Hi Matthieu,
I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did.
As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorialhttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id):
recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>
The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes.
All the best,
Bram
Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598
If you haven't already, you may want to run the subject through recon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following the directions in this tutorialhttps://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations. Then run the following command (again, substituting <subj_id> for your subject's id):
recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>
I would try this before doing the wm.mgz edits I suggested in my previous email.
Best, Bram ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu Sent: Friday, September 14, 2018 11:07:42 AM To: matthieuvanhoutte@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubles to determine the type of recon editing needed
Hi Matthieu,
I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did.
As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorialhttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id):
recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>
The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes.
All the best,
Bram
Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598
External Email - Use Caution
Dear Bram,
Thank you for your answer. As soon as possible I will run recon-all with the -bigventricles flag.
Concerning the manual editing I don't understand well the aim of editing aseg.mgz since it seems to most concern subcortical structures and statistics and not have an impact on surfaces computed ?
Best, Matthieu
Le ven. 14 sept. 2018 à 17:35, Diamond, Bram Ryder < BRDIAMOND@mgh.harvard.edu> a écrit :
If you haven't already, you may want to run the subject through recon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following the directions in this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations. Then run the following command (again, substituting <subj_id> for your subject's id):
recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>
I would try this before doing the wm.mgz edits I suggested in my previous email.
Best, Bram
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Diamond, Bram Ryder < BRDIAMOND@mgh.harvard.edu> *Sent:* Friday, September 14, 2018 11:07:42 AM *To:* matthieuvanhoutte@gmail.com *Cc:* freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Troubles to determine the type of recon editing needed
Hi Matthieu,
I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did.
As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id):
recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>
The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes.
All the best,
Bram
*Bram R. Diamond, BSc* Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598
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 Partners Compliance HelpLine at http://www.partners.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.
Hi Matthieu,
The initial estimate for surfaces is based off the wm.mgz. Since you're wm.mgz is incorrect (due to the large ventricles and wm abnormalities) the first pass at a surface reconstruction is way off. The wm.mgz is created in-part from the aseg.mgz, so it is important that you ensure your aseg.mgz is accurate. Additionally, it will be useful to have an accurate aseg.mgz for subcortical analyses.
I hope that answers your question.
Bram
________________________________ From: Matthieu Vanhoutte matthieuvanhoutte@gmail.com Sent: Friday, September 14, 2018 4:48:36 PM To: Diamond, Bram Ryder Cc: Freesurfer support list Subject: Re: Troubles to determine the type of recon editing needed
External Email - Use Caution
Dear Bram,
Thank you for your answer. As soon as possible I will run recon-all with the -bigventricles flag.
Concerning the manual editing I don't understand well the aim of editing aseg.mgz since it seems to most concern subcortical structures and statistics and not have an impact on surfaces computed ?
Best, Matthieu
Le ven. 14 sept. 2018 à 17:35, Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edumailto:BRDIAMOND@mgh.harvard.edu> a écrit : If you haven't already, you may want to run the subject through recon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following the directions in this tutorialhttps://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations. Then run the following command (again, substituting <subj_id> for your subject's id):
recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>
I would try this before doing the wm.mgz edits I suggested in my previous email.
Best, Bram ________________________________ 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 Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edumailto:BRDIAMOND@mgh.harvard.edu> Sent: Friday, September 14, 2018 11:07:42 AM To: matthieuvanhoutte@gmail.commailto:matthieuvanhoutte@gmail.com Cc: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edumailto:astevens@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubles to determine the type of recon editing needed
Hi Matthieu,
I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did.
As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorialhttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id):
recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>
The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes.
All the best,
Bram
Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598
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 Partners Compliance HelpLine at http://www.partners.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.
Hi Matthieu
the aseg is used to automatically edit the wm.mgz, which helps the creation of cortical surfaces. For example, the ventricles are filled using the aseg. I think in your case with greatly expanded ventricles, some of the ventricular voxels were incorrectly labeled in the aseg and hence resulted in incorrect surfaces.
cheers Bruce
On Fri, 14 Sep 2018, Matthieu Vanhoutte wrote:
External Email - Use Caution
Dear Bram, Thank you for your answer. As soon as possible I will run recon-all with the -bigventricles flag.
