depends on the nature of AICHA. Are these labels on a group of subjects? If so, you can build your own gcs file with train-gcs-atlas.
If it is just a label set, then you should run recon-all on the template subject, sample the labels onto the surface (mri_vol2surf), then convert the resulting surface segmentation to an annotation (mris_seg2annot), then map the annot to other subjects with mris_apply_reg

On 2/22/2021 8:59 AM, THIBEAU SUTRE Elina wrote:

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Hello freesurfer experts,

I would like to use freesurfer recon-all to obtain the regional cortical thicknesses of subjects of ADNI dataset. I launched freesurfer recon-all and obtained the parcellations according to Destrieux and Desikan-Killiany atlases. I would like to know how to obtain the same parcellations with another atlas, AICHA (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.gin.cnrs.fr/en/tools/aicha/), which is only available in nifti format.

I understood that I should create a .gcs file from the nifti version but I am not sure how. I saw that mris_ca_train could be used to create such a file from a a manually labelled dataset but I don’t know how to create these labelled subjects from the nifti atlas.

If anyone has already this kind of conversion .nii -> .gcs I would be really interested to know how you have done that!

Best regards,

Elina
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