HI Maxime
check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled Bruce On Fri, 10 Aug 2018, Maxime Perron wrote:
External Email - Use Caution
Hello FreeSurfer Developers, I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that is the midline does not go through exactly the center of the brain in coronal cut. For example, the midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've searched in the mail list and I don't find the way to fix it. Does anyone have any idea to fix it? Thank you,
Maxime Perron
External Email - Use Caution
Hi Freesurfer Experts,
I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you have an idea?
Best, Maxime
On Aug 10, 2018, at 5:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
HI Maxime
check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled Bruce On Fri, 10 Aug 2018, Maxime Perron wrote:
External Email - Use CautionHello FreeSurfer Developers,
I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that is the midline does not go through exactly the center of the brain in coronal cut. For example, the midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've searched in the mail list and I don't find the way to fix it. Does anyone have any idea to fix it? Thank you, Maxime Perron
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.
Hi Maxime
if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
cheers Bruce On Thu, 13 Sep 2018, Maxime Perron wrote:
External Email - Use CautionHi Freesurfer Experts,
I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you have an idea?
Best, Maxime
On Aug 10, 2018, at 5:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
HI Maxime
check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled Bruce On Fri, 10 Aug 2018, Maxime Perron wrote:
External Email - Use CautionHello FreeSurfer Developers,
I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that is the midline does not go through exactly the center of the brain in coronal cut. For example, the midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've searched in the mail list and I don't find the way to fix it. Does anyone have any idea to fix it? Thank you, Maxime Perron
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
External Email - Use Caution
Hi Bruce,
I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.
The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.
Thank you for all your help, Maxime
On Sep 13, 2018, at 10:08 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Maxime
if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
cheers Bruce On Thu, 13 Sep 2018, Maxime Perron wrote:
External Email - Use CautionHi Freesurfer Experts,
I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you have an idea?
Best, Maxime
On Aug 10, 2018, at 5:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
HI Maxime
check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled Bruce On Fri, 10 Aug 2018, Maxime Perron wrote:
External Email - Use CautionHello FreeSurfer Developers,
I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that is the midline does not go through exactly the center of the brain in coronal cut. For example, the midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've searched in the mail list and I don't find the way to fix it. Does anyone have any idea to fix it? Thank you, Maxime Perron
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
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
Hi Freesurfer Experts,
I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.
Best regards, Maxime ________________________________________ De : Maxime Perron Envoyé : 13 septembre 2018 22:29 À : Freesurfer support list Objet : Re: [Freesurfer] Midline errors
Hi Bruce,
I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.
The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.
Thank you for all your help, Maxime
On Sep 13, 2018, at 10:08 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Maxime
if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
cheers Bruce On Thu, 13 Sep 2018, Maxime Perron wrote:
External Email - Use CautionHi Freesurfer Experts,
I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you have an idea?
Best, Maxime
On Aug 10, 2018, at 5:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
HI Maxime
check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled Bruce On Fri, 10 Aug 2018, Maxime Perron wrote:
External Email - Use CautionHello FreeSurfer Developers,
I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that is the midline does not go through exactly the center of the brain in coronal cut. For example, the midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've searched in the mail list and I don't find the way to fix it. Does anyone have any idea to fix it? Thank you, Maxime Perron
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
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
Hi Freesurfer Experts,
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline.
I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
Since 10 of my subjects show this error, a solution is much needed.
Many thanks for your help!
Best, Maxime ________________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Maxime Perron maxime.perron.6@ulaval.ca Envoyé : 17 septembre 2018 10:00 À : Freesurfer support list Objet : Re: [Freesurfer] Midline errors
External Email - Use Caution
Hi Freesurfer Experts,
I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.
Best regards, Maxime ________________________________________ De : Maxime Perron Envoyé : 13 septembre 2018 22:29 À : Freesurfer support list Objet : Re: [Freesurfer] Midline errors
Hi Bruce,
I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.