Concerning the manual editing I don't understand well the aim of editing aseg.mgz since it seems to most concern subcortical structures and statistics and not have an impact on surfaces computed ?
Best, Matthieu
Le ven. 14 sept. 2018 à 17:35, Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu a écrit : If you haven't already, you may want to run the subject through recon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following the directions in this tutorial. Then run the following command (again, substituting <subj_id> for your subject's id): recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>
I would try this before doing the wm.mgz edits I suggested in my previous email.
Best, Bram
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu Sent: Friday, September 14, 2018 11:07:42 AM To: matthieuvanhoutte@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubles to determine the type of recon editing needed
Hi Matthieu,
I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did.
As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorial for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id):
recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>
The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes.
All the best,
Bram
Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598
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 Partners Compliance HelpLine at http://www.partners.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.
External Email - Use Caution
Dear Bram,
It looks like the -bigventricles flag fixed my problem with my specific subject. Not only, this took into account large ventricles but also corrected grey matter segmentation from extra Dura tissue that was erroneously segmented in GM.
I understand the first point of amelioration allowed by the flag but don't understand where the second point come from ?
If I used the -bigventricles flag for all my atrophied and large ventricles patients and not for my healthy patients, wouldn't it introduce a bias when further statistically comparing groups between them ?
Best, Matthieu
2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu:
If you haven't already, you may want to run the subject through recon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following the directions in this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations. Then run the following command (again, substituting <subj_id> for your subject's id):
recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>
I would try this before doing the wm.mgz edits I suggested in my previous email.
Best, Bram
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Diamond, Bram Ryder < BRDIAMOND@mgh.harvard.edu> *Sent:* Friday, September 14, 2018 11:07:42 AM *To:* matthieuvanhoutte@gmail.com *Cc:* freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Troubles to determine the type of recon editing needed
Hi Matthieu,
I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did.
As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id):
recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>
The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes.
All the best,
Bram
*Bram R. Diamond, BSc* Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street https://maps.google.com/?q=149+13th+Street+%0D%0A+Charlestown,+MA+02129&entry=gmail&source=g
Charlestown, MA 02129 https://maps.google.com/?q=149+13th+Street+%0D%0A+Charlestown,+MA+02129&entry=gmail&source=g (p): 617-726-6598
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 Partners Compliance HelpLine at http://www.partners.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.
Hi Matthieu
yes, you will want to run all of your subjects with it
cheers Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
External Email - Use Caution
Dear Bram,
It looks like the -bigventricles flag fixed my problem with my specific subject. Not only, this took into account large ventricles but also corrected grey matter segmentation from extra Dura tissue that was erroneously segmented in GM.
I understand the first point of amelioration allowed by the flag but don't understand where the second point come from ?
If I used the -bigventricles flag for all my atrophied and large ventricles patients and not for my healthy patients, wouldn't it introduce a bias when further statistically comparing groups between them ?
Best, Matthieu
2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu: If you haven't already, you may want to run the subject through recon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following the directions in this tutorial. Then run the following command (again, substituting <subj_id> for your subject's id): recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>
I would try this before doing the wm.mgz edits I suggested in my previous email.
Best, Bram
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu Sent: Friday, September 14, 2018 11:07:42 AM To: matthieuvanhoutte@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubles to determine the type of recon editing needed
Hi Matthieu,
I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did.
As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorial for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id):
recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>
The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes.
All the best,
Bram
Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598
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 Partners Compliance HelpLine at http://www.partners.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.
External Email - Use Caution
Hi Bruce,
Thanks, but in this case will recon-all with -bigventricles flag work well on normal patients without big ventricles ?
Best, Matthieu
2018-09-18 15:56 GMT+00:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Matthieu
yes, you will want to run all of your subjects with it
cheers Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
External Email - Use CautionDear Bram,
It looks like the -bigventricles flag fixed my problem with my specific subject. Not only, this took into account large ventricles but also corrected grey matter segmentation from extra Dura tissue that was erroneously segmented in GM.
I understand the first point of amelioration allowed by the flag but don't understand where the second point come from ?
