After running the dHCP structural pipeline, we are having trouble running the command that will give us the actual measurements. The errors suggest that the command cannot find our imaging data even though the structural pipeline has already been completed
Hello, the struct pipeline should create a directory full of images for you. Were these not created?
For example, I see:
$ pwd
/home/john/vol/dhcp-derived-data/derived_09Jan2019/derivatives/sub-CC00105XX06/ses-35801/anat
$ ls -R
.:
Native
sub-CC00105XX06_ses-35801_brainmask_bet.nii.gz
sub-CC00105XX06_ses-35801_brainmask_drawem.nii.gz
sub-CC00105XX06_ses-35801_drawem_all_labels.nii.gz
sub-CC00105XX06_ses-35801_drawem_tissue_labels.nii.gz
sub-CC00105XX06_ses-35801_ribbon.nii.gz
sub-CC00105XX06_ses-35801_T1w_biasfield.nii.gz
sub-CC00105XX06_ses-35801_T1wdividedbyT2w.nii.gz
sub-CC00105XX06_ses-35801_T1wdividedbyT2w_ribbon.nii.gz
sub-CC00105XX06_ses-35801_T1w.nii.gz
sub-CC00105XX06_ses-35801_T1w_restore_brain.nii.gz
sub-CC00105XX06_ses-35801_T1w_restore.nii.gz
sub-CC00105XX06_ses-35801_T2w_biasfield.nii.gz
sub-CC00105XX06_ses-35801_T2w.nii.gz
sub-CC00105XX06_ses-35801_T2w_restore_brain.nii.gz
sub-CC00105XX06_ses-35801_T2w_restore.nii.gz
xfms
./Native:
sub-CC00105XX06_ses-35801_corr_thickness.dscalar.nii
sub-CC00105XX06_ses-35801_curvature.dscalar.nii
sub-CC00105XX06_ses-35801_drawem.dlabel.nii
sub-CC00105XX06_ses-35801_left_corr_thickness.shape.gii
sub-CC00105XX06_ses-35801_left_curvature.shape.gii
sub-CC00105XX06_ses-35801_left_drawem.label.gii
sub-CC00105XX06_ses-35801_left_inflated.surf.gii
sub-CC00105XX06_ses-35801_left_midthickness.surf.gii
sub-CC00105XX06_ses-35801_left_myelin_map.func.gii
sub-CC00105XX06_ses-35801_left_pial.surf.gii
sub-CC00105XX06_ses-35801_left_roi.shape.gii
sub-CC00105XX06_ses-35801_left_smoothed_myelin_map.func.gii
sub-CC00105XX06_ses-35801_left_sphere.surf.gii
sub-CC00105XX06_ses-35801_left_sulc.shape.gii
sub-CC00105XX06_ses-35801_left_thickness.shape.gii
sub-CC00105XX06_ses-35801_left_very_inflated.surf.gii
sub-CC00105XX06_ses-35801_left_white.surf.gii
sub-CC00105XX06_ses-35801_myelin_map.dscalar.nii
sub-CC00105XX06_ses-35801_right_corr_thickness.shape.gii
sub-CC00105XX06_ses-35801_right_curvature.shape.gii
sub-CC00105XX06_ses-35801_right_drawem.label.gii
sub-CC00105XX06_ses-35801_right_inflated.surf.gii
sub-CC00105XX06_ses-35801_right_midthickness.surf.gii
sub-CC00105XX06_ses-35801_right_myelin_map.func.gii
sub-CC00105XX06_ses-35801_right_pial.surf.gii
sub-CC00105XX06_ses-35801_right_roi.shape.gii
sub-CC00105XX06_ses-35801_right_smoothed_myelin_map.func.gii
sub-CC00105XX06_ses-35801_right_sphere.surf.gii
sub-CC00105XX06_ses-35801_right_sulc.shape.gii
sub-CC00105XX06_ses-35801_right_thickness.shape.gii
sub-CC00105XX06_ses-35801_right_very_inflated.surf.gii
sub-CC00105XX06_ses-35801_right_white.surf.gii
sub-CC00105XX06_ses-35801_smoothed_myelin_map.dscalar.nii
sub-CC00105XX06_ses-35801_sulc.dscalar.nii
sub-CC00105XX06_ses-35801_thickness.dscalar.nii
sub-CC00105XX06_ses-35801_wb.spec
./xfms:
sub-CC00105XX06_ses-35801_anat2std39w.nii.gz
sub-CC00105XX06_ses-35801_anat2std40w.nii.gz
sub-CC00105XX06_ses-35801_std39w2anat.nii.gz
sub-CC00105XX06_ses-35801_std40w2anat.nii.gzYes, those were created. However, after this, I attempted to run the commands * . [dHCP_structural_pipeline_path]/parameters/path.sh followed by * ./pipeline.sh [derivatives_dir] [dataset_csv] ( --reporting ) ( -t [num_threads] ) in order to receive the quantitative data. I did create the csv file in excel before but was still receiving an error