diff --git a/docs/TUTORIAL.md b/docs/TUTORIAL.md index c759c98..f7d583e 100644 --- a/docs/TUTORIAL.md +++ b/docs/TUTORIAL.md @@ -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 @@ -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. + +