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edickie / ciftify

The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets
https://edickie.github.io/ciftify/
MIT License
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ciftify_PINT_vertices command not found #135

Closed renxili closed 4 years ago

renxili commented 4 years ago

Hi all:

I was trying to run the PINT on one of our subject but my bash could not find the command "ciftify_PINT_vertices". I have checked other commands like "cifti_vis_PINT" and they works fine. I have checked the /Users/renxili/opt/anaconda3/lib/python3.7/site-packages/bin and I can find ciftify_PINT_vertices.py and its executable file. Do you have any suggestions on what might go wrong? Many thanks!

edickie commented 4 years ago

sorry, I'm stumped.. cifti_vis_PINT and ciftify_PINT_vertices are installed the same way so I have no idea why one would work and not the other..

On Mon, May 18, 2020 at 10:48 PM renxili notifications@github.com wrote:

Hi all:

I was trying to run the PINT on one of our subject but my bash could not find the command "ciftify_PINT_vertices". I have checked other commands like "cifti_vis_PINT" and they works fine. I have checked the /Users/renxili/opt/anaconda3/lib/python3.7/site-packages/bin and I can find ciftify_PINT_vertices.py and its executable file. Do you have any suggestions on what might go wrong? Many thanks!

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renxili commented 4 years ago

That is exactly what I was thinking and confused about. It there any way we can re-install the ciftify package?

renxili commented 4 years ago

Okay, I re-installed ciftify and it now works. Thanks!

renxili commented 4 years ago

Hi: I have a follow-up problem for the PINT. I tried ciftify_PINT_vertices on one of the example subject but it always gives me an error of access the file while I have already set all folders and files to Read&Write in Finder. Would you mind take a look of what might go wrong?

(base) Renxis-Mac-mini:ciftify_demo_01 renxili$ ciftify_PINT_vertices --pcorr \${CIFTIFY_WORKDIR}/sub-50005/MNINonLinear/clean.dtseries.nii \${CIFTIFY_WORKDIR}/sub-50005/MNINonLinear/fsaverage_LR32k/sub-50005.L.midthickness.32k_fs_LR.surf.gii \${CIFTIFY_WORKDIR}/sub-50005/MNINonLinear/fsaverage_LR32k/sub-50005.R.midthickness.32k_fs_LR.surf.gii /Yeo7_2011_80verts.csv /sub-50005_task-rest Traceback (most recent call last): File "/Users/renxili/opt/anaconda3/bin/ciftify_PINT_vertices", line 10, in sys.exit(main()) File "/Users/renxili/opt/anaconda3/lib/python3.7/site-packages/ciftify/bin/ciftify_PINT_vertices.py", line 517, in main fh = logging.FileHandler('{}_pint.log'.format(output_prefix)) File "/Users/renxili/opt/anaconda3/lib/python3.7/logging/init.py", line 1087, in init StreamHandler.init(self, self._open()) File "/Users/renxili/opt/anaconda3/lib/python3.7/logging/init.py", line 1116, in _open return open(self.baseFilename, self.mode, encoding=self.encoding) OSError: [Errno 30] Read-only file system: '/sub-50005_task-rest_pint.log'