If I used the -bigventricles flag for all my atrophied and large ventricles patients and not for my healthy patients, wouldn't it introduce a bias when further statistically comparing groups between them ?
Best, Matthieu
2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu
:
If you haven't already, you may want to run the subject throughrecon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following the directions in this tutorial. Then run the following command (again, substituting <subj_id> for your subject's id): recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>
I would try this before doing the wm.mgz edits I suggested in my previous email.
Best, Bram
From: freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu Sent: Friday, September 14, 2018 11:07:42 AM To: matthieuvanhoutte@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubles to determine the type of recon editing needed
Hi Matthieu,
I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did.
As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorial for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id):
recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>
The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes.
All the best,
Bram
Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598
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 Partners Compliance HelpLine at http://www.partners.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.
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 Partners Compliance HelpLine at http://www.partners.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.
I think it should be ok. It will be a bit slower, but shouldn't reduce accuracy I don't think. Try it and see Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hi Bruce,
Thanks, but in this case will recon-all with -bigventricles flag work well on normal patients without big ventricles ?
Best, Matthieu
2018-09-18 15:56 GMT+00:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Matthieu
yes, you will want to run all of your subjects with it cheers Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote: External Email - Use Caution Dear Bram, It looks like the -bigventricles flag fixed my problem with my specific subject. Not only, this took into account large ventricles but also corrected grey matter segmentation from extra Dura tissue that was erroneously segmented in GM. I understand the first point of amelioration allowed by the flag but don't understand where the second point come from ? If I used the -bigventricles flag for all my atrophied and large ventricles patients and not for my healthy patients, wouldn't it introduce a bias when further statistically comparing groups between them ? Best, Matthieu 2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu>: If you haven't already, you may want to run the subject through recon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following the directions in this tutorial. Then run the following command (again, substituting <subj_id> for your subject's id): recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id> I would try this before doing the wm.mgz edits I suggested in my previous email. Best, Bram
_ From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu> Sent: Friday, September 14, 2018 11:07:42 AM To: matthieuvanhoutte@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubles to determine the type of recon editing needed Hi Matthieu, I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did. As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorial for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id): recon-all -autorecon2-wm -autorecon3 -subjid <subj_id> The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes. All the best, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598 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 Partners Compliance HelpLine at http://www.partners.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.
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 Partners Compliance HelpLine at http://www.partners.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.
External Email - Use Caution
Ok I will test it on normal subjects.
Do I have to put this -bigventricles flag on all recon-all commands following manual editing of brainmask, white matter,...etc or just once at the first recon-all -all command ?
Best, Matthieu
Le mar. 18 sept. 2018 à 18:03, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit :
I think it should be ok. It will be a bit slower, but shouldn't reduce accuracy I don't think. Try it and see Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Bruce,
Thanks, but in this case will recon-all with -bigventricles flag work
well on normal patients
without big ventricles ?
Best, Matthieu
2018-09-18 15:56 GMT+00:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Matthieu
yes, you will want to run all of your subjects with it cheers Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote: External Email - Use Caution Dear Bram, It looks like the -bigventricles flag fixed my problem withmy specific
subject. Not only, this took into account large ventricles but also corrected grey mattersegmentation
from extra Dura tissue that was erroneously segmented in GM. I understand the first point of amelioration allowed by theflag but don't
understand where the second point come from ? If I used the -bigventricles flag for all my atrophied andlarge ventricles
patients and not for my healthy patients, wouldn't it introduce a bias when furtherstatistically
comparing groups between them ? Best, Matthieu 2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu>:
If you haven't already, you may want to run thesubject through
recon-all with the -bigventricles flag since it looks like thelateral ventricle was
significantly mislabeled in the aseg. If using the -bigventriclesflag doesn't fix
your problem, you can edit the aseg.mgz manually by following thedirections in this
tutorial. Then run the following command (again, substituting <subj_id>for your
