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
>
>
>
>
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