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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