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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| September 29, 2021 06:25PM | |
Registered: 3 years ago Posts: 29 |
Hi AFNI team,
I am preprocessing resting state data using AFNI_21.2.04. I've copied my proc.py command below. In my HTML output there are no images generated in the motion block. While I can generate these images independently using 1dplot it would be handy to have them in the QC output for all participants for the review process. I am attaching the output generate from running the motion blocks of the @ss_review_html script. Do you have any suggestions on what may need to change so that these plots can be generated?
Thank you!
Jenna
I am preprocessing resting state data using AFNI_21.2.04. I've copied my proc.py command below. In my HTML output there are no images generated in the motion block. While I can generate these images independently using 1dplot it would be handy to have them in the QC output for all participants for the review process. I am attaching the output generate from running the motion blocks of the @ss_review_html script. Do you have any suggestions on what may need to change so that these plots can be generated?
Thank you!
Jenna
++ FOR: motion_sub01_enorm.1D: 1 arrays with 136 pts
++ FOR: outcount_rall.1D: 1 arrays with 136 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..135]
++ Plotting: enorm (~mm)
++ Plotting: outlier frac
Traceback (most recent call last):
File "/gpfs/runtime/opt/afni/21.2.04/1dplot.py", line 65, in <module>
ok_fig = lpod.make_1dplot_figure(bigfig)
File "/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_plot_1D.py", line 498, in make_1dplot_figure
bbox_inches='tight')
File "/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 695, in savefig
res = fig.savefig(*args, **kwargs)
File "/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/figure.py", line 2062, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py", line 2173, in print_figure
canvas = self._get_output_canvas(format)
File "/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py", line 2105, in _get_output_canvas
.format(fmt, ", ".join(sorted(self.get_supported_filetypes()))))
ValueError: Format 'jpg' is not supported (supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz)
++ FOR: dfile_rall.1D: 6 arrays with 136 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..135]
++ Plotting: dP
(mm)
++ Plotting: dL
(mm)
++ Plotting: dS
(mm)
++ Plotting: yaw
(deg)
++ Plotting: pitch
(deg)
++ Plotting: roll
(deg)
Traceback (most recent call last):
File "/gpfs/runtime/opt/afni/21.2.04/1dplot.py", line 65, in <module>
ok_fig = lpod.make_1dplot_figure(bigfig)
File "/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_plot_1D.py", line 498, in make_1dplot_figure
bbox_inches='tight')
File "/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 695, in savefig
res = fig.savefig(*args, **kwargs)
File "/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/figure.py", line 2062, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py", line 2173, in print_figure
canvas = self._get_output_canvas(format)
File "/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py", line 2105, in _get_output_canvas
.format(fmt, ", ".join(sorted(self.get_supported_filetypes()))))
ValueError: Format 'jpg' is not supported (supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz)
++ 3dGrayplot: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
+ Loading dataset ./errts.sub01.fanaticor+tlrc.HEAD
+ Number of voxels in mask = 62801
+ 3dGrayplot: Elapsed = 3.5 s
++ pbar name has known extension: jpg
++ My command:
@chauffeur_afni -ulay mask_epi_anat.sub01+tlrc.HEAD -olay mask_epi_anat.sub01+tlrc.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar gray_scale -func_range 3.29 -blowup 1 -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_sub01/media/qc_08_mot_grayplot.pbar.jpg -pbar_comm_range for normal distr, bounds of 0.001 prob tail -prefix __tmp_ZXCV_img -save_ftype JPEG -montx 1 -monty 1 -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
++ Using AFNI ver : AFNI_21.2.04
++ chauffeur ver : 6.26
------------------ start of optionizing ------------------
++ Found input file: mask_epi_anat.sub01+tlrc.HEAD
++ Found input file: mask_epi_anat.sub01+tlrc.HEAD
++ Using blowup factor: 1
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ./__tmp_chauf_YNZcvkMHJbF
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1.000000]
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_YNZcvkMHJbF/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_YNZcvkMHJbF/tmp_olay.nii
++ User-entered function range value value (3.29)
++ Dimensions (xyzt): 64 76 64 1
++ (initial) Slice spacing ordered (x,y,z) is: 64 76 64
++ 3dAutomask: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: Emperor Zhark
++ 3dAutobox: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Auto bbox: x=0..63 y=0..75 z=0..63
++ THD_zeropad: all pad values are zero - just copying dataset
++ 3dAutobox: output dataset = ./__tmp_chauf_YNZcvkMHJbF/ulay_box_0.nii
++ 3dmaskdump: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=./__tmp_chauf_YNZcvkMHJbF/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_XYZ_uh_XsyAJiXcm1HNaMN9hUQ argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.2.04 (Jul 28 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0: no scale factor
++ Computing output statistics
++ Output dataset /tmp/3dcalc_XYZ_uh_XsyAJiXcm1HNaMN9hUQ+tlrc.BRIK
++ 311296 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ How many coors? 3
++ Will have the ref box central coors : SET_DICOM_XYZ 1.5 19.5 19.5
++ Will have the ref box central gapord: 64 76 64
------------------- end of optionizing -------------------
-- trying to start Xvfb :535
[1] 121869
+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=9 mont=1x1:64:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=1x1:76:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=1x1:64:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 1 gray_scale -com PBAR_SAVEIM QC_sub01/media/qc_08_mot_grayplot.pbar.jpg dim=64x512H -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 3.29 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 1.5 19.5 19.5 -com SAVE_JPEG sagittalimage ./__tmp_ZXCV_img.sag blowup=1 -com SAVE_JPEG coronalimage ./__tmp_ZXCV_img.cor blowup=1 -com SAVE_JPEG axialimage ./__tmp_ZXCV_img.axi blowup=1 -com QUITT ./__tmp_chauf_YNZcvkMHJbF
+/gpfs/data/hoh23/jblujus/Redundancy/derivatives/AFNI_03_Proc_DerivCensBPOut/sub01/sub01.results/__tmp_chauf_YNZcvkMHJbF++ Writing palette image to QC_sub01/media/qc_08_mot_grayplot.pbar.jpg
++ Writing one 76x64 image to filter '/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > ./__tmp_ZXCV_img.sag.jpg'
++ Writing one 64x64 image to filter '/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > ./__tmp_ZXCV_img.cor.jpg'
++ Writing one 64x76 image to filter '/gpfs/runtime/opt/afni/21.2.04/cjpeg -quality 95 > ./__tmp_ZXCV_img.axi.jpg'
AFNI QUITTs!
