Hi,

Perfect, thank you for the quick response!

Best,

Gustav

On 2017-02-10 14:37, Iglesias Gonzalez, Eugenio wrote: Hi Gustav, No problem at all (ingen fara!). The idea is that, when our new joint atlas of the hippocampal subfields and amygdala nuclei is ready to be released, we’ll just need to replace the atlas files, without having to touch the code. It was my fault not to wrap that move command inside an IF statement to avoid that suspicious output. 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 10 Feb 2017, at 09:45, Gustav Mårtensson <gustav.martensson@ki.semailto:gustav.martensson@ki.se> wrote:

Hi,

I'm planning to run hippocampal subfield segmentation in FreeSurfer 6.0. I have already run the recon-all -all pipeline and are running

recon-all -s bert -hippocampal-subfields-T1

as described in https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields . The output, as far as I can see, looks fine but in the very end of hippocampal-subfields-T1.log I get

mri_convert.bin discreteLabels.mgz discreteLabelsResampledT1.mgz -rt nearest -odt float -rl /home/gustav/Desktop/preprocessing_h70/bert/mri/norm.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from discreteLabels.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) reading template info from volume /home/gustav/Desktop/preprocessing_h70/bert/mri/norm.mgz... Reslicing using nearest writing to discreteLabelsResampledT1.mgz... mv: cannot stat 'volumesAmygdala.txt': No such file or directory Everything done! It took 1305.6951 seconds

Does anyone know what this error ("mv: cannot stat 'volumesAmygdala.txt': No such file or directory") means and if it is of any importance? We are planning on run this command on a few thousand images and we are curious to know this to avoid the risk of re-running everything.

We are running on Ubuntu 16.04 LTS with FS version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I've included recon-all.log and hippocampal-subfields-T1.log in case it is of interest.

Thank you for your help!

-- Gustav Mårtensson | PhD student Division of Clinical Geriatrics Department of Neurobiology, Care Sciences and Society Karolinska Institutet Novum plan 5, 114 57 Huddinge Phone: +46-703-087614 E-mail: gustav.martensson@ki.semailto:gustav.martensson@ki.se | ki.sehttp://ki.se ___________________________________ Karolinska Institutet – a medical university <recon-all.log><hippocampal-subfields-T1.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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