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.se ___________________________________ Karolinska Institutet – a medical university