Thanks !

Cheers, Pierre On Jul 8, 2016 1:14 PM, "Iglesias, Eugenio" e.iglesias@ucl.ac.uk wrote:

I think I identified the problem; hopefully this will be sorted out very soon. Cheers, Eugenio

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis < RPEREACAMARGO@mgh.harvard.edu> wrote:

*Warning: This message has had one or more attachments removed (recon-all.cmd). Please read the "UCL-Attachment-Warning.txt" attachment(s) for more information.* Hi all, I am currently trying to run hippocampal subfields in a couple of my participants using FreeSurfer6.0 (located at *nmr*:/usr/local/freesurfer/stable6).

It did run successfully for many of my subjects earlier in the year but some of them only had a let hemisphere segmentation. So I decided to re-run them using launchpad and also my local nmr computer.

Now, none of the hippocampal sufields segmentations appear (no rh/lh.hippoSfLabels-T1-T2.*.mgz appears). I looked at <FSSUBJECT>/scripts/scripts/hippocampal-subfields-T1T2.log and the error I get is:

Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf

Could a missing *.ctf cause the error? (btw, the re-run happened after the major hardware crash).

Thanks in advance for your help, Rodrigo

PS: I am attaching the *log files as suggested in the bug reporting page.

--- Rodrigo Dennis Perea Research Fellow Department of Radiology Athinoula A. Martinos Center Massachusetts General Hospital rpereacamargo@mgh.harvard.edu

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