You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
There is a problem getting the exact bundles specified in the recon spec under track_id when using autotrack.
Specifically it is not possible to get results for 'parent bundles', i.e. the overarching bundle for bundles made up of sub bundles.
Example below for the CorpusCallosum.
Additional details
QSIRecon version: 0.23.1
Singularity version: apptainer version 1.1.8-1.el7
What were you trying to do?
Get autotrack results for the bundle Commissure_CorpusCallosum.
What did you expect to happen?
The expected outcome would have been a .tck.gz file for the Commissure_CorpusCallosum bundle and a row in the bundle stats .csv file for this bundle in the qsirecon output directory.
What actually happened?
There is no .tck.gz file in the output directory. In the bundle stats file there is no information on the Commissure_CorpusCallosum. Instead, there are four empty rows, one for each of the Corpus Callosum sub bundles.
In DSI Studio, by default the parent bundle will be reconstructed when only specifying a part of the bundle name. To track sub bundles these need to be named explicitly, i.e., Commissure_CorpusCallosum_ForcepsMinor .
The problem seems to be that qsirecon iterates through this list of bundles: https://github.com/frankyeh/data-atlas/blob/main/ICBM152_adult/ICBM152_adult.tt.gz.txt to extract the bundles to track from the given track_ids. This list, however, doesn't contain the parent bundles. For the CC it only contains the four sub bundles. So qsiprep will get the four sub bundles from the list but DSI Studio will only track the parent bundle. qsirecon will then look for the sub bundles to copy to the output directory and the stats file but there are only results for the parent bundle.
Summary
There is a problem getting the exact bundles specified in the recon spec under
track_id
when using autotrack.Specifically it is not possible to get results for 'parent bundles', i.e. the overarching bundle for bundles made up of sub bundles.
Example below for the
CorpusCallosum
.Additional details
What were you trying to do?
Get autotrack results for the bundle
Commissure_CorpusCallosum
.What did you expect to happen?
The expected outcome would have been a
.tck.gz
file for theCommissure_CorpusCallosum
bundle and a row in the bundle stats.csv
file for this bundle in the qsirecon output directory.What actually happened?
There is no
.tck.gz
file in the output directory. In the bundle stats file there is no information on theCommissure_CorpusCallosum
. Instead, there are four empty rows, one for each of the Corpus Callosum sub bundles.Reproducing the bug
This is the recon spec I used:
I get the same issue when setting
track_id: Commissure_CorpusCallosum
And this is the qsirecon call
The text was updated successfully, but these errors were encountered: