Hi Peter,
Thank you so much for picking up on this. Yes, I guess I mean template - I am still new to FS and get some of the terms/procedures mixed up. Jenni Pacheco at NIH (copied) is helping to bring our group up to speed. Hopefully she can clarify further.
I would appreciate being able to use those data in our research with FS. It would be good for hear what the FS staff have to say also.
Jack
-----Original Message----- From: Molfese, Peter [mailto:peter.molfese@yale.edu] Sent: Friday, May 26, 2017 9:57 AM To: john.hettema@vcuhealth.org Cc: jenni.pacheco@nih.gov; freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] Haskins Pediatric Atlas use in FS
Hi Jack-
I created the Haskins Pediatric Atlas and saw your message on the Freesurfer list. I’m not sure I fully understand your question, would you like to use the Haskins Template (Atlas is technically the label/segmentation) as your template in Freesurfer? If it’s “as simple as” running through the steps on this page (https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates), I suspect I can generate that in a couple of weeks.
The GCS file seems to be more useful for actual atlas labeling. It may be possible for us to do some of this with the tools that exist (https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceLabelAtlas).
Freesurfer experts, would you be willing to weigh in on options? All of these pediatric data (N=75) were run through Freesurfer 5.3 with manual edits.
Best, Peter
To FreeSurfer team,
I have child MRI data for which it would be best to use a pediatric atlas/template for warping, alignment, and labeling. I am aware of the Haskins Pediatric Atlas that AFNI includes as an optional dataset for this purpose in the FreeSurfer anatomical rendering it performs before running functional analyses.
However, the AFNI team were unable to tell me how to connect to this atlas outside of AFNI. I.e., when I just run FreeSurfer for volume and surface reconstruction.
How may I include this atlas in the usual running of FreeSurfer?
Is there a specific command line flag I can use to specify it instead of the default adult one?
Do I need to download some specific .gcs file?
Thanks.
Jack