subject's id): recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id> I would try this before doing the wm.mgz edits I suggestedin my previous
email. Best, Bram
_ From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu> Sent: Friday, September 14, 2018 11:07:42 AM To: matthieuvanhoutte@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu;astevens@nmr.mgh.harvard.edu
Subject: [Freesurfer] Troubles to determine the type ofrecon editing needed
Hi Matthieu, I've taken a look through the files you shared with us and Isee the poor
surfaces in the posterior right hemisphere you were referring to in yourmessage. It looks
like your subject has a combination of abnormally large ventricles andsignificant wm
abnormalities, so I'm surprised FreeSurfer did as well as it did. As for the recon editing - I would recommend editing thewm.mgz to more
accurately represent the wm from slice 84 to 39. You can take a look at the whitematter edits
tutorial for details on how to do that. Then run the following command(substituting <subj_id>
for your subject's id): recon-all -autorecon2-wm -autorecon3 -subjid <subj_id> The surface reconstruction may also benefit from labelingthe right lateral
ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain sinceyou didn't send
us the surfaces for the left hemisphere. Before you do that, edit the wm.mgzas explained in
the tutorial and tell us how that goes. All the best, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598 The information in this e-mail is intended only for theperson to whom it is
addressed. If you believe this e-mail was sent to you inerror and the
e-mail contains patient information, please contact the PartnersCompliance
HelpLine at http://www.partners.org/complianceline . If the e-mail wassent to you in
error but does not contain patient information, please contact thesender and
properly dispose of the e-mail.
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.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.
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 Partners Compliance HelpLine at http://www.partners.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.
Yes - if you've used the -bigventricles flag, you should always include it with the recon-all command.
Bram
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Matthieu Vanhoutte matthieuvanhoutte@gmail.com Sent: Tuesday, September 18, 2018 12:45:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Troubles to determine the type of recon editing needed
External Email - Use Caution
Ok I will test it on normal subjects.
Do I have to put this -bigventricles flag on all recon-all commands following manual editing of brainmask, white matter,...etc or just once at the first recon-all -all command ?
Best, Matthieu
Le mar. 18 sept. 2018 à 18:03, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> a écrit : I think it should be ok. It will be a bit slower, but shouldn't reduce accuracy I don't think. Try it and see Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Bruce,
Thanks, but in this case will recon-all with -bigventricles flag work well on normal patients without big ventricles ?
Best, Matthieu
2018-09-18 15:56 GMT+00:00 Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu>: Hi Matthieu
yes, you will want to run all of your subjects with it cheers Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote: External Email - Use Caution Dear Bram, It looks like the -bigventricles flag fixed my problem with my specific subject. Not only, this took into account large ventricles but also corrected grey matter segmentation from extra Dura tissue that was erroneously segmented in GM. I understand the first point of amelioration allowed by the flag but don't understand where the second point come from ? If I used the -bigventricles flag for all my atrophied and large ventricles patients and not for my healthy patients, wouldn't it introduce a bias when further statistically comparing groups between them ? Best, Matthieu 2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu<mailto:BRDIAMOND@mgh.harvard.edu>>: If you haven't already, you may want to run the subject through recon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following the directions in this tutorial. Then run the following command (again, substituting <subj_id> for your subject's id): recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id> I would try this before doing the wm.mgz edits I suggested in my previous email. Best, Bram
_ 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 Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu<mailto:BRDIAMOND@mgh.harvard.edu>> Sent: Friday, September 14, 2018 11:07:42 AM To: matthieuvanhoutte@gmail.com<mailto:matthieuvanhoutte@gmail.com> Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>; astevens@nmr.mgh.harvard.edu<mailto:astevens@nmr.mgh.harvard.edu> Subject: [Freesurfer] Troubles to determine the type of recon editing needed Hi Matthieu, I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did. As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorial for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id): recon-all -autorecon2-wm -autorecon3 -subjid <subj_id> The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes. All the best, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598 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 Partners Compliance HelpLine at http://www.partners.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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 Partners Compliance HelpLine at http://www.partners.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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 Partners Compliance HelpLine at http://www.partners.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.
External Email - Use Caution
Dear Bram,
According recon-all help "If a subject has enlarged ventricles due to atrophy, include the -bigventricles flag with the -autorecon2 stage in order to prevent surfaces extending into the ventricle regions. The flag directly affects the binary mri_ca_register, and mris_make_surfaces indirectly via aseg.presurf.mgz.
