Hi Freesurfer Developers,
Our group is hoping to obtain the cortical thickness, surface area, and volume for various cortical regions (as well as some subcortical volumes); however, we would like these values to be outputted with respect to the regions delineated in the Hammersmith atlas. This atlas is available for free online (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-m...) and I’ve included a screenshot to show you what files are included in the download. Based on this information, what is the best and/or most straight forward to move forward?
Thank you for your time. I look forward to hearing from you.
1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 2. Platform: macOS High Sierra (Version 10.13.1)
Best,
Ryan -- Ryan Flores Clinical Research Coordinator
There is not an easy way to do this. If you have access to the original hammersmith data, you can run each subject through FS, copy/convert the manual labels into the conformed space for each subject, then build your own volume-based atlas. If that is something you are up for, let me know and I can give you more details.
On 4/16/18 3:14 PM, Ryan Flores wrote:
Hi Freesurfer Developers,
Our group is hoping to obtain the cortical thickness, surface area, and volume for various cortical regions (as well as some subcortical volumes); however, we would like these values to be outputted with respect to the regions delineated in the Hammersmith atlas. This atlas is available for free online (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-m...) and I’ve included a screenshot to show you what files are included in the download. Based on this information, what is the best and/or most straight forward to move forward?
Thank you for your time. I look forward to hearing from you.
- FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119
- Platform: macOS High Sierra (Version 10.13.1)
Best,
Ryan
--
Ryan Flores
Clinical Research Coordinator
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, just seeing that you also want cortical summaries. Those might be easier. You should run recon-all on the T1 template for the hammersmith. You can then create your own hammersmith annotation by mapping the atlas labels onto the surface (mri_vol2surf) and then mris_seg2annot. You can then use mris_apply_reg to map the annotation to the surface of an individual (or fsaverage).
On 4/16/18 3:14 PM, Ryan Flores wrote:
Hi Freesurfer Developers,
Our group is hoping to obtain the cortical thickness, surface area, and volume for various cortical regions (as well as some subcortical volumes); however, we would like these values to be outputted with respect to the regions delineated in the Hammersmith atlas. This atlas is available for free online (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-m...) and I’ve included a screenshot to show you what files are included in the download. Based on this information, what is the best and/or most straight forward to move forward?
Thank you for your time. I look forward to hearing from you.
- FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119
- Platform: macOS High Sierra (Version 10.13.1)
Best,
Ryan
--
Ryan Flores
Clinical Research Coordinator
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thank you for your response. I attempted to run recon-all on the Hammersmith nifti file as suggested, but unfortunately it appears to have run into some issues. I’ve attached the recon-all.log for reference.
Best,
Ryan -- Ryan Flores Clinical Research Coordinator From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 17, 2018 at 9:33 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all w/ Hammersmith atlas
Sorry, just seeing that you also want cortical summaries. Those might be easier. You should run recon-all on the T1 template for the hammersmith. You can then create your own hammersmith annotation by mapping the atlas labels onto the surface (mri_vol2surf) and then mris_seg2annot. You can then use mris_apply_reg to map the annotation to the surface of an individual (or fsaverage).
On 4/16/18 3:14 PM, Ryan Flores wrote: Hi Freesurfer Developers,
Our group is hoping to obtain the cortical thickness, surface area, and volume for various cortical regions (as well as some subcortical volumes); however, we would like these values to be outputted with respect to the regions delineated in the Hammersmith atlas. This atlas is available for free online (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-m...) and I’ve included a screenshot to show you what files are included in the download. Based on this information, what is the best and/or most straight forward to move forward?
Thank you for your time. I look forward to hearing from you.
1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 2. Platform: macOS High Sierra (Version 10.13.1)
Best,
Ryan -- Ryan Flores Clinical Research Coordinator
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
can you send me Hammers_mith_atlas_n30r83_SPM5.nii.gz ?
On 04/17/2018 07:55 PM, Ryan Flores wrote:
Hi Doug,
Thank you for your response. I attempted to run recon-all on the Hammersmith nifti file as suggested, but unfortunately it appears to have run into some issues. I’ve attached the recon-all.log for reference.
Best,
Ryan
--
Ryan Flores
Clinical Research Coordinator
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Tuesday, April 17, 2018 at 9:33 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Recon-all w/ Hammersmith atlas
Sorry, just seeing that you also want cortical summaries. Those might be easier. You should run recon-all on the T1 template for the hammersmith. You can then create your own hammersmith annotation by mapping the atlas labels onto the surface (mri_vol2surf) and then mris_seg2annot. You can then use mris_apply_reg to map the annotation to the surface of an individual (or fsaverage).
