Re: [Freesurfer] how to generate aparc.annotion files?
Hi Shahin you'll need a monkey atlas based on manually labeled monkey folding patterns. we don't have one, but it's possible that someone else on the list does (it would be a lot easier to do for monkey than it was for human as the folds are so much simpler) cheers Bruce On Mon, 8 Nov 2010, Shahin wrote: Hi Freesurfers, Anybody knows how can I make lh and rh.annotation.aparc files for a monkey? I need them initiate an brain averaging process. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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.
Re: [Freesurfer] how to generate aparc.annotion files?
Hi Shahin have you run spherical registration? If so, to what target? I don't think the monkey-to-human atlas aligment is that robust, so you would need a monkey geometry atlas (which is a lot easier to build as you don't need to do manual labeling for it). Probably someone on list has one? Bruce On Mon, 8 Nov 2010, Shahin wrote: Thanks Bruce, To avoid this problem, is there anyway to run make_average_subject without having lh and rh.aparc.annot files? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Shahin sha...@nmr.mgh.harvard.edu Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Mon, November 8, 2010 12:10:38 PM Subject: Re: [Freesurfer] how to generate aparc.annotion files? Hi Shahin you'll need a monkey atlas based on manually labeled monkey folding patterns. we don't have one, but it's possible that someone else on the list does (it would be a lot easier to do for monkey than it was for human as the folds are so much simpler) cheers Bruce On Mon, 8 Nov 2010, Shahin wrote: Hi Freesurfers, Anybody knows how can I make lh and rh.annotation.aparc files for a monkey? I need them initiate an brain averaging process. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School 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.
Re: [Freesurfer] how to generate aparc.annotion files?
Thanks Bruce, To avoid this problem, is there anyway to run make_average_subject without having lh and rh.aparc.annot files? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Shahin sha...@nmr.mgh.harvard.edu Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Mon, November 8, 2010 12:10:38 PM Subject: Re: [Freesurfer] how to generate aparc.annotion files? Hi Shahin you'll need a monkey atlas based on manually labeled monkey folding patterns. we don't have one, but it's possible that someone else on the list does (it would be a lot easier to do for monkey than it was for human as the folds are so much simpler) cheers Bruce On Mon, 8 Nov 2010, Shahin wrote: Hi Freesurfers, Anybody knows how can I make lh and rh.annotation.aparc files for a monkey? I need them initiate an brain averaging process. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School 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.
Re: [Freesurfer] how to generate aparc.annotion files?
Yes, I have made a template on the basis of many monkeys (mris_make_template) and then I have done spherical registeration for each individual monkey (to this template) by using mris_register. Now it is the final step and I have to run the make_average_subject but it generates an error saying that I don't have a lh and rh.aparc.annot files. Apparently very old versions of freesurfer (version 3) didnt need these files. Am I right? Do you suggest to use old versions? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Shahin sha...@nmr.mgh.harvard.edu Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Mon, November 8, 2010 12:33:03 PM Subject: Re: [Freesurfer] how to generate aparc.annotion files? Hi Shahin have you run spherical registration? If so, to what target? I don't think the monkey-to-human atlas aligment is that robust, so you would need a monkey geometry atlas (which is a lot easier to build as you don't need to do manual labeling for it). Probably someone on list has one? Bruce On Mon, 8 Nov 2010, Shahin wrote: Thanks Bruce, To avoid this problem, is there anyway to run make_average_subject without having lh and rh.aparc.annot files? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Shahin sha...@nmr.mgh.harvard.edu Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Mon, November 8, 2010 12:10:38 PM Subject: Re: [Freesurfer] how to generate aparc.annotion files? Hi Shahin you'll need a monkey atlas based on manually labeled monkey folding patterns. we don't have one, but it's possible that someone else on the list does (it would be a lot easier to do for monkey than it was for human as the folds are so much simpler) cheers Bruce On Mon, 8 Nov 2010, Shahin wrote: Hi Freesurfers, Anybody knows how can I make lh and rh.annotation.aparc files for a monkey? I need them initiate an brain averaging process. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School 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.
Re: [Freesurfer] how to generate aparc.annotion files?
It is needed in make_average_surface. I've created a new version that does not use the aparc (thought I have not tested it). You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc Make a backup of your current version of make_average_surface and then copy this one over it douig Shahin wrote: Yes, I have made a template on the basis of many monkeys (mris_make_template) and then I have done spherical registeration for each individual monkey (to this template) by using mris_register. Now it is the final step and I have to run the make_average_subject but it generates an error saying that I don't have a lh and rh.aparc.annot files. Apparently very old versions of freesurfer (version 3) didnt need these files. Am I right? Do you suggest to use old versions? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School *From:* Bruce Fischl fis...@nmr.mgh.harvard.edu *To:* Shahin sha...@nmr.mgh.harvard.edu *Cc:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Mon, November 8, 2010 12:33:03 PM *Subject:* Re: [Freesurfer] how to generate aparc.annotion files? Hi Shahin have you run spherical registration? If so, to what target? I don't think the monkey-to-human atlas aligment is that robust, so you would need a monkey geometry atlas (which is a lot easier to build as you don't need to do manual labeling for it). Probably someone on list has one? Bruce On Mon, 8 Nov 2010, Shahin wrote: Thanks Bruce, To avoid this problem, is there anyway to run make_average_subject without having lh and rh.aparc.annot files? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School From: Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu To: Shahin sha...@nmr.mgh.harvard.edu mailto:sha...@nmr.mgh.harvard.edu Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Sent: Mon, November 8, 2010 12:10:38 PM Subject: Re: [Freesurfer] how to generate aparc.annotion files? Hi Shahin you'll need a monkey atlas based on manually labeled monkey folding patterns. we don't have one, but it's possible that someone else on the list does (it would be a lot easier to do for monkey than it was for human as the folds are so much simpler) cheers Bruce On Mon, 8 Nov 2010, Shahin wrote: Hi Freesurfers, Anybody knows how can I make lh and rh.annotation.aparc files for a monkey? I need them initiate an brain averaging process. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to generate aparc.annotion files?