So doesn't this mean that we should only out the -bigventricles flag for the -autorecon2 stage of recon-all ?
Best, Matthieu
Le mer. 19 sept. 2018 à 15:17, Diamond, Bram Ryder < BRDIAMOND@mgh.harvard.edu> a écrit :
Yes - if you've used the -bigventricles flag, you should always include it with the recon-all command.
Bram
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthieu Vanhoutte < matthieuvanhoutte@gmail.com> *Sent:* Tuesday, September 18, 2018 12:45:23 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Troubles to determine the type of recon editing needed
External Email - Use CautionOk I will test it on normal subjects.
Do I have to put this -bigventricles flag on all recon-all commands following manual editing of brainmask, white matter,...etc or just once at the first recon-all -all command ?
Best, Matthieu
Le mar. 18 sept. 2018 à 18:03, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit :
I think it should be ok. It will be a bit slower, but shouldn't reduce accuracy I don't think. Try it and see Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Bruce,
Thanks, but in this case will recon-all with -bigventricles flag work
well on normal patients
without big ventricles ?
Best, Matthieu
2018-09-18 15:56 GMT+00:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Matthieu
yes, you will want to run all of your subjects with it cheers Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote: External Email - Use Caution Dear Bram, It looks like the -bigventricles flag fixed my problem withmy specific
subject. Not only, this took into account large ventricles but also corrected grey mattersegmentation
from extra Dura tissue that was erroneously segmented in GM. I understand the first point of amelioration allowed by theflag but don't
understand where the second point come from ? If I used the -bigventricles flag for all my atrophied andlarge ventricles
patients and not for my healthy patients, wouldn't it introduce a bias when furtherstatistically
comparing groups between them ? Best, Matthieu 2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu>:
If you haven't already, you may want to run thesubject through
recon-all with the -bigventricles flag since it looks like thelateral ventricle was
significantly mislabeled in the aseg. If using the -bigventriclesflag doesn't fix
your problem, you can edit the aseg.mgz manually by following thedirections in this
tutorial. Then run the following command (again, substituting <subj_id>for your
subject's id): recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id> I would try this before doing the wm.mgz edits I suggestedin my previous
email. Best, Bram
_ From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu> Sent: Friday, September 14, 2018 11:07:42 AM To: matthieuvanhoutte@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu;astevens@nmr.mgh.harvard.edu
Subject: [Freesurfer] Troubles to determine the type ofrecon editing needed
Hi Matthieu, I've taken a look through the files you shared with us and Isee the poor
surfaces in the posterior right hemisphere you were referring to in yourmessage. It looks
like your subject has a combination of abnormally large ventricles andsignificant wm
abnormalities, so I'm surprised FreeSurfer did as well as it did. As for the recon editing - I would recommend editing thewm.mgz to more
accurately represent the wm from slice 84 to 39. You can take a look at the whitematter edits
tutorial for details on how to do that. Then run the following command(substituting <subj_id>
for your subject's id): recon-all -autorecon2-wm -autorecon3 -subjid <subj_id> The surface reconstruction may also benefit from labelingthe right lateral
ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain sinceyou didn't send
us the surfaces for the left hemisphere. Before you do that, edit the wm.mgzas explained in
the tutorial and tell us how that goes. All the best, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598 The information in this e-mail is intended only for theperson to whom it is
addressed. If you believe this e-mail was sent to you inerror and the
e-mail contains patient information, please contact the PartnersCompliance
HelpLine at http://www.partners.org/complianceline . If the e-mail wassent to you in
error but does not contain patient information, please contact thesender and
properly dispose of the e-mail.
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.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.
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 Partners Compliance HelpLine at http://www.partners.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.
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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 Partners Compliance HelpLine at http://www.partners.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.
Hi Matthieu
only recon2 will use it, but you can specify it for all of them cheers Bruce
On Wed, 19 Sep 2018, Matthieu Vanhoutte wrote:
External Email - Use Caution
Dear Bram, According recon-all help "If a subject has enlarged ventricles due to atrophy, include the -bigventricles flag with the -autorecon2 stage in order to prevent surfaces extending into the ventricle regions. The flag directly affects the binary mri_ca_register, and mris_make_surfaces indirectly via aseg.presurf.mgz.
