Re: [Freesurfer] Recon-all w/ Hammersmith atlas
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" <rya...@stanford.edu> wrote: > > Yes, of course. Please see attached. > > Best, > > Ryan > > -- > Ryan Flores > Clinical Research Coordinator > On 4/18/18, 10:39 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf > of Douglas N. Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > dgr...@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-boun...@nmr.mgh.harvard.edu> on behalf of > Douglas > > Greve <dgr...@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 > > _
Re: [Freesurfer] Recon-all w/ Hammersmith atlas
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" <rya...@stanford.edu> wrote:
Yes, of course. Please see attached.
Best,
Ryan
--
Ryan Flores
Clinical Research Coordinator
On 4/18/18, 10:39 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N. Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgr...@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-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
> Greve <dgr...@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
___
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contains patient information, please contact the Partners Compliance
HelpLine at
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Re: [Freesurfer] Recon-all w/ Hammersmith atlas
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-boun...@nmr.mgh.harvard.edu> on behalf of Douglas > Greve <dgr...@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.
Re: [Freesurfer] Recon-all w/ Hammersmith atlas
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-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@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 recon-all.log Description: recon-all.log ___ 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] 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 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.
Re: [Freesurfer] Recon-all w/ Hammersmith atlas
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-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 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.
