Hello Freesurfer Experts,
I am trying to view stats generated with FsFast in fslview/MNIspace, and in doing so I have run mni152reg to generate the registration matrix.
That said, mni152reg did not complete correctly and below I have pasted the terminal output:
Thu Jul 17 09:58:10 EDT 2014
setenv SUBJECTS_DIR /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s CD_cerv_pat4_sess1_recon
Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux fslregister --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz --s CD_cerv_pat4_sess1_recon --reg /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat --dof 12 mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833': Permission denied
Log file is /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log
Thu Jul 17 09:58:11 EDT 2014 --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz --s CD_cerv_pat4_sess1_recon --reg /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat --dof 12 $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ purkinje Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons mri_convert /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii mri_convert /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii niiWrite(): error opening file /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz... TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (-0, -0, -1) k_ras = (0, 1, 0) writing to /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii... ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
I tried to run the fslregister command from within the subject's directory (in hopes to possible correct what may be a permissions issue), but this produces the same final error, "ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii."
Lastly, probably to no surprise, the /.../mri/transforms/reg.mni152.2mm.dat file was never generated.
Any ideas how I may be able to correct these errors?
Thank you for the help!
Jacob