Can you send the recon-all.log file for some of the failures?
On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote:
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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... -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
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 http://ki.se/en/startpage ______________________________________ Karolinska Institutet – a medical university
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