fieldtrip / fieldtrip/website

use ft_transform_geometry instead of ft_warp_apply in the documentation

Open
#907 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
44
Forks
107
PR merge metrics
No merged PRs in 30d

Description

with https://github.com/fieldtrip/fieldtrip/commit/b385d992d3be427286b1572fa20ef1fe7ff29cd5 I updated ft_transform_geometry, since I was using it in the OPM helmet tutorial, but mixed with ft_warp_apply. From now on it is possible to use ft_transform_geometry most of the time, and that should be promoted in the tutorials.

I suggest not to change it immediately, since people will not have the latest version of the fieldtrip code on their computer yet.

I found the following cases in the online documentation, some of these can be updated in the future (although not the ones using "sn2individual").

```
mac084> find . -name \*.md -exec grep -H ft_warp_apply {} \;
./workshop/chieti2015/virtualchannel.md: lh_seed_pos = ft_warp_apply(individual_mri.transform, lh_seed_vox, 'homogeneous');
./workshop/chieti2015/virtualchannel.md: rh_seed_pos = ft_warp_apply(individual_mri.transform, rh_seed_vox, 'homogeneous');
./workshop/meg-uk-2015/fieldtrip-beamformer-demo.md: vox_fids = ft_warp_apply(inv(mri_orig.transform), mri_fids);
./tutorial/connectivity/connectivity_aef.md:Next, we normalise the individual MRI to derive parameters allowing to convert the mni- coordinates of the desired parcels into individual coordinates. For this we use **[ft_warp_apply](/reference/utilities/ft_warp_apply)**.
./tutorial/connectivity/connectivity_aef.md: posback=ft_warp_apply(norm.params,posCML,'sn2individual');
./tutorial/connectivity/connectivity_aef.md: btiposCML= ft_warp_apply(pinv(norm.initial),posback); % xyz positions in individual coordinates
./tutorial/connectivity/connectivity_aef.md: posback=ft_warp_apply(norm.params,posHGL,'sn2individual');
./tutorial/connectivity/connectivity_aef.md: btiposHGL= ft_warp_apply(pinv(norm.initial),posback); % xyz positions in individual coordinates
./tutorial/connectivity/connectivity_aef.md: posback=ft_warp_apply(norm.params,posHGR,'sn2individual');
./tutorial/connectivity/connectivity_aef.md: btiposHGR= ft_warp_apply(pinv(norm.initial),posback); % xyz positions in individual coordinates
./example/source/electrodes2bem.md: head_Nas = ft_warp_apply(vox2head, vox_Nas, 'homogenous'); % nasion
./example/source/electrodes2bem.md: head_Lpa = ft_warp_apply(vox2head, vox_Lpa, 'homogenous'); % Left preauricular
./example/source/electrodes2bem.md: head_Rpa = ft_warp_apply(vox2head, vox_Rpa, 'homogenous'); % Right preauricular
./getting_started/othersoftware/bioimage.md:Once the CT and MRI are coregistered, warp the electrode coordinates in elec (corresponding to the raw CT coordinate system) to the fused CT-MRI head space using **[ft_warp_apply](/reference/utilities/ft_warp_apply)**.
./getting_started/othersoftware/bioimage.md: elec_vox.elecpos = ft_warp_apply(inv(ct. transform), elec.elecpos);
./getting_started/othersoftware/bioimage.md: elec_acpc_f.elecpos = ft_warp_apply(ct_acpc_f.transform, elec_vox.elecpos);
./getting_started/meg/ricoh.md: hpi_vox = ft_warp_apply(inv(mri.transform), hpi_mri);
./getting_started/meg/ricoh.md: fid_mri = ft_warp_apply(mri.transform, fid_vox, 'homogeneous');
./getting_started/meg/ricoh.md: fid_pos = ft_warp_apply(meg2head, fid_pos, 'homogeneous');
./getting_started/meg/ricoh.md: fid_mri = ft_warp_apply(mri_coreg.transform, fid_vox, 'homogeneous');
./getting_started/meg/ricoh.md: hpi_mri = ft_warp_apply(mri_coreg.transform, hpi_vox, 'homogeneous');
```

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.