The QC output is outstanding and very helpful.
I'm trying to run Example 0 on the website you provided, but nothing is saving to my QC folder.
Here's my command:
set opref = QC/anat
@chauffeur_afni -ulay 2072_test.T1+orig -prefix ${opref} -set_xhairs MULTI -montx 3 -monty 3 -label_mode 1 -label_mode 4
The command seems to run fine (see terminal output below). But when I go into QC folder, there's nothing there.
++ My command:
@chauffeur_afni -ulay 2072_test.T1+orig -prefix QC/anat -set_xhairs MULTI -montx 3 -monty 3 -label_mode 1 -label_mode 4
++ Using AFNI ver : AFNI_22.3.05
++ chauffeur ver : 6.51
\n------------------ start of optionizing ------------------\n
++ Found input file: 2072_test.T1+orig
+* Noting: you did NOT provide an overlay, and yet
you did NOT turn off the overlay with '-olay_off'
--> so I assume you just want to view the underlay.
++ Using blowup factor: 2
++ Using opacity: 6
++ Making temporary work directory to copy vis files: QC/__tmp_chauf_RzN4p7uicct
++ Converted 0 to labels
++ Final subbrick indices: -1 -1 -1
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 2408.000000]
++ 3dcalc: AFNI version=AFNI_22.3.05 (Nov 9 2022) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC/__tmp_chauf_RzN4p7uicct/tmp_ulay.nii
++ No overlay viewing
++ Dimensions (xyzt): 256 256 188 1
++ (initial) Slice spacing ordered (x,y,z) is: 28 28 20
++ 3dmaskdump: AFNI version=AFNI_22.3.05 (Nov 9 2022) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=2072_test.T1+orig[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/y5/gzw6hjys3_90fqb0mdfm0q2m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_qs-ZU95XqkCGUUmM0dkiyg argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_22.3.05 (Nov 9 2022) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.021250
++ Computing output statistics
++ Output dataset /var/folders/y5/gzw6hjys3_90fqb0mdfm0q2m0000gn/T/3dcalc_AFN_qs-ZU95XqkCGUUmM0dkiyg+orig.BRIK
++ 12320768 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 127 127 94
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :284
[1] 74485
+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_ulay.nii -com SEE_OVERLAY - -com OPEN_WINDOW sagittalimage opacity=6 mont=3x3:28:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=6 mont=3x3:28:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=6 mont=3x3:20:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 1 Plasma -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 2408.000000 -com SET_FUNC_RANGE 0 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS MULTI -com SET_XHAIR_GAP -1 -com SET_IJK 127 127 94 -com SAVE_PNG axialimage QC/anat.axi blowup=2 -com SAVE_PNG sagittalimage QC/anat.sag blowup=2 -com SAVE_PNG coronalimage QC/anat.cor blowup=2 -com QUITT QC/__tmp_chauf_RzN4p7uicct
+/Users/amlung/neuro/rescue/2072_test/QC/__tmp_chauf_RzN4p7uicct
AFNI QUITTs!
\n+* Removing temporary image directory 'QC/__tmp_chauf_RzN4p7uicct'.\n
[1] Done Xvfb :284 -screen 0 1024x768x24
++ DONE (good exit)
see: QC/anat*