The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.
Thank you for all your help, Maxime
On Sep 13, 2018, at 10:08 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Maxime
if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
cheers Bruce On Thu, 13 Sep 2018, Maxime Perron wrote:
External Email - Use CautionHi Freesurfer Experts,
I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you have an idea?
Best, Maxime
On Aug 10, 2018, at 5:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
HI Maxime
check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled Bruce On Fri, 10 Aug 2018, Maxime Perron wrote:
External Email - Use CautionHello FreeSurfer Developers,
I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that is the midline does not go through exactly the center of the brain in coronal cut. For example, the midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've searched in the mail list and I don't find the way to fix it. Does anyone have any idea to fix it? Thank you, Maxime Perron
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
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
Hi Maxime,
I'll take a look at your data and the issue you're having and get back to you after the weekend.
Best,
Bram
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maxime Perron maxime.perron.6@ulaval.ca Sent: Tuesday, September 25, 2018 1:14:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correction Needed for the Midline
External Email - Use Caution
Hi Freesurfer Experts,
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline.
I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
Since 10 of my subjects show this error, a solution is much needed.
Many thanks for your help!
Best, Maxime ________________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Maxime Perron maxime.perron.6@ulaval.ca Envoyé : 17 septembre 2018 10:00 À : Freesurfer support list Objet : Re: [Freesurfer] Midline errors
External Email - Use Caution
Hi Freesurfer Experts,
I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.
Best regards, Maxime ________________________________________ De : Maxime Perron Envoyé : 13 septembre 2018 22:29 À : Freesurfer support list Objet : Re: [Freesurfer] Midline errors
Hi Bruce,
I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.
The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.
Thank you for all your help, Maxime
On Sep 13, 2018, at 10:08 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Maxime
if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
cheers Bruce On Thu, 13 Sep 2018, Maxime Perron wrote:
External Email - Use CautionHi Freesurfer Experts,
I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you have an idea?
Best, Maxime
On Aug 10, 2018, at 5:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
HI Maxime
check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled Bruce On Fri, 10 Aug 2018, Maxime Perron wrote:
External Email - Use CautionHello FreeSurfer Developers,
I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that is the midline does not go through exactly the center of the brain in coronal cut. For example, the midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've searched in the mail list and I don't find the way to fix it. Does anyone have any idea to fix it? Thank you, Maxime Perron
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
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Maxime,
I'm having trouble finding your data - can you please use the filedrop instead?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks, Bram
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maxime Perron maxime.perron.6@ulaval.ca Sent: Friday, October 12, 2018 11:17:07 AM To: Freesurfer support list Subject: Re: [Freesurfer] Correction Needed for the Midline
External Email - Use Caution
Hi Bram,
Thank you very much for the reply, I'm glad you'll have some time to look at the issue. Please don't hesitate to contact me should anything specific be needed. I'll be happy to contribute!
Many thanks, Maxime ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu Envoyé : 11 octobre 2018 13:18 À : Freesurfer support list Objet : Re: [Freesurfer] Correction Needed for the Midline
Hi Maxime,
I'll take a look at your data and the issue you're having and get back to you after the weekend.
Best,
Bram
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maxime Perron maxime.perron.6@ulaval.ca Sent: Tuesday, September 25, 2018 1:14:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correction Needed for the Midline
External Email - Use Caution
Hi Freesurfer Experts,
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline.
I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
Since 10 of my subjects show this error, a solution is much needed.
Many thanks for your help!
Best, Maxime ________________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Maxime Perron maxime.perron.6@ulaval.ca Envoyé : 17 septembre 2018 10:00 À : Freesurfer support list Objet : Re: [Freesurfer] Midline errors
External Email - Use Caution
Hi Freesurfer Experts,
I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.
Best regards, Maxime ________________________________________ De : Maxime Perron Envoyé : 13 septembre 2018 22:29 À : Freesurfer support list Objet : Re: [Freesurfer] Midline errors
Hi Bruce,
I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.