On 4/16/18 3:14 PM, Ryan Flores wrote:
Hi Freesurfer Developers, Our group is hoping to obtain the cortical thickness, surface area, and volume for various cortical regions (as well as some subcortical volumes); however, we would like these values to be outputted with respect to the regions delineated in the Hammersmith atlas. This atlas is available for free online (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-map-hammers-mith-atlas-n30r83-in-mni-space/) and I’ve included a screenshot to show you what files are included in the download. Based on this information, what is the best and/or most straight forward to move forward? Thank you for your time. I look forward to hearing from you. 1. FreeSurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 2. Platform: macOS High Sierra (Version 10.13.1) Best, Ryan -- Ryan Flores Clinical Research Coordinator _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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
Yes, of course. Please see attached.
Best,
Ryan
-- Ryan Flores Clinical Research Coordinator On 4/18/18, 10:39 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote:
can you send me Hammers_mith_atlas_n30r83_SPM5.nii.gz ?
On 04/17/2018 07:55 PM, Ryan Flores wrote: > > Hi Doug, > > Thank you for your response. I attempted to run recon-all on the > Hammersmith nifti file as suggested, but unfortunately it appears to > have run into some issues. I’ve attached the recon-all.log for reference. > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical Research Coordinator > > *From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas > Greve dgreve@mgh.harvard.edu > *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu > *Date: *Tuesday, April 17, 2018 at 9:33 AM > *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu > *Subject: *Re: [Freesurfer] Recon-all w/ Hammersmith atlas > > Sorry, just seeing that you also want cortical summaries. Those might > be easier. You should run recon-all on the T1 template for the > hammersmith. You can then create your own hammersmith annotation by > mapping the atlas labels onto the surface (mri_vol2surf) and then > mris_seg2annot. You can then use mris_apply_reg to map the annotation > to the surface of an individual (or fsaverage). > > On 4/16/18 3:14 PM, Ryan Flores wrote: > > Hi Freesurfer Developers, > > Our group is hoping to obtain the cortical thickness, surface > area, and volume for various cortical regions (as well as some > subcortical volumes); however, we would like these values to be > outputted with respect to the regions delineated in the > Hammersmith atlas. This atlas is available for free online > (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-m...) > and I’ve included a screenshot to show you what files are included > in the download. Based on this information, what is the best > and/or most straight forward to move forward? > > Thank you for your time. I look forward to hearing from you. > > 1. FreeSurfer version: > freesurfer-i386-apple-darwin11.4.2-stable6-20170119 > 2. Platform: macOS High Sierra (Version 10.13.1) > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical Research Coordinator > > > > > _______________________________________________ > > 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.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 Doug,
I just wanted to follow up on this. Were you able to download the zip file ok?
Best,
Ryan
On 4/18/18, 10:46 AM, "Ryan Flores" ryan10@stanford.edu wrote:
Yes, of course. Please see attached.
Best,
Ryan
-- Ryan Flores Clinical Research Coordinator On 4/18/18, 10:39 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote:
can you send me Hammers_mith_atlas_n30r83_SPM5.nii.gz ?
On 04/17/2018 07:55 PM, Ryan Flores wrote: > > Hi Doug, > > Thank you for your response. I attempted to run recon-all on the > Hammersmith nifti file as suggested, but unfortunately it appears to > have run into some issues. I’ve attached the recon-all.log for reference. > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical Research Coordinator > > *From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas > Greve dgreve@mgh.harvard.edu > *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu > *Date: *Tuesday, April 17, 2018 at 9:33 AM > *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu > *Subject: *Re: [Freesurfer] Recon-all w/ Hammersmith atlas > > Sorry, just seeing that you also want cortical summaries. Those might > be easier. You should run recon-all on the T1 template for the > hammersmith. You can then create your own hammersmith annotation by > mapping the atlas labels onto the surface (mri_vol2surf) and then > mris_seg2annot. You can then use mris_apply_reg to map the annotation > to the surface of an individual (or fsaverage). > > On 4/16/18 3:14 PM, Ryan Flores wrote: > > Hi Freesurfer Developers, > > Our group is hoping to obtain the cortical thickness, surface > area, and volume for various cortical regions (as well as some > subcortical volumes); however, we would like these values to be > outputted with respect to the regions delineated in the > Hammersmith atlas. This atlas is available for free online > (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-m...) > and I’ve included a screenshot to show you what files are included > in the download. Based on this information, what is the best > and/or most straight forward to move forward? > > Thank you for your time. I look forward to hearing from you. > > 1. FreeSurfer version: > freesurfer-i386-apple-darwin11.4.2-stable6-20170119 > 2. Platform: macOS High Sierra (Version 10.13.1) > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical Research Coordinator > > > > > _______________________________________________ > > 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.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.
sorry, did not get it. Can you resend?
On 4/23/18 8:25 PM, Ryan Flores wrote:
External Email - Use CautionHi Doug,
I just wanted to follow up on this. Were you able to download the zip file ok?
