Hi All,

I can't seem to get V6 hipposubfields to run on my new Yosemite install. Data was processed with V5.3 under 10.6.8. Attached log..but no error occurred.

Thanks for your help!

Carl

<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract@gmail.com; carl_anderson@hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

Command line:

vermisii:Only_5_3 carlanderson$ recon-all -s RB_139 -hippocampal-subfields-T1

INFO: FreeSurfer build stamps do not match

Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/Only_5_3

Actual FREESURFER_HOME /Applications/freesurfer

-rw-rw-r-- 1 carlanderson wheel 632773 Jan 21 09:41 /Applications/freesurfer/subjects/Only_5_3/RB_139/scripts/recon-all.log

Darwin vermisii.mclean.harvard.edu 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64

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

#@# Hippocampal Subfields processing (T1 only) left Thu Jan 21 09:57:22 EST 2016

\n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 /Applications/freesurfer RB_139 /Applications/freesurfer/subjects/Only_5_3 left \n

See log file: /Applications/freesurfer/subjects/Only_5_3/RB_139/scripts/hippocampal-subfields-T1.log

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

Setting up environment variables

---

DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:

Warning: application is running on a locale different from the original platform locale.

Registering imageDump.mgz to hippocampal mask from ASEG

dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib

Referenced from: /Applications/freesurfer/bin//kvlAutoCrop

Reason: image not found

/bin/bash: line 1: 5956 Trace/BPT trap: 5 /Applications/freesurfer/bin//kvlAutoCrop /Applications/freesurfer/subjects/Only_5_3/RB_139/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask.mgz 6 > /dev/null

/Applications/freesurfer/bin//kvlAutoCrop /Applications/freesurfer/subjects/Only_5_3/RB_139/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask.mgz 6 >/dev/null: Trace/breakpoint trap

/Applications/freesurfer/subjects/Only_5_3/RB_139/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory

ERROR: problem reading fname

SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 588)

Error in myMRIread>myMRIread_aux (line 85)

Error in myMRIread (line 56)

Error in segmentSubjectT1_autoEstimateAlveusML (line 174)

MATLAB:badSwitchExpression

--