Corresponding Stats output of FastSurfer to "Recon-all" about fastsurfer HOT 6 OPEN

Generally, the file naming conventions between FreeSurfer and FastSurfer are the same. So you should be able to run the same commands with FastSurfer outputs as with FreeSurfer outputs.

Here, I would recommend to use change --subjects `cat done.txt` to --subjectsfile done.txt (assuming done.txthas one subject per line). You also need to make sure the SUBJECTS_DIR enviroment variable is set correctly.

from fastsurfer.

Thanks a lot for the answer. After running recon-all with freesurfer I have a lot more files in the surf folder e.g.

as after running FastSurfer (files mentioned above).
Do I need to give extra arguments to FastSurfer to get the same results?

I currently use

..
 --fs_license /fs_license/license.txt \
           --t1 /xy.nii \
           --sid xy --sd /output \
           --parallel --3T

with no extra arguments.

from fastsurfer.

The thickness, curvature, etc. information is stored in the {rh,lh}.{thick,curv,... } files. The other files produced by FreeSurfer mostly concern other segmentation protocols (like a2009s -- FastSurfer only generates the aparc.DKTatlas surface segmentation) or smoothing of statistics (see fwhm).

I am not really sure, why you generated this many smoothed statistics in your reference run, but generally this is not the default FreeSurfer behavior. In any way, it is not necessary to have this statistic.

So I would expect you do not need to manually create other atlas-surface segmentations (call mris_ca_label) as your command only processes the default (--parc <...>not specified).

from fastsurfer.

I see.

But in the stats output of FastSurfer is no e.g. rh.aparc.stats and running:

aparcstats2table --subjects xy/ --hemi rh  --meas thickness  --tablefile rh_aparc_stats_thickness.tx
SUBJECTS_DIR : /FastSurfer
Parsing the .stats files

ERROR: Cannot find stats file /FastSurfer/xy/stats/rh.aparc.stats

(paths are correct)

from fastsurfer.

FastSurfer uses the the DKTatlas, so adding --parc aparc.DTKatlas.mapped should solve this.

from fastsurfer.

Yes, we should document all this a little better. Freesurfer also generates the DKTatlas but it is not the default (although many people think it should be). The DKT it is only a minor modification from the older aparc with some clean up and a few unreliable labels merged.
In FastSurfer, you can use the --fs-aparc flag which will generate more stats files, but will be a little slower obviously. For most applications the default DKTatlas.mapped one will be fine. This is the volume based DKT atlas segmentation mapped to the surface, so it does not even require a spherical non-linear registration.

from fastsurfer.