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#1301 changed BASIL input parameters #1360

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Merged
jan-petr merged 29 commits into from
Apr 14, 2023
Merged

#1301 changed BASIL input parameters #1360

jan-petr merged 29 commits into from
Apr 14, 2023

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@jan-petr jan-petr commented Mar 28, 2023

Linked issue

Close #1301

@jan-petr jan-petr self-assigned this Mar 28, 2023
@jan-petr jan-petr linked an issue Mar 28, 2023 that may be closed by this pull request
BASIL ATT quantification settings are wrong #1301
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@jan-petr jan-petr force-pushed the bug-#1301_BasilFix branch 2 times, most recently from fc5e9b7 to 5407e8c Compare March 28, 2023 15:56
MDijsselhof
MDijsselhof reviewed Mar 29, 2023
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MDijsselhof
MDijsselhof reviewed Mar 29, 2023
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MDijsselhof
MDijsselhof reviewed Mar 29, 2023
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MDijsselhof reviewed Mar 29, 2023
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MDijsselhof reviewed Mar 29, 2023
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MDijsselhof reviewed Mar 29, 2023
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MDijsselhof
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Answering most comments. But I still need to check units for ABV and the correct quantificaiton.

MDijsselhof
MDijsselhof reviewed Mar 29, 2023
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@jan-petr jan-petr requested a review from MDijsselhof March 30, 2023 15:51
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BeatrizPadrela commented Apr 7, 2023

BASIL is working perfectly, so it is running for multiPLD (ASL_2 for DEBBIE)

image

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BeatrizPadrela commented Apr 7, 2023

Okay, so between step 3 and step4 (where we do spatial regularization) the maps become weird, the FTISS output from FSL (used later on to obtain CBF.nii by dividing it by M0) becomes weird:

[step3]
WhatsApp Image 2023-04-07 at 11 47 32

[step4]
WhatsApp Image 2023-04-07 at 11 47 57

But this doesn't mean there's some kind of error, I think that all is working very well, maybe we just need to turn off the bSpai

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BeatrizPadrela commented Apr 11, 2023 •
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Okay, for fabber quantification, it was giving this error:
Screenshot 2023-04-11 at 13 37 39

So, comparing to an older branch (#927), I realised that the fabber command line should be as simple as 'fabber_asl -@ txt_path ' and then all of the options should be inside the txt, including the output path and the PWI input path as well. I've now added a new input to the xASL_sub_FSLOptions:
image

... so that we can have these two commands inside the txt file:
image

Additionally, since we don't need nothing else than this orange command line, we can define these cmdlineOptions (in green) only for non-Fabber quantification:
image

@jan-petr jan-petr removed the request for review from BeatrizPadrela April 14, 2023 07:36
jan-petr and others added 24 commits April 14, 2023 09:37
@jan-petr
#1301 Rename to xASL_quant_FSL
ba04ab6
@jan-petr
#1301 Merge FSL and FABBER calls
d6d58a6
@jan-petr
#1301 Define FSL i/o paths
2b8e002
@jan-petr
#1301 quant_FSL basic options
3410120
@jan-petr
#1301 Fix BASIL extras
c2cdfb3
@jan-petr
#1301 Fix Mathijs comments
4c2ade4
@jan-petr
#1301 Fix ABV scaling
42533fc
@jan-petr
#1301 Restructure BASIL options
06129cb
@jan-petr
#1301 xASL_quant_FSL: Clean future ideas
1604703
@jan-petr
#1301 Fix missing maps
c02faf0
@jan-petr
#1301 Restructure basic model parameters
23309d2
@jan-petr
#1301 xASL_quant_FSL: Reorganize basic parameters
806d71c
@jan-petr
#1301 Minor fix
2d5815e
@jan-petr
#1301 Merging FABBER and BASIL parameters
022cf30
@jan-petr
#1301 Restructure FABBER and BASIL
7eb5ea1
@MDijsselhof @jan-petr
#1301 minor change
ac8e39a
@MDijsselhof @jan-petr
#1301 removed code to keep PWI4D
94f748d
@jan-petr
#1301 Revert deleting Pop-PWI4D
a6a4fbd
@jan-petr
#1301 Change BASIL spatial defaults
8b161c3
@BeatrizPadrela @jan-petr
#1301 Correcting command line for fabber quantification
7088965
@jan-petr
#1301 Clean FSL options
e6ee68b
@jan-petr
#1301 Minor fix
b355e6d
@jan-petr
#1301 Enable BASIL options for multi-PLD
6b8f94c
@jan-petr
#1301 xASL_quant_FSL: Fix paths
be1deb8
@jan-petr jan-petr force-pushed the bug-#1301_BasilFix branch from 2f202a3 to be1deb8 Compare April 14, 2023 07:38
@jan-petr jan-petr merged commit be1deb8 into develop Apr 14, 2023
@jan-petr jan-petr deleted the bug-#1301_BasilFix branch April 14, 2023 07:39
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BASIL ATT quantification settings are wrong

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