Estimate response #425
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Estimate response #425
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…ams set as in the paper.
Previously the calibrator assumed a homogeneous delta function field. This change considers that the FOD amplitude for different paths may change due to both the orientation and the position within the field, by assuming that the voxels adjacent to the calibration position have zero amplitude.
- Allow the user to set -number 0 or -maxnum 0, and the program will ignore the relevant criterion.
Should fix issue #385.
Much like the binary commands, the scripts will now print the relevant citation details at the end of the help page. This has been implemented in such a way that new scripts and new articles can be easily added. If a script contains relevant citations, and the script is run in normal or verbose mode, a note will be printed to the user at the commencement of the script reminding them of the fact. The scripts will now also print the full help page if there is an error in parsing the arguments and options, rather than the default brief error message.
as discussed in #397
These are mapped to Ctrl+/-, as discussed in #397
Clarify the expectations for a 5TT image, and how to add the pathology mask to the 5TT image.
Previously, wherever a progress bar was created, the programmer may or may not have added an ellipsis to the end of the message, and there may or may not have been a space after the ellipsis (which offsets the cursor). This commit removes this variability, and therefore makes the overall MRtrix terminal appearance more consistent, by handling the ellipsis display within the ProgressInfo class. If a functor is used to update the text, however, no ellipsis is displayed. Additionally, the ellipsis disappears once the relevant processing is completed. Closes #30.
The colour of ODFs when not colouring by direction is now handled using an explicit menu action in shview, and a colour button in mrview's ODF tool, rather than being a part of the lighting settings dock. Closes #408.
By default, the maximum number of streamline attempts is implicitly set to 100 times the number of desired streamlines. Alternatively, the user may set this maximum number of attempts explicitly. If tracking is terminated due to the implicit setting of this value, and the user has requested a particular number of streamlines and not received it, a warning will now be issued. Closes #367.
Global tractography
as discussed in #400. Not sure how 5ttgen ended up on this branch anyway - I have a feeling someone's been doing some cherry-picking from master...
Rename command option -tod to -fod, to be consistent with the terminology used in the journal paper. The distinction between both is mute in global tractography, and therefore simplified to users.
as discussed in #31.
This is the correct thing to do: https://gcc.gnu.org/onlinedocs/cpp/System-Headers.html It also kills quite a few warnings generated from system headers, including Qt and Eigen.
…digits as discussed in #420
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Sorry, wasn't supposed to be against |
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As discussed in #422. This is currently a very simple proof of concept script, just to get feedback on whether the approach is worth implementing properly. Feedback welcome...