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suggestion about deletion of latest command
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tashrifbillah committed May 27, 2020
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Expand Up @@ -1015,6 +1015,38 @@ they propagate to subsequent non FA TBSS (altogether or separate).
For `--study` branch, note that `template/template0.nii.gz` file may be created even if template creation fails midway.
So, before trying again, make sure to delete that or use `--force` flag.


(8) `log/commands.txt` stores all the command you attempt on `--outDir`. When nonFA TBSS is run separately,
the latest command is [parsed](https://github.com/pnlbwh/TBSS/blob/21f8bb116fae917d22c7e62a52101da4570bb933/lib/tbss_all#L205)
to figure out the following attributes that are same for all modalities:

```python
for i, entity in enumerate(lastArgs):
if entity=='--caselist':
args.caselist= lastArgs[i+1]
elif entity=='--space':
args.space= lastArgs[i+1]
elif entity=='--labelMap':
args.labelMap= lastArgs[i+1]
elif entity=='--lut':
args.lut= lastArgs[i+1]
elif entity=='--SKEL_THRESH':
args.SKEL_THRESH= lastArgs[i+1]
elif entity=='--SEARCH_RULE_MASK':
args.SEARCH_RULE_MASK= lastArgs[i+1]
elif entity=='--avg':
args.avg= True
elif entity=='--noFillHole':
args.noFillHole= True
elif entity=='--noAllSkeleton':
args.noAllSkeleton= True
elif entity=='--noHtml':
args.noHtml= True
```

If you have made a 'blatant' mistake in your attempt of nonFA TBSS, it might be useful to delete the last line
from `log/commands.txt` lest that line should become the reference command for future nonFA TBSS.


# Reference

Expand All @@ -1030,3 +1062,5 @@ Frontiers in Neuroinformatics, vol. 8, p. 8, Frontiers, 2014.

Billah, Tashrif; Bouix, Sylvain, Rathi, Yogesh; Various MRI Conversion Tools,
https://github.com/pnlbwh/conversion, 2019, DOI: 10.5281/zenodo.2584003.


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