+* Removing temporary image directory './__tmp_chauf_YNZcvkMHJbF'.
[1] + Done Xvfb :535 -screen 0 1024x768x24
++ DONE (good exit)
see: ./__tmp_ZXCV_img*
++ FOR: motion_sub01_enorm.1D: 1 arrays with 136 pts
++ FOR: outcount_rall.1D: 1 arrays with 136 pts
*+ No ylabels entered
*+ No input x-axis; making values based on length of data: [0..135]
++ Will scale each time series by censor_hline
++ Apply scale: 3.33333333333
++ Apply scale: 10.0
++ Will apply same y-axis range '[0.0, 3.0]' to all dsets
++ Plotting:
++ Plotting:
Traceback (most recent call last):
File "/gpfs/runtime/opt/afni/21.2.04/1dplot.py", line 65, in <module>
ok_fig = lpod.make_1dplot_figure(bigfig)
File "/gpfs/rt/7.2/opt/afni/21.2.04/afnipy/lib_plot_1D.py", line 495, in make_1dplot_figure
plt.savefig( bf.fname, dpi=bf.dpi, facecolor=bf.bkgd_color)
File "/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 695, in savefig
res = fig.savefig(*args, **kwargs)
File "/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/figure.py", line 2062, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py", line 2173, in print_figure
canvas = self._get_output_canvas(format)
File "/gpfs/runtime/opt/matplotlib/2.2.4/lib/python2.7/site-packages/matplotlib-2.2.4-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py", line 2105, in _get_output_canvas
.format(fmt, ", ".join(sorted(self.get_supported_filetypes()))))
ValueError: Format 'jpg' is not supported (supported formats: eps, pdf, pgf, png, ps, raw, rgba, svg, svgz)
djpeg: can't open __tmp_img_enorm.jpg
pnmcat: Error reading magic number from Netpbm image stream. Most often, this means your input file is empty.
Empty input file
+* Removing temporary files '__tmp_gluing*'
++ DONE! Image output:
QC_sub01/media/qc_08_mot_grayplot.jpg
rm: cannot remove \u2018__tmp_img_enorm.jpg\u2019: No such file or directory
afni_proc.py \
-subj_id sub01 -script proc.sub01 -scr_overwrite -out_dir sub01.results \
-blocks despike tshift align tlrc volreg blur mask scale \
regress \
-radial_correlate_blocks tcat volreg \
-copy_anat ${ss_dir}/anatSS.sub01.nii \
-anat_has_skull no \
-anat_follower anat_w_skull anat ${ss_dir}/anatU.sub01.nii \
-anat_follower_ROI aaseg anat ${fs_dir}/aparc.a2009s+aseg.nii.gz \
-anat_follower_ROI aeseg epi ${fs_dir}/aparc.a2009s+aseg.nii.gz \
-anat_follower_ROI FSvent epi ${fs_dir}/fs_ap_latvent.nii.gz \
-anat_follower_ROI FSWe epi ${fs_dir}/fs_ap_wm.nii.gz \
-anat_follower_erode FSvent FSWe \
-dsets ${raw_epi} \
-tcat_remove_first_trs 4 \
-tshift_opts_ts -tpattern altplus \
-align_opts_aea -cost lpc+ZZ -giant_move -check_flip \
-tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets ${ss_dir}/anatQQ.sub01.nii ${ss_dir}/anatQQ.sub01.aff12.1D \
${ss_dir}/anatQQ.sub01_WARP.nii \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_size 4 \
-mask_epi_anat yes \
-regress_motion_per_run \
-regress_ROI_PC FSvent 3 \
-regress_ROI_PC_per_run FSvent \
-regress_make_corr_vols aeseg FSvent \
-regress_anaticor_fast \
-regress_anaticor_label FSWe \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.1 \
-regress_bandpass 0.01 0.1 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_epits \
-regress_est_blur_errts \
-html_review_style pythonic
| Subject | Author | Posted |
|---|---|---|
|
jkblujus | September 29, 2021 06:25PM |
|
ptaylor | September 30, 2021 09:29AM |