You'll probably have to do it by hand with tkregister2. Someone on the list may have solved this problem before. doug Shahin wrote: Ok now I faced another problem saying that I dont have talairach.xfm for monkeys. Would you tell me how can I generate it for monkeys? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Shahin sha...@nmr.mgh.harvard.edu *Cc:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Mon, November 8, 2010 12:55:37 PM *Subject:* Re: [Freesurfer] how to generate aparc.annotion files? It is needed in make_average_surface. I've created a new version that does not use the aparc (thought I have not tested it). You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc Make a backup of your current version of make_average_surface and then copy this one over it douig Shahin wrote: Yes, I have made a template on the basis of many monkeys (mris_make_template) and then I have done spherical registeration for each individual monkey (to this template) by using mris_register. Now it is the final step and I have to run the make_average_subject but it generates an error saying that I don't have a lh and rh.aparc.annot files. Apparently very old versions of freesurfer (version 3) didnt need these files. Am I right? Do you suggest to use old versions? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School *From:* Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu *To:* Shahin sha...@nmr.mgh.harvard.edu mailto:sha...@nmr.mgh.harvard.edu *Cc:* Freesurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Mon, November 8, 2010 12:33:03 PM *Subject:* Re: [Freesurfer] how to generate aparc.annotion files? Hi Shahin have you run spherical registration? If so, to what target? I don't think the monkey-to-human atlas aligment is that robust, so you would need a monkey geometry atlas (which is a lot easier to build as you don't need to do manual labeling for it). Probably someone on list has one? Bruce On Mon, 8 Nov 2010, Shahin wrote: Thanks Bruce, To avoid this problem, is there anyway to run make_average_subject without having lh and rh.aparc.annot files? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School From: Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu To: Shahin sha...@nmr.mgh.harvard.edu mailto:sha...@nmr.mgh.harvard.edu mailto:sha...@nmr.mgh.harvard.edu mailto:sha...@nmr.mgh.harvard.edu Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Sent: Mon, November 8, 2010 12:10:38 PM Subject: Re: [Freesurfer] how to generate aparc.annotion files? Hi Shahin you'll need a monkey atlas based on manually labeled monkey folding patterns. we don't have one, but it's possible that someone else on the list does (it would be a lot easier to do for monkey than it was for human as the folds are so much simpler) cheers Bruce On Mon, 8 Nov 2010, Shahin wrote: Hi Freesurfers, Anybody knows how can I make lh and rh.annotation.aparc files for a monkey? I need them initiate an brain averaging process. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu
Re: [Freesurfer] how to generate aparc.annotion files?
Ok now I faced another problem saying that I dont have talairach.xfm for monkeys. Would you tell me how can I generate it for monkeys? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Shahin sha...@nmr.mgh.harvard.edu Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Mon, November 8, 2010 12:55:37 PM Subject: Re: [Freesurfer] how to generate aparc.annotion files? It is needed in make_average_surface. I've created a new version that does not use the aparc (thought I have not tested it). You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc Make a backup of your current version of make_average_surface and then copy this one over it douig Shahin wrote: Yes, I have made a template on the basis of many monkeys (mris_make_template) and then I have done spherical registeration for each individual monkey (to this template) by using mris_register. Now it is the final step and I have to run the make_average_subject but it generates an error saying that I don't have a lh and rh.aparc.annot files. Apparently very old versions of freesurfer (version 3) didnt need these files. Am I right? Do you suggest to use old versions? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School *From:* Bruce Fischl fis...@nmr.mgh.harvard.edu *To:* Shahin sha...@nmr.mgh.harvard.edu *Cc:* Freesurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Mon, November 8, 2010 12:33:03 PM *Subject:* Re: [Freesurfer] how to generate aparc.annotion files? Hi Shahin have you run spherical registration? If so, to what target? I don't think the monkey-to-human atlas aligment is that robust, so you would need a monkey geometry atlas (which is a lot easier to build as you don't need to do manual labeling for it). Probably someone on list has one? Bruce On Mon, 8 Nov 2010, Shahin wrote: Thanks Bruce, To avoid this problem, is there anyway to run make_average_subject without having lh and rh.aparc.annot files? Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School From: Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu To: Shahin sha...@nmr.mgh.harvard.edu mailto:sha...@nmr.mgh.harvard.edu Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Sent: Mon, November 8, 2010 12:10:38 PM Subject: Re: [Freesurfer] how to generate aparc.annotion files? Hi Shahin you'll need a monkey atlas based on manually labeled monkey folding patterns. we don't have one, but it's possible that someone else on the list does (it would be a lot easier to do for monkey than it was for human as the folds are so much simpler) cheers Bruce On Mon, 8 Nov 2010, Shahin wrote: Hi Freesurfers, Anybody knows how can I make lh and rh.annotation.aparc files for a monkey? I need them initiate an brain averaging process. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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
