Ciao Eugenio,
I've just checked the presence of the file T1resampled.mgz and it doesn't show
up in tmp/ folder as well as in other folders of the same subject.
Morover, the T1resampled.mgz file is not present in ever subjects folder at
every time point as well as for the base/template folder.
Daniele
Message: 11
Date: Mon, 7 Nov 2016 16:47:02 +0000
From: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk>
Subject: Re: [Freesurfer] FreeSurfer 6.0 (beta) Error in
segmentSubjectT1_autoEstimateAlveusML (line 588)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <aed2f588-0f26-4361-bea8-3162d0a86...@ucl.ac.uk>
Content-Type: text/plain; charset="utf-8"
Ciao Daniele,
This is weird. Would you mind verifying that file T1resampled.mgz actually
exists in the temporary directory of the subject? You can do that by CDing to
$SUBJECT_DIR/[SUBJECT_NAME]/tmp and running the command:
find . -name ?T1resampled.mgz?
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 7 Nov 2016, at 16:39, Daniele Orlandi
<dorla...@fatebenefratelli.eu<mailto:dorla...@fatebenefratelli.eu>> wrote:
Dear experts,
I've finished FSv5.3 longitudinal analysis and I'm now running FSv6.0(beta) for
hippocampal subfield features extraction (always on Ubuntu 14.01 environment).
After several trial I realized that before pipeline ends I've got the following
error:
/opt/FreeSurfer-6-Beta/bin//mri_mask -T 0.5 T1resampled.mgz
hippoMaskResampledDilated.mgz T1resampled.mgz >/dev/null: Signal 127
Error using kvlGEMSMatlab
/cluster/koen/eugenio/GEMS/itkMGHImageIO.cxx:216:
itk::ERROR: MGHImageIO(0x7fe88bcda050): Can't find/open file: T1resampled.mgz
Error in kvlReadCroppedImage (line 11)
Error in segmentSubjectT1_autoEstimateAlveusML (line 588)
Could you help me?
Best
Daniele
PS: Even though one of the last row display " finished without error", no
output is generated in the /mri/ folder.
--
--
Daniele Orlandi, PsyD
IRCCS Fatebenefratelli
Via Pilastroni 4
25125 Brescia - Italy
tel: +39 030 35 01 563
e-mail: dorla...@fatebenefratelli.eu<mailto:dorla...@fatebenefratelli.eu>
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