The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.
Thank you for all your help, Maxime
On Sep 13, 2018, at 10:08 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Maxime
if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
cheers Bruce On Thu, 13 Sep 2018, Maxime Perron wrote:
External Email - Use CautionHi Freesurfer Experts,
I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you have an idea?
Best, Maxime
On Aug 10, 2018, at 5:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
HI Maxime
check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled Bruce On Fri, 10 Aug 2018, Maxime Perron wrote:
External Email - Use CautionHello FreeSurfer Developers,
I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that is the midline does not go through exactly the center of the brain in coronal cut. For example, the midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've searched in the mail list and I don't find the way to fix it. Does anyone have any idea to fix it? Thank you, Maxime Perron
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
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Maxime,
What did you edit in the aseg? It looks like the CC_* have been mislabeled.
Bram
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maxime Perron maxime.perron.6@ulaval.ca Sent: Tuesday, October 16, 2018 2:23:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correction Needed for the Midline
External Email - Use Caution
Sorry. Here are the good links :
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t
Maxime
On Oct 16, 2018, at 2:22 PM, Maxime Perron <maxime.perron.6@ulaval.camailto:maxime.perron.6@ulaval.ca> wrote:
External Email - Use Caution
Hi Bram,
No worries.
Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h
Thanks, Maxime
On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edumailto:BRDIAMOND@mgh.harvard.edu> wrote:
Hi Maxime,
I'm having trouble finding your data - can you please use the filedrop instead?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks, 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 Maxime Perron <maxime.perron.6@ulaval.camailto:maxime.perron.6@ulaval.ca> Sent: Friday, October 12, 2018 11:17:07 AM To: Freesurfer support list Subject: Re: [Freesurfer] Correction Needed for the Midline
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Hi Bram,
Thank you very much for the reply, I'm glad you'll have some time to look at the issue. Please don't hesitate to contact me should anything specific be needed. I'll be happy to contribute!
Many thanks, Maxime ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edumailto:BRDIAMOND@mgh.harvard.edu> Envoyé : 11 octobre 2018 13:18 À : Freesurfer support list Objet : Re: [Freesurfer] Correction Needed for the Midline
Hi Maxime,
I'll take a look at your data and the issue you're having and get back to you after the weekend.
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 Maxime Perron <maxime.perron.6@ulaval.camailto:maxime.perron.6@ulaval.ca> Sent: Tuesday, September 25, 2018 1:14:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correction Needed for the Midline
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Hi Freesurfer Experts,
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline.
I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
Since 10 of my subjects show this error, a solution is much needed.
Many thanks for your help!
Best, Maxime ________________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Maxime Perron <maxime.perron.6@ulaval.camailto:maxime.perron.6@ulaval.ca> Envoyé : 17 septembre 2018 10:00 À : Freesurfer support list Objet : Re: [Freesurfer] Midline errors
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Hi Freesurfer Experts,
I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.
Best regards, Maxime ________________________________________ De : Maxime Perron Envoyé : 13 septembre 2018 22:29 À : Freesurfer support list Objet : Re: [Freesurfer] Midline errors
Hi Bruce,
I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.
The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.
Thank you for all your help, Maxime
On Sep 13, 2018, at 10:08 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Maxime
if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
cheers Bruce On Thu, 13 Sep 2018, Maxime Perron wrote:
External Email - Use CautionHi Freesurfer Experts,
I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you have an idea?
Best, Maxime
On Aug 10, 2018, at 5:09 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
HI Maxime
check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled Bruce On Fri, 10 Aug 2018, Maxime Perron wrote:
External Email - Use CautionHello FreeSurfer Developers,
I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that is the midline does not go through exactly the center of the brain in coronal cut. For example, the midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've searched in the mail list and I don't find the way to fix it. Does anyone have any idea to fix it? Thank you, Maxime Perron
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
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Possibly - I would definitely start there. The surfaces are following the corpus callosum into the right hemisphere because the aseg labeling is off.
