Annelies van't Westeinde | PHD Candidate
Department of Women's and Children's Health | Karolinska Institutet
171 77 Solna | Karolinskavägen 37A
+46 760967499
annelies.vant.westeinde@ki.se | ki.se
______________________________________
Karolinska Institutet – a medical university

Dear list,

As described by others on this list, recon-all with Freesurfer 7.1 on a Mac operating system seems to fail for around 10% of the subjects.

The following solution was offered:

sudo curl 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
 -o rca-long-tp-init 
sudo chmod +x rca-long-tp-init

However, this did not solve the problem for me.

I re-ran recon-all for the same subjects, but it still failed, some of them at the following step:

"#######################################

GCADIR /Applications/freesurfer/average

GCA RB_all_2020-01-02.gca

GCASkull RB_all_withskull_2020_01_02.gca

AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif

GCSDIR /Applications/freesurfer/average

GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs

#######################################"

It simply stopped running there.

Others did finish running, but instead got a segmentation fault error.

What could I do? I have Mac High Sierra.

Annelies