Hmmm, OK. I ran the following in the Bootcamp data (AFNI_data6/FT_analysis/FT directory) OK, and got the attached image:
3dTqual -range -automask FT_epi_r1+orig | 1dplot -one -stdin -png NAME
However, if I ran without the extension:
3dTqual -range -automask FT_epi_r1 | 1dplot -one -stdin -png NAME
… then I got the error you are seeing:
*** Can't open dataset FT_epi_r1
** FATAL ERROR: Can't read from stdin!
So, whether your input is NIFTI or BRIK/HEAD format, can you try putting the more complete name: NAME.nii, NAME.nii.gz, NAME+orig, NAME+orig.HEAD, etc.?
Hmmm, I get the same bad behavior. I cannot produce a png file (even with Paul’s command). Maybe that means there is some shell program that is needed that I do not have installed.
Thank you both for trying and replicating the command!
So adding the complete name (NAME.nii, NAME.nii.gz, NAME+orig, NAME+orig.HEAD) was still giving the error, and running the brew install netpbm didn’t install the package for some reason, same thing with updating the binaries.
The command:
Will try the afni_system_check.py -check_all next. But update, the -jpg function works and produces an output! Thank you for the suggestion, will replace -png with -jpg in the script moving forward.
Your help is much appreciated!
Best,
RJ
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