpg@01D77649.2DEE96A0]
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@01D77649.2DEE96A0][cid:image011.jpg@01D77649.2DEE96A0]
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@01D77649.2DEE96A0][cid:image013.jpg@01D77649.2DEE96A0]
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@01D77649.2DEE96A0][cid:image015.png@01D77649.2DEE96A0] [cid:image016.jpg@01D77649.2DEE96A0]
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@01D77649.2DEE96A0][cid:image018.jpg@01D77649.2DEE96A0][cid:image019.jpg@01D77649.2DEE96A0]
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@01D77649.2DEE96A0] [cid:image021.jpg@01D77649.2DEE96A0] [cid:image022.png@01D77649.2DEE96A0] [cid:image023.png@01D77649.2DEE96A0] &nb sp; [cid:image024.png@01D77649.2DEE96A0][cid:image025.jpg@01D77649.2DEE96A0]
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That probably means you are being too aggressive with the CP placement. Try putting them more towards the interior not so far out where the voxels are probably partial-volumed. I expect you are pushing the WM intensity in that region too high. Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Monday, June 7, 2021 4:26 PM To: Freesurfer support list 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:image001.jpg@01D75BBD.A030D3A0][cid:image002.jpg@01D75BBD.A030D3A0]
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:image003.png@01D75BBD.A030D3A0][cid:image004.jpg@01D75BBD.A030D3A0]
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:image005.jpg@01D75BBD.A030D3A0][cid:image006.jpg@01D75BBD.A030D3A0]
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:image007.png@01D75BBD.A030D3A0][cid:image008.png@01D75BBD.A030D3A0] [cid:image009.jpg@01D75BBD.A030D3A0]
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:image010.jpg@01D75BBD.A030D3A0][cid:image011.jpg@01D75BBD.A030D3A0][cid:image012.jpg@01D75BBD.A030D3A0]
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
* External Email - Caution *
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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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:image013.png@01D75BBD.A030D3A0] [cid:image014.jpg@01D75BBD.A030D3A0] [cid:image015.png@01D75BBD.A030D3A0] [cid:image016.png@01D75BBD.A030D3A0] &nb sp; [cid:image017.png@01D75BBD.A030D3A0][cid:image018.jpg@01D75BBD.A030D3A0]
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Hi Jim, I know it has been a while, but I have tracked down the source of the problem with the pial surface. I can go into detail if you want, but the fix is to add -no-numakeuchar to recon-all. I noticed that there are some places where the white surface does not extend far enough. This is due to the WM strands being very thin and partial voluming with GM. The fix for this is to edit the wm.mgz and rerun recon-all with -autorecon-wm -autorecon3. doug
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
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External Email - Use Caution
Thx Doug, much appreciated.
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, August 31, 2021 12:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
* External Email - Caution * Hi Jim, I know it has been a while, but I have tracked down the source of the problem with the pial surface. I can go into detail if you want, but the fix is to add -no-numakeuchar to recon-all. I noticed that there are some places where the white surface does not extend far enough. This is due to the WM strands being very thin and partial voluming with GM. The fix for this is to edit the wm.mgz and rerun recon-all with -autorecon-wm -autorecon3. doug
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@01D79E6C.D1C47A10] [cid:image002.jpg@01D79E6C.D1C47A10] [cid:image003.png@01D79E6C.D1C47A10] [cid:image004.png@01D79E6C.D1C47A10] &nb sp; [cid:image005.png@01D79E6C.D1C47A10][cid:image006.jpg@01D79E6C.D1C47A10]
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________________________________ 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.
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Doug,
It appears as though using the -no-numakeuchar flag does correct the global normalization issue, however, the resulting surfaces are not early a good/crisp as the ones generated without the flag. Results are on 2yo subjects using 7.1.1. adult with -hires. Illustrations of the left/right hems are below. Comments?
Left Hem - without the -no-numakeuchar flag. Note superior/anterior darker regions [cid:image001.jpg@01D7A3DB.0B109380]
Left Hem - including the -no-numakeuchar flag [cid:image002.jpg@01D7A3DB.0B109380]
Right Hem - including the -no-numakeuchar flag [cid:image003.jpg@01D7A3DB.0B109380]
Right Hem - without the -no-numakeuchar flag [cid:image004.png@01D7A3DB.0B109380]
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, August 31, 2021 12:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
* External Email - Caution * Hi Jim, I know it has been a while, but I have tracked down the source of the problem with the pial surface. I can go into detail if you want, but the fix is to add -no-numakeuchar to recon-all. I noticed that there are some places where the white surface does not extend far enough. This is due to the WM strands being very thin and partial voluming with GM. The fix for this is to edit the wm.mgz and rerun recon-all with -autorecon-wm -autorecon3. doug
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:image005.png@01D7A3DB.0B109380] [cid:image006.jpg@01D7A3DB.0B109380] [cid:image007.png@01D7A3DB.0B109380] [cid:image008.png@01D7A3DB.0B109380] &nb sp; [cid:image009.png@01D7A3DB.0B109380][cid:image010.jpg@01D7A3DB.0B109380]
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Is the same case you sent before (MOD1533_Y2_a_fs7)?
On 9/7/2021 12:24 PM, Alexopoulos, Dimitrios wrote:
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External Email - Use Caution
Doug,
It appears as though using the -no-numakeuchar flag does correct the global normalization issue, however, the resulting surfaces are not early a good/crisp as the ones generated without the flag. Results are on 2yo subjects using 7.1.1. adult with –hires. Illustrations of the left/right hems are below. Comments?
