Export of group-level tables for aparc- and aseg-stats #26
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run.py
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| if os.path.isdir(os.path.join(output_dir, "sub-" + s)): | ||
| subjects.append("sub-" + s) | ||
| else: | ||
| warn("No freesurfer subject found for %s in %s" % (s, output_dir)) |
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Shouldn't this be an error?
run.py
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| # create subcortical stats | ||
| table_file = os.path.join(table_dir, "aseg.tsv") | ||
| if os.path.isfile(table_file): | ||
| warn("Table file exists, delete if you want to recompute it. %s" % table_file) |
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shouldn't recomputing be the default?
run.py
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| '(in parallel) using the same output_dir.', | ||
| choices=['participant', 'group']) | ||
| '(in parallel) using the same output_dir. ' | ||
| '"goup1" creates study specific group template. ' |
| # make freesurfer python scripts python3 ready | ||
| RUN 2to3-3.4 -w $FREESURFER_HOME/bin/aparcstats2table | ||
| RUN 2to3-3.4 -w $FREESURFER_HOME/bin/asegstats2table | ||
| RUN 2to3-3.4 -w $FREESURFER_HOME/bin/*.py |
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the other option would be to install python2. is that you preference?
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The only problem of this option is that it breaks the possibility to run the script outside of docker.
People without root privileges cannot run docker so it is a problem for them.
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Why would you want to run python scripts from inside the container using python interpreter from outside the container (host). How are you using this App without Docker? Are you using Singularity?
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I don't know if it is intended for but I just run the app by calling run.py from a server with freesurfer installed.
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Oh I see. It's intended to be run via Docker or Singualrity. The latter works on clusters/hpc without root. You should check it out: http://singularity.lbl.gov/ http://bids-apps.neuroimaging.io/tutorial/
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OK but my cluster does not have singularity installed and if I install it myself with my user privileges I get this error when I try to execute the image:
-bash-4.1$ ./bids_example-2016-10-27-709845fcdcd0.img
ERROR : Singularity must be executed in privileged mode to use images
ABORT : Retval = 255
Anyway it is not a big problem for me because I can easily modify this part of the script myself since everything else is working fine without the need to be in a container.
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I recommend contacting your admins and asking them to install singularity system wide. It will make both of your life's easier!
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Nope. If this works I'm happy!
…On Thu, Feb 9, 2017 at 10:34 AM, Franz Liem ***@***.***> wrote:
***@***.**** commented on this pull request.
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In Dockerfile <#26>:
> @@ -60,6 +60,11 @@ ENV PATH /opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:
ENV PYTHONPATH=""
RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
+# make freesurfer python scripts python3 ready
+RUN 2to3-3.4 -w $FREESURFER_HOME/bin/aparcstats2table
+RUN 2to3-3.4 -w $FREESURFER_HOME/bin/asegstats2table
+RUN 2to3-3.4 -w $FREESURFER_HOME/bin/*.py
the other option would be to install python2. is that you preference?
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Is there anything else I can do here or on #24? Could you otherwise please create a new release? Thanks. |
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I'm merging this - after tests pass on master I will make a new release. |
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Thanks |
My proposition for #19.
groupis renamedgroup1group200_group2_stats_tablesfolder inoutput_dir