search

kmcgregor123456 / CVNRimagingCore

CVNR Imaging Core Issues List
2 stars 1 forks source link

Script alternately runs on lens and ralph...? #51

Closed awoodbu closed 6 years ago

awoodbu commented 6 years ago

Error message: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 awoodbury@ralph:~/Woodbury_CDA1/05.scripts$ ./11_rsfMRI_mask_ventricles_in_MNI.sh run ventricle segmentation on subject PENFS01 post /usr/share/fsl/5.0/bin/first_flirt: 1: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/imtest: not found /usr/share/fsl/5.0/bin/first_flirt: 89: [: =: unexpected operator /usr/share/fsl/5.0/bin/first_flirt: 1: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/remove_ext: not found /usr/share/fsl/5.0/bin/first_flirt: 1: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/remove_ext: not found initial registration 1 /usr/share/fsl/5.0/bin/first_flirt: 123: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/flirt: not found Stage 2: use subcortical mask /usr/share/fsl/5.0/bin/first_flirt: 127: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/flirt: not found /usr/share/fsl/5.0/bin/first_flirt: 128: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/convert_xfm: not found /usr/share/fsl/5.0/bin/first_flirt: 132: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/flirt: not found Alternate Stage 2: Use brain mask /usr/share/fsl/5.0/bin/first_flirt: 137: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/flirt: not found /usr/share/fsl/5.0/bin/first_flirt: 139: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/convert_xfm: not found /usr/share/fsl/5.0/bin/first_flirt: 141: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/flirt: not found /bin/rm: cannot remove '_tmp_stage*': No such file or directory run segmentation of L-vent PENFS01 post /usr/share/fsl/5.0/bin/run_first: 1: /usr/share/fsl/5.0/bin/run_first: /usr/lib/fsl/5.0/bin/remove_ext: not found /usr/share/fsl/5.0/bin/run_first: 1: /usr/share/fsl/5.0/bin/run_first: /usr/lib/fsl/5.0/bin/imtest: not found /usr/share/fsl/5.0/bin/run_first: 140: [: =: unexpected operator linear transformation matrix file not found run segmentation of R-vent PENFS01 post /usr/share/fsl/5.0/bin/run_first: 1: /usr/share/fsl/5.0/bin/run_first: /usr/lib/fsl/5.0/bin/remove_ext: not found /usr/share/fsl/5.0/bin/run_first: 1: /usr/share/fsl/5.0/bin/run_first: /usr/lib/fsl/5.0/bin/imtest: not found /usr/share/fsl/5.0/bin/run_first: 140: [: =: unexpected operator linear transformation matrix file not found combine the ventricles into one volume PENFS01 post ++ 3dcalc: AFNI version=Debian-18.0.05+git24-gb25b21054~dfsg.1-1~nd14.04+1 (Jan 23 2018) [64-bit] ++ Authored by: A cast of thousands ERROR (nifti_image_read): failed to find header file for 'PENFS01_MPRAGE_deoblq_axRPI_optiBET_brain_rmbias_toMNI-R_LatVent_first.nii.gz' FATAL ERROR: can't open dataset PENFS01_MPRAGE_deoblq_axRPI_optiBET_brain_rmbias_toMNI-R_LatVent_first.nii.gz ** Program compile date = Jan 23 2018 ++ 3dAutomask: AFNI version=Debian-18.0.05+git24-gb25b21054~dfsg.1-1~nd14.04+1 (Jan 23 2018) [64-bit] ++ Authored by: Emperor Zhark ++ Loading dataset /data/qb/Atlanta/Woodbury_CDA1/06.Imaging_data/PENFS/PENFS01/post/preprocfiles/rsfMRI/PENFS01_rsfMRI_post_Tshift_volreg_applytopup_denoised_t

kmcgregor123456 commented 6 years ago

oh. that's the .profile error. I will fix.

