ICA component images do not load in functional report

[danlurie]

MRIQC v. 0.9.2 (not running via Docker/Singularity, unfortunately).

Running with --ica produces a melodic_reportlet.svg image in the working directory...

...but the ICA plots don't load at all in the report page.

Here's the command-line call used for this run.

mriqc \
    --participant_label $SUB_ID \
    -m T1w bold \
    --n_procs 5 \
    --mem_gb 8 \
    --ica \
    --ants-nthreads 3\
    -w /home/despoB/dlurie/Projects/despolab_lesion/qc/work \
    --report-dir /home/despoB/dlurie/Projects/despolab_lesion/qc/report \
    --verbose-reports \
    /home/despoB/lesion/data/original/bids/ \
    /home/despoB/dlurie/Projects/despolab_lesion/qc/out \
    participant 

I've attached the HTML report page as a .zip. Let me know if there is any other info I can provide to help track down the cause.

sub-193_task-rest_acq-64px_run-02_bold.html.zip

[chrisgorgo]

That is bizzare. Was this run outside without a container? Do you have SVGO and CWEBP installed (they should be optional)?

On Tue, May 2, 2017 at 8:52 PM, Daniel Lurie [email protected] wrote:

MRIQC v. 0.9.2 (not running via Docker/Singularity, unfortunately).

Running with --ica produces a melodic_reportlet.svg image in the working directory...

[image: screenshot_5_2_17__20_50] https://cloud.githubusercontent.com/assets/1873103/25647681/03b431c6-2f79-11e7-813c-4e5954bea441.jpg

...but the ICA plots don't load at all in the report page.

[image: mriqc__individual_bold_report] https://cloud.githubusercontent.com/assets/1873103/25647608/353e6186-2f78-11e7-8fe6-cafd9c7ed11a.jpg

Here's the command-line call used for this run.

mriqc
--participant_label $SUB_ID
-m T1w bold
--n_procs 5
--mem_gb 8
--ica
--ants-nthreads 3
-w /home/despoB/dlurie/Projects/despolab_lesion/qc/work
--report-dir /home/despoB/dlurie/Projects/despolab_lesion/qc/report
--verbose-reports
/home/despoB/lesion/data/original/bids/
/home/despoB/dlurie/Projects/despolab_lesion/qc/out
participant

I've attached the HTML report page as a .zip. Let me know if there is any other info I can provide to help track down the cause.

sub-193_task-rest_acq-64px_run-02_bold.html.zip https://github.com/poldracklab/mriqc/files/972418/sub-193_task-rest_acq-64px_run-02_bold.html.zip

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[danlurie]

Run on a manual install. svgo and cwebp were not installed when I first encountered the issue, so I just installed them and then re-generated the reports, but the issue persists.

(Still working on getting Singularity running on our server.)

[danlurie]

Update: It seems like the ICA images are there, but something goes wrong when the browser tries to display them. If I scroll down to the ICA section of the report and refresh the page, the component images and plots appear very briefly (<500ms) when the page loads, and then disappear. It's hard to be sure, but during their brief appearance, it looks like the component images much larger than they should be (~5x larger). The plots look like they're the right size.

Not sure if this helps at all, and I haven't yet had a chance to try running the latest version of mriqc or running in a container, but I figured I'd report back just in case.

[stjep]

I have the same issue with the ICA output when running the current version of mriqc (0.9.6) inside a container, if the .html is moved away from the reports directory. All other images load fine.

[stjep]

The ICA plots seem to render fine for me only if I open the individual reports in Chrome on Windows and Ubuntu. They don't show running Chrome on Mac OS or in Firefox on any OS.

[chrisgorgo]

That's useful info. We might need to consider a different codec for raster file compression.

Which version of chrome does it fail on Mac?

On Aug 23, 2017 11:10 AM, "Dan Stjepanović" [email protected] wrote:

The ICA plots seem to render fine for me only if I open the individual reports in Chrome on Windows and Ubuntu. They don't show running Chrome on Mac OS or in Firefox on any OS.

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[stjep]

I just tried Mac OS again and it works fine on this version of Chrome (it's auto-updating, so not sure if this is a change or I was mis-remembering). No other browsers work. Same deal on Windows, the most recent version of Chrome is fine but IE and Firefox don't work.

Might be that Chrome works always but other rendering engines trip up with the ICA output.

[chrisgorgo]

Yes - this makes sense considering we use WEBP.

On Thu, Aug 24, 2017 at 4:10 AM, Dan Stjepanović [email protected] wrote:

I just tried Mac OS again and it works fine on this version of Chrome, but no other browser. Same deal on Windows, the most recent version of Chrome is fine but IE and Firefox don't work.

Might be that Chrome works always but other rendering engines trip up with the ICA output.

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