Hi,

Perfect, thank you for the quick response!

Best,

Gustav

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.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.se | ki.se
___________________________________
Karolinska Institutet – a medical university

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