Best,
Bram
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maxime Perron maxime.perron.6@ulaval.ca Sent: Tuesday, October 16, 2018 2:48:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correction Needed for the Midline
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Hi Bram,
I modified the label of the lateral ventricules because they were mislabeled too (Freesurfer_S043_test). I didn't change the label of the CC_*. Do you think that can fix the middle line?
Thanks, Maxime
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Diamond, Bram Ryder BRDIAMOND@mgh.harvard.edu Envoyé : 16 octobre 2018 14:36 À : Freesurfer support list Objet : Re: [Freesurfer] Correction Needed for the Midline
Hi Maxime,
What did you edit in the aseg? It looks like the CC_* have been mislabeled.
Bram
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Maxime Perron maxime.perron.6@ulaval.ca Sent: Tuesday, October 16, 2018 2:23:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correction Needed for the Midline
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Sorry. Here are the good links :
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0 http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t
Maxime
On Oct 16, 2018, at 2:22 PM, Maxime Perron <maxime.perron.6@ulaval.camailto:maxime.perron.6@ulaval.ca> wrote:
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Hi Bram,
No worries.
Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h
Thanks, Maxime
On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edumailto:BRDIAMOND@mgh.harvard.edu> wrote:
Hi Maxime,
I'm having trouble finding your data - can you please use the filedrop instead?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks, 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 Maxime Perron <maxime.perron.6@ulaval.camailto:maxime.perron.6@ulaval.ca> Sent: Friday, October 12, 2018 11:17:07 AM To: Freesurfer support list Subject: Re: [Freesurfer] Correction Needed for the Midline
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Hi Bram,
Thank you very much for the reply, I'm glad you'll have some time to look at the issue. Please don't hesitate to contact me should anything specific be needed. I'll be happy to contribute!
Many thanks, Maxime ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edumailto:BRDIAMOND@mgh.harvard.edu> Envoyé : 11 octobre 2018 13:18 À : Freesurfer support list Objet : Re: [Freesurfer] Correction Needed for the Midline
Hi Maxime,
I'll take a look at your data and the issue you're having and get back to you after the weekend.
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 Maxime Perron <maxime.perron.6@ulaval.camailto:maxime.perron.6@ulaval.ca> Sent: Tuesday, September 25, 2018 1:14:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correction Needed for the Midline
External Email - Use Caution
Hi Freesurfer Experts,
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline.
I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
Since 10 of my subjects show this error, a solution is much needed.
Many thanks for your help!
Best, Maxime ________________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Maxime Perron <maxime.perron.6@ulaval.camailto:maxime.perron.6@ulaval.ca> Envoyé : 17 septembre 2018 10:00 À : Freesurfer support list Objet : Re: [Freesurfer] Midline errors
External Email - Use Caution
Hi Freesurfer Experts,
I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.
Best regards, Maxime ________________________________________ De : Maxime Perron Envoyé : 13 septembre 2018 22:29 À : Freesurfer support list Objet : Re: [Freesurfer] Midline errors
Hi Bruce,
I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.
The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.
Thank you for all your help, Maxime
On Sep 13, 2018, at 10:08 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Maxime
if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
cheers Bruce On Thu, 13 Sep 2018, Maxime Perron wrote:
External Email - Use CautionHi Freesurfer Experts,
I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you have an idea?
Best, Maxime
On Aug 10, 2018, at 5:09 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
HI Maxime
check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled Bruce On Fri, 10 Aug 2018, Maxime Perron wrote:
External Email - Use CautionHello FreeSurfer Developers,
I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that is the midline does not go through exactly the center of the brain in coronal cut. For example, the midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've searched in the mail list and I don't find the way to fix it. Does anyone have any idea to fix it? Thank you, Maxime Perron
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
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Maxime Perron