On 7/21/15 10:04 AM, Silas wrote:
Dear Freesurfer team,
I've created my own labels using tksurfer and common anatomical
guidelines - and my next step is to apply these labels to my subjects
and analyze (ROI) cortical thickness or volume (first of all),
functional data and myelination data.
1 - Do you suggest drawing a label on the surface of fsaverage and
applying this label to the other subjects (e.g. using mri_label2label)
- or drawing a label on each subjects surface?
It depends on how accurately you think you can make it and how much
accuracy you need. Drawing it on fsaverage will be much easier than
doing it on each subject, though the accuracy may suffer a little bit
when mapping it to the individual. I would do it this way and see if the
output labels meet your expectations and then make edits to the
individual if not. Use mri_label2label to map the label from fsaverage
to an individual. Run with --help for examples.
2 - What is my next step? Do i have to run recon-all again with my new
label in the labels folder - or should i experiment with mri_label2vol
and mri_label2annot?
You do not need to run recon-all again. You can run
mris_anatomical_stats to get thickness, surface area, and volume
estimates for this label (like the .stats files). When using it with
functional data, you can run mri_label2vol to map the label into the
functional space. Run with --help for examples.
3 - Do you have an existing guide in this kind of analysis?
I'm not sure of one to do specifically these steps, though look at the
multimodal integration tutorials and the ROI tuturials.
doug
Thanks! Best, Silas
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