*Left Hem – without the -no-numakeuchar flag. Note superior/anterior darker regions*
*Left Hem – including **the **-no-numakeuchar flag*
*Right Hem – including **the **-no-numakeuchar flag*
*Right Hem – without the -no-numakeuchar flag*
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Tuesday, August 31, 2021 12:00 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] WM or Pial edits to correct surfaces
** External Email - Caution **
Hi Jim, I know it has been a while, but I have tracked down the source of the problem with the pial surface. I can go into detail if you want, but the fix is to add -no-numakeuchar to recon-all. I noticed that there are some places where the white surface does not extend far enough. This is due to the WM strands being very thin and partial voluming with GM. The fix for this is to edit the wm.mgz and rerun recon-all with -autorecon-wm -autorecon3. doug
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 &nb sp; ------------------------------------------------------------------------ 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 <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>
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Yes, the same subject was run using the same input DCM files. The only diff is top figure was run with -hire -all, the bottom run with -no-numakeuchar flag as well. I have uploaded the output using the -no-numakeuchar to transfer/incoming as MOD1533_Y2_a_fs7_no-numakeuchar.zip
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, September 07, 2021 8:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
* External Email - Caution * Is the same case you sent before (MOD1533_Y2_a_fs7)? On 9/7/2021 12:24 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
External Email - Use Caution Doug,
It appears as though using the -no-numakeuchar flag does correct the global normalization issue, however, the resulting surfaces are not early a good/crisp as the ones generated without the flag. Results are on 2yo subjects using 7.1.1. adult with -hires. Illustrations of the left/right hems are below. Comments?
Left Hem - without the -no-numakeuchar flag. Note superior/anterior darker regions [cid:image001.jpg@01D7A653.B4B64720]
Left Hem - including the -no-numakeuchar flag [cid:image002.jpg@01D7A653.B4B64720]
Right Hem - including the -no-numakeuchar flag [cid:image003.jpg@01D7A653.B4B64720]
Right Hem - without the -no-numakeuchar flag [cid:image004.png@01D7A653.B4B64720]
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: Tuesday, August 31, 2021 12:00 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 * Hi Jim, I know it has been a while, but I have tracked down the source of the problem with the pial surface. I can go into detail if you want, but the fix is to add -no-numakeuchar to recon-all. I noticed that there are some places where the white surface does not extend far enough. This is due to the WM strands being very thin and partial voluming with GM. The fix for this is to edit the wm.mgz and rerun recon-all with -autorecon-wm -autorecon3. doug
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:image005.png@01D7A653.B4B64720] [cid:image006.jpg@01D7A653.B4B64720] [cid:image007.png@01D7A653.B4B64720] [cid:image008.png@01D7A653.B4B64720] &n bsp; &nb sp; [cid:image009.png@01D7A653.B4B64720][cid:image010.jpg@01D7A653.B4B64720]
________________________________ 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.
_______________________________________________
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________________________________ 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.
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Hi,
Just wondering if you've had a chance to evaluate these differences?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Friday, September 10, 2021 3:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces
* External Email - Caution *
External Email - Use Caution Yes, the same subject was run using the same input DCM files. The only diff is top figure was run with -hire -all, the bottom run with -no-numakeuchar flag as well. I have uploaded the output using the -no-numakeuchar to transfer/incoming as MOD1533_Y2_a_fs7_no-numakeuchar.zip
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 Douglas N. Greve Sent: Tuesday, September 07, 2021 8:45 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 * Is the same case you sent before (MOD1533_Y2_a_fs7)? On 9/7/2021 12:24 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
External Email - Use Caution Doug,
It appears as though using the -no-numakeuchar flag does correct the global normalization issue, however, the resulting surfaces are not early a good/crisp as the ones generated without the flag. Results are on 2yo subjects using 7.1.1. adult with -hires. Illustrations of the left/right hems are below. Comments?
Left Hem - without the -no-numakeuchar flag. Note superior/anterior darker regions [cid:image001.jpg@01D7B399.EFD87EB0]
Left Hem - including the -no-numakeuchar flag [cid:image002.jpg@01D7B399.EFD87EB0]
Right Hem - including the -no-numakeuchar flag [cid:image003.jpg@01D7B399.EFD87EB0]
Right Hem - without the -no-numakeuchar flag [cid:image004.png@01D7B399.EFD87EB0]
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: Tuesday, August 31, 2021 12:00 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 * Hi Jim, I know it has been a while, but I have tracked down the source of the problem with the pial surface. I can go into detail if you want, but the fix is to add -no-numakeuchar to recon-all. I noticed that there are some places where the white surface does not extend far enough. This is due to the WM strands being very thin and partial voluming with GM. The fix for this is to edit the wm.mgz and rerun recon-all with -autorecon-wm -autorecon3. doug
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:image005.png@01D7B399.EFD87EB0] [cid:image006.jpg@01D7B399.EFD87EB0] [cid:image007.png@01D7B399.EFD87EB0] [cid:image008.png@01D7B399.EFD87EB0] &n bsp; &nb sp; [cid:image009.png@01D7B399.EFD87EB0][cid:image010.jpg@01D7B399.EFD87EB0]
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Alexopoulos, Dimitrios -
Douglas N. Greve -
Fischl, Bruce