Hi Ju - Are you using the same computer and are logged in in as the same user when you create the directory manually and when you run trac-all? It's hard to replicate this error. What the program does at that point is run the system call mkdir -p /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr and check if the return status is 0 (no error). When you do this on the command line and then "echo $status" what do you get?

Best, a.y

On Tue, 17 Nov 2015, jupiter wrote:

Hi,

I am running freesurfer 6.0 beta with cuda 6.5 and FSL 5.0.9 on Linux platform, I've got following error:

$ trac-all -path -c /scratchTRAC_TEST/dmrirc_first_exp_2.example

.........

INFO: Found 8 baseline images (b = 0) out of a total of 136 frames INFO: Found 169534 voxels in brain mask INFO: Resolution of DWI space relative to base space is (1, 1, 1) Loading atlas reference volume from /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz Loading affine registration from /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dmri/xfms/diff2mni.bbr.mat Loading segmentation map from /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dlabel/mni/aparc+aseg.nii.gz Creating output directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr ERROR: Could not create directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr Linux m2cvlnode17 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

The directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath is fully acceptable, I even tried manually create the directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr, then run the command, it deleted /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr, and never created it even the message was "Creating output directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr". Could it be a bug or could it be some thing I am missing? Appreciate clues to fix it.

Thank you.

Kind regards,

• ju