3D FLASH T1w slope about brkraw

[egarza]

Great! thanks again

[gdevenyi]

I think if its not already there --ignore-offset should go with this.

[gdevenyi]

I think we should try to implement the spec as-is, even if we've never seen values for some things. This kind of correction is important for quantitative acquisions.

I think rather, I'd like three options
--ignore-slope
--ignore-offset
--ignore-rescaling

Where --ignore-rescaling disables both.

[dvm-shlee]

@gdevenyi It makes sense to me. I will implement those three options on the next update. Thank you for the suggestion!

[dvm-shlee]

@egarza It seems what you are asking is the way to remove data slope.

I just add the option --ignore_slope
just add it to your command. such as

pip install --upgrade git+https://github.com/brkraw/bruker
then
brkraw gui --ignore_slope
or
brkraw tonii --ignore_slope <raw data path>

Hope this can solve your issue.

[dvm-shlee]

@egarza Since I had an additional update, you can use this function from 0.3.3rc8

[dvm-shlee]

Could you close this issue if you don't have any problem with the new option? Thank you!

[dvm-shlee]

@gdevenyi I've already made the changes but if the term --ignore-offset is more suitable, I will update it for 0.3.3 release version.

Thank you for your comment!

[gdevenyi]

sorry, thats not what I mean. The bruker specifies a scaling as an offset + a slope to remap the on-disk data into a different data range. If we have an --ignore-slope parameter, we should also have an --ignore-offset parameter

[gdevenyi]

See https://github.com/SebastianoF/bruker2nifti/blob/6cf20451a135e9d001a39ad2bd6efc81c253c609/bruker2nifti/_cores.py for example

[dvm-shlee]

@gdevenyi I got what your point now. The reason I only handled this is before I haven't seen any offset value assigned on Bruker data so far. And these two would be better to go together since it's just for correcting the value into the data type (16bit) by combining two (slope and offset).

So if there is any good idea to cover both (for example --ignore-correction), it would be more suitable I think?

[egarza]

Thank you, that would help a lot. This is a big issue specially for volumetric analysis.

[dvm-shlee]

@gdevenyi @egarza 0.3.3 released version will have those functions.
--ignore-rescale, or --ignore-slope and --ignore-offset
I will close this issue, but please let me know if other issues occurred related to this change.