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dsistudio autotrack recon not saving out all bundles #749
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In my experience, DSI Studio AutoTrack GQI does not always reconstruct all requested tracts with the default number of seeds or streamlines. This can be related to data quality or large anatomical differences (e.g. damaged ipsilesional CST post-stroke) from the young adults atlas used in DSI Studio. I would recommend trying to run AutoTrack in the DSI Studio GUI using the qsiprep preprocessed data for a few participants in your dataset and adjusting the tracking parameters. If you find a set of parameters that works for all your participants, these could be used for a custom reconstruction workflow in QSIPrep. Best of luck! |
@hamsiradhakrishnan can you confirm that there are trk files in those directories? And are there entries for them in the bundlesummaries.tsv? |
Yes there are .trk files and non-empty stat values in the *stat.txt files in the work directory- but the entries for the missing bundles in bundlestats.csv in the qsirecon-DSIStudio output directory has no metrics. The rows are still there, but it looks something like this: |
Are there any streamlines in the .trk files if you load them in DSI Studio or another .trk viewer (e.g. DIPY Horizon)? |
Summary
Not all segmented bundles are being saved out in the recon directory when using the dsi_studio_autotrack recon workflow.
Additional details
What were you trying to do and what actually happened?
I'm using the latest version of QSIprep (0.21.4) to run the dsi_studio_autotrack recon pipeline- and it looks like some of the bundles (CorpusCallosum, Cingulum, SLF, CST) aren't being saved out in the final output directory. Some of the missing ones do seem to be present in the work directory, but not in subsegments (i.e., just "CorpusCallosum" and not "CorpusCallosumForcepsMinor" etc), and they're not ported over to the main output directory. There are no errors thrown in the logs. The call from qsiprep is
I also checked whether it was a dsistudio bug and it seems like not:
https://groups.google.com/g/dsi-studio/c/zx4u739EWGc
Even more info:
The output log throws no error, and claims that it's trying to reconstruct all the bundles:
However, only the following output folders can be found in qsirecon-DSIstudio:
Contents of the dsistudio working directory *_recon_wf/autotrackgqi/actual_trk/) for your reference:
Thank you so much for your help!
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