# Transform stc from head to MRI coordinate system? **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [May 28, 2018, 9:42pm UTC](https://mne.discourse.group/t/transform-stc-from-head-to-mri-coordinate-system/1533 "2018-05-28T21:42:10Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 28, 2018, 9:42pm UTC](https://mne.discourse.group/t/transform-stc-from-head-to-mri-coordinate-system/1533/1 "2018-05-28T21:42:10Z")
External Email - Use Caution Hi, I would like my volumetric source estimate to be in MRI coordinates, is there a way to easily transform my stc, before I save it into nifti? Thank you for any advice! Best, Lori ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 29, 2018, 4:12pm UTC](https://mne.discourse.group/t/transform-stc-from-head-to-mri-coordinate-system/1533/2 "2018-05-29T16:12:44Z")
External Email - Use Caution I think that if you constructed your volume source space with the `mri` argument and `add_interpolator=True`, then you should be able to do `stc.save_as_volume(...)` or `as_volume` that will already properly be in the same MRI coordinates as the `mri` you originally supplied. Does that help? Eric ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 29, 2018, 7:45pm UTC](https://mne.discourse.group/t/transform-stc-from-head-to-mri-coordinate-system/1533/3 "2018-05-29T19:45:32Z")
External Email - Use Caution Thanks Eric! I will give it a try. Best, Lori ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 30, 2018, 9:15pm UTC](https://mne.discourse.group/t/transform-stc-from-head-to-mri-coordinate-system/1533/4 "2018-05-30T21:15:08Z")
External Email - Use Caution Unfortunately, it seems to revert back to head coordinates at the fwd step. Any other possibilities? Thanks, Lori ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [May 30, 2018, 9:56pm UTC](https://mne.discourse.group/t/transform-stc-from-head-to-mri-coordinate-system/1533/5 "2018-05-30T21:56:56Z")
External Email - Use Caution Hi Lori, Are you definitely using the volume source space to compute the forward solution and inverse operator? There's not a separate '\_volume\_' function for the forward solution or inverse inverse operator, so if you're also setting up the surface models in the same script it would be very easy to inadvertently use the surface model or even overwrite the volume output files (speaking from experience...). Here's what mine currently looks like: head = setup\_volume\_source\_space(subject, mri=fname\_t1, bem=fname\_bem, mindist=mindist,                          subjects\_dir=subjects\_dir, add\_interpolator=True) mne.write\_source\_spaces(fname\_volsrc, head, overwrite=True) forward = mne.make\_forward\_solution(fname\_raw, fname\_trans, head, fname\_bem,                     meg=True, eeg=False, mindist=mindist,                     n\_jobs=8) mne.write\_forward\_solution(fname\_volfwd, forward, overwrite=True) inverse\_operator = make\_inverse\_operator(raw.info, forward, noise\_cov, loose=1, depth=None, fixed=False) write\_inverse\_operator(fname\_volinv, inverse\_operator, verbose=True) Jon