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.iglesias@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-BEA8-3162D0A861A9@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 <dorlandi@fatebenefratelli.eumailto:dorlandi@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: dorlandi@fatebenefratelli.eumailto:dorlandi@fatebenefratelli.eu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.