Hi everyone,
Freesurfer uses DKT atlas for volumetric analysis by default.
Brainnetome is our favorite one, is there a way to use that?
Best,
Majid
Hi Majid,
You can find some help here:
https://www.nitrc.org/projects/bn_atlas
Choose: BN_Atlas_freesurfer_Usage.pdf
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Many thanks @jsein
Unfortunately, I’m confused about the first step of that. It gives me bellow error. Could you help me?
mris_ca_label ‐l /Users/majid/TEST/01/label/lh.cortex.label 01 lh /Users/majid/TEST/01/surf/lh.sphere.reg /Users/majid/TEST/lh.BN_Atlas.gcs /Users/majid/TEST/01/label/lh.BN_Atlas.annot
7.2.0
7.2.0
reading atlas from lh…
error: No such file or directory
error: GCSAread(lh): could not open file
error: No such file or directory
error: mris_ca_label: could not read classifier from lh
Actually I never used these tools but I recently heard about the Brainnetome atlas from a colleague and remembered seeing this document when I read your question.
I tried to reproduce your error and got stuck at the same point with the same error message. Then I understood: If you copy paste the command lines from the PDF, beware of the character ‘-’ ! The ‘-’ you paste from the PDF is not the same than the ‘-’ you type in your terminal. You have to replace them and then it works.
Thank you so much JSein,
I used “mapping_to_subjects.sh” commands and that worked.
Maybe it is necessary to set “SUBJECTS_DIR” first.
Hello! I am using “mapping_to_subjects.sh” and it has worked fine for most of my participants’ data. However, for some subjects, I get some cortical areas with only have one vertex and are often the areas encircled in red in the image below.
Has anyone encountered this too and managed to solve the problem?