Re: [Freesurfer] WM or Pial edits to correct surfaces
External Email - Use Caution Thx Doug, much appreciated. Jim From: freesurfer-boun...@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] sp; [cid:image005.png@01D79E6C.D1C47A10][cid:image006.jpg@01D79E6C.D1C47A10] The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1YPN3hs4SyjZclyss7RMMOissR1aZ8Uwn4a_0Jq5vYrfci6A59120SXSb0sKe_KiChRMyqT03GrtjEpvMXK-ID5_mFZyeiQW6IG4tERBD-TqUOpRAGbH-1tIOXEjrDmjPZYO8KFRoKksLscaqeKhf8kwlTdmb9durYYaCWLRq0NN_oIT4bj7kKl_ewjL6zWkMJu06W9cB4RqOf7el-gq6aPYY2ymbPYfSb4euBdJd-oi8BCKHdsWPI0QIbfan138P5vOHDmVV_iX0y5a0q2olUg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] WM or Pial edits to correct surfaces
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 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_0Jq5vYrfci6A59120SXSb0sKe_KiChRMyqT03GrtjEpvMXK-ID5_mFZyeiQW6IG4tERBD-TqUOpRAGbH-1tIOXEjrDmjPZYO8KFRoKksLscaqeKhf8kwlTdmb9durYYaCWLRq0NN_oIT4bj7kKl_ewjL6zWkMJu06W9cB4RqOf7el-gq6aPYY2ymbPYfSb4euBdJd-oi8BCKHdsWPI0QIbfan138P5vOHDmVV_iX0y5a0q2olUg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] WM or Pial edits to correct surfaces
External Email - Use Caution Thanks Doug. Will try with difference distances. Where is the expert file placed? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Thursday, May 27, 2021 5:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces * External Email - Caution * There might be a couple things happening. First, I would try adding a few control points in that area; make sure they are in true WM in voxels that have a value less than 110 on the brain.mgz file. This might help push the white surface further out (the WM in that gyrus is very thin). It might also help push the pial surface out. The next thing you can try is to increase the maximum distance over which the edge is searched for. These young subjects have very plump/thick cortices. You can do that with an expert options file. Create a text file with the following content: PlaceT1PialSurf --max-cbv-dist 6 Where "6" tells it to search 6 mm rather than the default 5. You may need to play with the number You can then run recon-all with recon-all -s subject -expert yourexpertoptions.txt -pial -lh The above command will run just the pial of just the lh hemi, so you should have your answer in a few minutes On 5/27/2021 2:19 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution External Email - Use Caution Hi users, We're having some issues with running some of our 2-3yo data (0.8mm isotropic) through FS7 with and without the -hires flag. There are persistent issues with the frontal lobe regions where the pial has not extended to outer surface as illustrated below. The WM surface contour look reasonable but the pial has underestimated the outer cortex resulting in an incorrect surface (below). I don't think control points will work (low intensity values in the 50-60s), and no WM to add to the WM.mgz. Any suggestion on how to push the pial surface out to capture the cortical surface?? Thx. Jim [cid:image001.png@01D753C2.9A297CD0] [cid:image002.jpg@01D753C2.9A297CD0] [cid:image003.png@01D753C2.9A297CD0] [cid:image004.png@01D753C2.9A297CD0] sp; [cid:image005.png@01D753C2.9A297CD0][cid:image006.jpg@01D753C2.9A297CD0] The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1YPN3hs4SyjZclyss7RMMOissR1aZ8Uwn4a_0Jq5vYrfci6A59120SXSb0sKe_KiChRMyqT03GrtjEpvMXK-ID5_mFZyeiQW6IG4tERBD-TqUOpRAGbH-1tIOXEjrDmjPZYO8KFRoKksLscaqeKhf8kwlTdmb9durYYaCWLRq0NN_oIT4bj7kKl_ewjL6zWkMJu06W9cB4RqOf7el-gq6aPYY2ymbPYfSb4euBdJd-oi8BCKHdsWPI0QIbfan138P5vOHDmVV_iX0y5a0q2olUg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] WM or Pial edits to correct surfaces
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_0Jq5vYrfci6A59120SXSb0sKe_KiChRMyqT03GrtjEpvMXK-ID5_mFZyeiQW6IG4tERBD-TqUOpRAGbH-1tIOXEjrDmjPZYO8KFRoKksLscaqeKhf8kwlTdmb9durYYaCWLRq0NN_oIT4bj7kKl_ewjL6zWkMJu06W9cB4RqOf7el-gq6aPYY2ymbPYfSb4euBdJd-oi8BCKHdsWPI0QIbfan138P5vOHDmVV_iX0y5a0q2olUg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
