Le 23 févr. 2021 à 16:52, THIBEAU SUTRE Elina <elina.thibeausutre@icm-institute.org> a écrit :

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Thank you for your answer!

I actually found a .gcs version of the atlas here MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://figshare.com/articles/dataset/multiAtlasTT_data/5998583.

I now try to reproduce the steps done in freesurfer recon-all with this atlas.

I now have another problem: when I try to reproduce the steps based on MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 with an atlas used by the pipeline (for example ?h.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs) I do not obtain the same result than with recon-all.

My freesurfer version is 6.0.0 and I tried to do the two steps leading to the creation of statistics for one particular subject:

mris_ca_label -l ../label/?h.cortex.label -aseg aseg.presurf.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ?h.aparc.annot

mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h

Can you confirm that these are the correct steps to perform ? And that the root directory here is $SUBJECTS_DIR/<subjid> /mri?

Le 23 févr. 2021 à 15:07, Douglas N. Greve <dgreve@mgh.harvard.edu> a écrit :

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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