So doesn't this mean that we should only out the -bigventricles flag for the -autorecon2 stage of recon-all ?
Best, Matthieu
Le mer. 19 sept. 2018 à 15:17, Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu a écrit :
Yes - if you've used the -bigventricles flag, you should always include it with the recon-all command. Bram
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Matthieu Vanhoutte matthieuvanhoutte@gmail.com Sent: Tuesday, September 18, 2018 12:45:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Troubles to determine the type of recon editing needed
External Email - Use Caution
Ok I will test it on normal subjects. Do I have to put this -bigventricles flag on all recon-all commands following manual editing of brainmask, white matter,...etc or just once at the first recon-all -all command ?
Best, Matthieu
Le mar. 18 sept. 2018 à 18:03, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit : I think it should be ok. It will be a bit slower, but shouldn't reduce accuracy I don't think. Try it and see Bruce On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:
> > External Email - Use Caution > > Hi Bruce, > > Thanks, but in this case will recon-all with -bigventricles flag work well on normal patients > without big ventricles ? > > Best, > Matthieu > > 2018-09-18 15:56 GMT+00:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: > Hi Matthieu > > yes, you will want to run all of your subjects with it > > cheers > Bruce > On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote: > > > External Email - Use Caution > > Dear Bram, > > It looks like the -bigventricles flag fixed my problem with my specific > subject. Not only, this took > into account large ventricles but also corrected grey matter segmentation > from extra Dura tissue > that was erroneously segmented in GM. > > I understand the first point of amelioration allowed by the flag but don't > understand where the > second point come from ? > > If I used the -bigventricles flag for all my atrophied and large ventricles > patients and not for my > healthy patients, wouldn't it introduce a bias when further statistically > comparing groups between > them ? > > Best, > Matthieu > > 2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu>: > If you haven't already, you may want to run the subject through > recon-all with the > -bigventricles flag since it looks like the lateral ventricle was > significantly > mislabeled in the aseg. If using the -bigventricles flag doesn't fix > your problem, you > can edit the aseg.mgz manually by following the directions in this > tutorial. Then run > the following command (again, substituting <subj_id> for your > subject's id): > recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id> > > I would try this before doing the wm.mgz edits I suggested in my previous > email. > > Best, > Bram > >___________________________________________________________________________________________________ > _ > From: freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces@nmr.mgh.harvard.edu> on > behalf of Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu> > Sent: Friday, September 14, 2018 11:07:42 AM > To: matthieuvanhoutte@gmail.com > Cc: freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu > Subject: [Freesurfer] Troubles to determine the type of recon editing needed > > > Hi Matthieu, > > > I've taken a look through the files you shared with us and I see the poor > surfaces in the > posterior right hemisphere you were referring to in your message. It looks > like your subject > has a combination of abnormally large ventricles and significant wm > abnormalities, so I'm > surprised FreeSurfer did as well as it did. > > > As for the recon editing - I would recommend editing the wm.mgz to more > accurately represent > the wm from slice 84 to 39. You can take a look at the white matter edits > tutorial for details > on how to do that. Then run the following command (substituting <subj_id> > for your > subject's id): > > > recon-all -autorecon2-wm -autorecon3 -subjid <subj_id> > > > The surface reconstruction may also benefit from labeling the right lateral > ventricle in the > wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send > us the surfaces > for the left hemisphere. Before you do that, edit the wm.mgz as explained in > the tutorial and > tell us how that goes. > > > All the best, > > Bram > > > Bram R. Diamond, BSc > Research Technician II > Laboratory for Computational Neuroimaging > Martinos Center for Biomedical Imaging > Massachusetts General Hospital > 149 13th Street > Charlestown, MA 02129 > (p): 617-726-6598 > > 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 Partners Compliance > HelpLine at > http://www.partners.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. > > > > > _______________________________________________ > 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 Partners Compliance HelpLine at > http://www.partners.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. > > > >_______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.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.
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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 Partners Compliance HelpLine at http://www.partners.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.
freesurfer@nmr.mgh.harvard.edu