Sorry, scratch that. Apparently it just didn’t realise that my subjects were in a subdirectory in the subjects directory.

Running now.

Note to self: “Think before you click send”

Kind regards,

FREDA SCHEFFLER

Research Assistant / PhD Candidate

MA Research Psychology

Faculty of Medicine and Health Sciences

Fakulteit Geneeskunde en Gesondheidswetenskappe

Universiteit Stellenbosch University

PO Box | Posbus 241, Cape Town | Kaapstad, 8000

Francie van Zijl Drive | -rylaan, Tygerberg, 7505

South Africa | Suid-Afrika

Tel: +27 21 938 9771

Email | E-pos: fredas@sun.ac.za

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Scheffler, F, Mev [fredas@sun.ac.za]" <fredas@sun.ac.za>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 26 October 2018 at 18:24
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Error in segmentHA_T1.sh

External Email - Use Caution

Dear Freesurfer Developers

I’ve run recon-all -all on a batch of 20 subjects on a linux based high performance computing setup and am now trying to run the segmentHA_T1 on them as well.

It sets up the environment and then complains about myMRIread and Error in segmentSubjectT1_autoEstimateAlveusML (line 157)

Here is the command line output:

#--------------------------------------------

#@# Hippocampal Subfields processing (T1) left Fri Oct 26 18:06:27 SAST 2018

------------------------------------------

Setting up environment variables

---

LD_LIBRARY_PATH is

<redacted, because I’m paranoid>

Error using myMRIread (line 16)

Error in myMRIread: temporary directory does not exist

Error in segmentSubjectT1_autoEstimateAlveusML (line 157)

@#@FSTIME 2018:10:26:18:06:27 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 107.33 S 6.58 U 8.77 P 14% M 145072 F 14363 R 298922 W 0 c 179 w 32314 I 33416 O 0 L 0.02 5.50 14.86

@#@FSLOADPOST 2018:10:26:18:08:14 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.78 4.16 13.38

Linux cnode0070 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Fri Oct 26 18:08:15 SAST 2018

What am I doing wrong here?

Thanks very much.