Best,
Ryan
On 4/18/18, 10:46 AM, "Ryan Flores" ryan10@stanford.edu wrote:
Yes, of course. Please see attached. Best, Ryan -- Ryan Flores Clinical Research Coordinator On 4/18/18, 10:39 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote: can you send me Hammers_mith_atlas_n30r83_SPM5.nii.gz ? On 04/17/2018 07:55 PM, Ryan Flores wrote: > > Hi Doug, > > Thank you for your response. I attempted to run recon-all on the > Hammersmith nifti file as suggested, but unfortunately it appears to > have run into some issues. I’ve attached the recon-all.log for reference. > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical Research Coordinator > > *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas > Greve <dgreve@mgh.harvard.edu> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Date: *Tuesday, April 17, 2018 at 9:33 AM > *To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] Recon-all w/ Hammersmith atlas > > Sorry, just seeing that you also want cortical summaries. Those might > be easier. You should run recon-all on the T1 template for the > hammersmith. You can then create your own hammersmith annotation by > mapping the atlas labels onto the surface (mri_vol2surf) and then > mris_seg2annot. You can then use mris_apply_reg to map the annotation > to the surface of an individual (or fsaverage). > > On 4/16/18 3:14 PM, Ryan Flores wrote: > > Hi Freesurfer Developers, > > Our group is hoping to obtain the cortical thickness, surface > area, and volume for various cortical regions (as well as some > subcortical volumes); however, we would like these values to be > outputted with respect to the regions delineated in the > Hammersmith atlas. This atlas is available for free online > (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-map-hammers-mith-atlas-n30r83-in-mni-space/) > and I’ve included a screenshot to show you what files are included > in the download. Based on this information, what is the best > and/or most straight forward to move forward? > > Thank you for your time. I look forward to hearing from you. > > 1. FreeSurfer version: > freesurfer-i386-apple-darwin11.4.2-stable6-20170119 > 2. Platform: macOS High Sierra (Version 10.13.1) > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical Research Coordinator > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto: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 _______________________________________________ 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
Yes, of course. It should be a zip file attached.
Best,
Ryan
-- Ryan Flores Clinical Research Coordinator On 4/24/18, 10:26 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote:
sorry, did not get it. Can you resend?
On 4/23/18 8:25 PM, Ryan Flores wrote: > External Email - Use Caution > > Hi Doug, > > I just wanted to follow up on this. Were you able to download the zip file ok? > > Best, > > Ryan > > On 4/18/18, 10:46 AM, "Ryan Flores" ryan10@stanford.edu wrote: > > Yes, of course. Please see attached. > > Best, > > Ryan > > -- > Ryan Flores > Clinical Research Coordinator > On 4/18/18, 10:39 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dgreve@mgh.harvard.edu> wrote: > > can you send me Hammers_mith_atlas_n30r83_SPM5.nii.gz ? > > > On 04/17/2018 07:55 PM, Ryan Flores wrote: > > > > Hi Doug, > > > > Thank you for your response. I attempted to run recon-all on the > > Hammersmith nifti file as suggested, but unfortunately it appears to > > have run into some issues. I’ve attached the recon-all.log for reference. > > > > Best, > > > > Ryan > > > > -- > > > > Ryan Flores > > > > Clinical Research Coordinator > > > > *From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas > > Greve dgreve@mgh.harvard.edu > > *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu > > *Date: *Tuesday, April 17, 2018 at 9:33 AM > > *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu > > *Subject: *Re: [Freesurfer] Recon-all w/ Hammersmith atlas > > > > Sorry, just seeing that you also want cortical summaries. Those might > > be easier. You should run recon-all on the T1 template for the > > hammersmith. You can then create your own hammersmith annotation by > > mapping the atlas labels onto the surface (mri_vol2surf) and then > > mris_seg2annot. You can then use mris_apply_reg to map the annotation > > to the surface of an individual (or fsaverage). > > > > On 4/16/18 3:14 PM, Ryan Flores wrote: > > > > Hi Freesurfer Developers, > > > > Our group is hoping to obtain the cortical thickness, surface > > area, and volume for various cortical regions (as well as some > > subcortical volumes); however, we would like these values to be > > outputted with respect to the regions delineated in the > > Hammersmith atlas. This atlas is available for free online > > (http://brain-development.org/brain-atlases/adult-brain-maximum-probability-m...) > > and I’ve included a screenshot to show you what files are included > > in the download. Based on this information, what is the best > > and/or most straight forward to move forward? > > > > Thank you for your time. I look forward to hearing from you. > > > > 1. FreeSurfer version: > > freesurfer-i386-apple-darwin11.4.2-stable6-20170119 > > 2. Platform: macOS High Sierra (Version 10.13.1) > > > > Best, > > > > Ryan > > > > -- > > > > Ryan Flores > > > > Clinical Research Coordinator > > > > > > > > > > _______________________________________________ > > > > 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.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
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N. Greve
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Ryan Flores