hey, using the FreeSurferPipline in the new version of the Pipelines i get the error bellow. furthermore, the fsaverage folder is empty, so nothing was created in there, so not only this file is missing...
Reporting on 70 segmentations Using PrintSegStat mri_segstats done /root/hcppilelines/piano_hcp/working_directory/103/T1w/103/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /root/hcppilelines/piano_hcp/working_directory/103/T1w; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - #-------------------------------------------- #@# BA_exvivo Labels lh Sat Mar 23 17:46:55 UTC 2019 mri_label2label --srcsubject fsaverage --srclabel /root/hcppilelines/piano_hcp/working_directory/103/T1w/fsaverage/label/lh.BA1_exvivo.label --trgsubject 103 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface No such file or directory mri_label2label.bin: could not open label file /root/hcppilelines/piano_hcp/working_directory/103/T1w/fsaverage/label/lh.BA1_exvivo.label srclabel = /root/hcppilelines/piano_hcp/working_directory/103/T1w/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = 103 trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /root/hcppilelines/piano_hcp/working_directory/103/T1w FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /root/hcppilelines/piano_hcp/working_directory/103/T1w/fsaverage/label/lh.BA1_exvivo.label Linux 55369391361f 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 103 exited with ERRORS at Sat Mar 23 17:46:55 UTC 2019 ------------------------------------------------------------------------------------------------------------- im also adding here my call to the pipeline: /root/hcppilelines/HCPpipelines-master/FreeSurfer/FreeSurferPipeline.sh --subject=103 --subjectDIR=/root/hcppilelines/piano_hcp/working_directory/103/T1w --t1=/root/hcppilelines/piano_hcp/working_directory/103/T1w/T1w_acpc_dc_restore.nii.gz --t1brain=/root/hcppilelines/piano_hcp/working_directory/103/T1w/T1w_acpc_dc_restore_brain.nii.gz --t2=/root/hcppilelines/piano_hcp/working_directory/103/T1w/T2w_acpc_dc_restore.nii.gz ------------------------------------------------------------------------------------------------------------------ hope to hear from you Shachar _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