================ Keith M. McGregor, PhD VA RR&D Atlanta CVNR Emory University, Department of Neurology 352.359.8084 www.varrd.emory.eduhttp://www.varrd.emory.edu

From: awoodbu notifications@github.com Sent: Thursday, August 9, 2018 3:03:18 PM To: kmcgregor123456/CVNRimagingCore Cc: Subscribed Subject: [kmcgregor123456/CVNRimagingCore] Script alternately runs on lens and ralph...? (#51)

Error message: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 awoodbury@ralph:/Woodbury_CDA1/05.scripts$ ./11_rsfMRI_mask_ventricles_in_MNI.sh run ventricle segmentation on subject PENFS01 post /usr/share/fsl/5.0/bin/first_flirt: 1: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/imtest: not found /usr/share/fsl/5.0/bin/first_flirt: 89: [: =: unexpected operator /usr/share/fsl/5.0/bin/first_flirt: 1: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/remove_ext: not found /usr/share/fsl/5.0/bin/first_flirt: 1: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/remove_ext: not found initial registration 1 /usr/share/fsl/5.0/bin/first_flirt: 123: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/flirt: not found Stage 2: use subcortical mask /usr/share/fsl/5.0/bin/first_flirt: 127: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/flirt: not found /usr/share/fsl/5.0/bin/first_flirt: 128: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/convert_xfm: not found /usr/share/fsl/5.0/bin/first_flirt: 132: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/flirt: not found Alternate Stage 2: Use brain mask /usr/share/fsl/5.0/bin/first_flirt: 137: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/flirt: not found /usr/share/fsl/5.0/bin/first_flirt: 139: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/convert_xfm: not found /usr/share/fsl/5.0/bin/first_flirt: 141: /usr/share/fsl/5.0/bin/first_flirt: /usr/lib/fsl/5.0/bin/flirt: not found /bin/rm: cannot remove '_tmp_stage*': No such file or directory run segmentation of L-vent PENFS01 post /usr/share/fsl/5.0/bin/run_first: 1: /usr/share/fsl/5.0/bin/run_first: /usr/lib/fsl/5.0/bin/remove_ext: not found /usr/share/fsl/5.0/bin/run_first: 1: /usr/share/fsl/5.0/bin/run_first: /usr/lib/fsl/5.0/bin/imtest: not found /usr/share/fsl/5.0/bin/run_first: 140: [: =: unexpected operator linear transformation matrix file not found run segmentation of R-vent PENFS01 post /usr/share/fsl/5.0/bin/run_first: 1: /usr/share/fsl/5.0/bin/run_first: /usr/lib/fsl/5.0/bin/remove_ext: not found /usr/share/fsl/5.0/bin/run_first: 1: /usr/share/fsl/5.0/bin/run_first: /usr/lib/fsl/5.0/bin/imtest: not found /usr/share/fsl/5.0/bin/run_first: 140: [: =: unexpected operator linear transformation matrix file not found combine the ventricles into one volume PENFS01 post ++ 3dcalc: AFNI version=Debian-18.0.05+git24-gb25b21054dfsg.1-1nd14.04+1 (Jan 23 2018) [64-bit] ++ Authored by: A cast of thousands ERROR (nifti_image_read): failed to find header file for 'PENFS01_MPRAGE_deoblq_axRPI_optiBET_brain_rmbias_toMNI-R_LatVent_first.nii.gz' FATAL ERROR: can't open dataset PENFS01_MPRAGE_deoblq_axRPI_optiBET_brain_rmbias_toMNI-R_LatVent_first.nii.gz ** Program compile date = Jan 23 2018 ++ 3dAutomask: AFNI version=Debian-18.0.05+git24-gb25b21054dfsg.1-1~nd14.04+1 (Jan 23 2018) [64-bit] ++ Authored by: Emperor Zhark ++ Loading dataset /data/qb/Atlanta/Woodbury_CDA1/06.Imaging_data/PENFS/PENFS01/post/preprocfiles/rsfMRI/PENFS01_rsfMRI_post_Tshift_volreg_applytopup_denoised_t

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/kmcgregor123456/CVNRimagingCore/issues/51, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AE21MJDiWdXoRjkFN6-xKS7w-cH7NhRIks5uPId2gaJpZM4V2PbW.

This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.

If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).