Re: [Freesurfer] Correction Needed for the Midline
External Email - Use Caution There surely seems to be a link indeed; I'll look at where to correct the labeling and will give you feedback on the result. In the meantime, should you have any advice on such an optimal way, I'll be glad to hear it. I'll keep you posted soon in all cases. Many thanks for your help, Maxime De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Diamond, Bram Ryder Envoyé : 16 octobre 2018 14:54 À : Freesurfer support list Objet : Re: [Freesurfer] Correction Needed for the Midline 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-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron Sent: Tuesday, October 16, 2018 2:48:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correction Needed for the Midline External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu de la part de Diamond, Bram Ryder 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-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron 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.perro...@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 <brdiam...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Diamond, Bram Ryder <brdiam...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Maxime Perron <maxime.perro...@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, M
Re: [Freesurfer] Correction Needed for the Midline
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-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron Sent: Tuesday, October 16, 2018 2:48:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correction Needed for the Midline External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu de la part de Diamond, Bram Ryder 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-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron 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 mailto:maxime.perro...@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 mailto:brdiam...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Maxime Perron mailto:maxime.perro...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> de la part de Diamond, Bram Ryder mailto:brdiam...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Maxime Perron mailto:maxime.perro...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> de la part de Maxime Perron mailto:maxime.perro...@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 th
Re: [Freesurfer] Correction Needed for the Midline
External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu de la part de Diamond, Bram Ryder 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-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron 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.perro...@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 <brdiam...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Diamond, Bram Ryder <brdiam...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Maxime Perron <maxime.perro...@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 <fis...@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: > >>
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-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron 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 mailto:maxime.perro...@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 mailto:brdiam...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Maxime Perron mailto:maxime.perro...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> de la part de Diamond, Bram Ryder mailto:brdiam...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Maxime Perron mailto:maxime.perro...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> de la part de Maxime Perron mailto:maxime.perro...@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 > mailto:fis...@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 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
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.perro...@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 <brdiam...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Diamond, Bram Ryder <brdiam...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Maxime Perron <maxime.perro...@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 <fis...@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 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 <fis...@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
Re: [Freesurfer] Correction Needed for the Midline
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 <brdiam...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Diamond, Bram Ryder <brdiam...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maxime Perron <maxime.perro...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Maxime Perron <maxime.perro...@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 <fis...@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 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 <fis...@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 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
Re: [Freesurfer] Correction Needed for the Midline
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-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron 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-boun...@nmr.mgh.harvard.edu de la part de Diamond, Bram Ryder 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-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron 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-boun...@nmr.mgh.harvard.edu de la part de Maxime Perron 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 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 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 >>> 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 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 >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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-boun...@nmr.mgh.harvard.edu de la part de Diamond, Bram Ryder 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-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron 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-boun...@nmr.mgh.harvard.edu de la part de Maxime Perron 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 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 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 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 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 >>> ___ >>> 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 s
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-boun...@nmr.mgh.harvard.edu on behalf of Maxime Perron 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-boun...@nmr.mgh.harvard.edu de la part de Maxime Perron 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 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 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 >>> 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 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 >>> ___ >>> 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 >> >> > ___ > Frees
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-boun...@nmr.mgh.harvard.edu de la part de Maxime Perron 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 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 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 >>> 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 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 >>> ___ >>> 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
