Back to the main page.
Bug 3171 - spm12 not installed
| Status | CLOSED FIXED |
| Reported | 2016-08-16 19:59:00 +0200 |
| Modified | 2019-08-10 12:40:32 +0200 |
| Product: | FieldTrip |
| Component: | core |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Windows |
| Importance: | P5 normal |
| Assigned to: | Arjen Stolk |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: | http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=3175 |
Diego Lozano Soldevilla - 2016-08-16 19:59:53 +0200
Doing the ECoG tutorial I encountered that spm12 is not installed. The tutorial suggests that at some point spm12 was integrated in fieldtrip: http://www.fieldtriptoolbox.org/tutorial/human_ecog#processing_of_anatomical_data % co-register the CT to the MRI cfg = []; cfg.method = 'spm'; cfg.spmversion = 'spm12'; cfg.viewresult = 'yes'; % view realignment result ct = ft_volumerealign(cfg, ct, mri); By the way, ft_volumerealign requires the desired head coordinate system in cfg.coordsys which makes the third input cofusing. For example, if ct is spm and mri tal, this combination does not work: cfg = []; cfg.method = 'spm'; cfg.spmversion = 'spm8'; cfg.viewresult = 'yes'; % view realignment result cfg.coordsys = 'tal'; ct = ft_volumerealign(cfg, ct, mri); but this one works: ct = ft_volumerealign(cfg, mri,ct);
Arjen Stolk - 2016-08-16 20:11:19 +0200
Lorenzo! Nice to see you're using/trying this freshly made pipeline. "The tutorial suggests that at some point spm12 was integrated in fieldtrip" > Actually, it says "We then fuse the CT with the MRI, which are now both described in the same coordinate space, using SPM12. Note: currently (February, 2016) this requires downloading and adding SPM12 to the MATLAB path." The integration of spm12 code is a separate bug/issue, file elsewhere. Of course, this tutorial would benefit from having it integrated. The "cfg.coordsys = 'tal';" part seems to be a requirement introduced recently. In sum, this should work (ensure you have spm12): % co-register the CT to the MRI cfg = []; cfg.method = 'spm'; cfg.spmversion = 'spm12'; cfg.viewresult = 'yes'; % view realignment result cfg.coordsys = 'tal'; ct = ft_volumerealign(cfg, ct, mri);
Arjen Stolk - 2016-08-16 20:12:15 +0200
considering it fixed - the tutorial is still work in progress and spm12 is explicitly stated to be downloaded
Arjen Stolk - 2017-01-25 18:56:05 +0100
Hey Lorenzo, Spm12 is no longer needed on the path as of today. A mini version has been added to the external folder. Ciao!
Diego Lozano Soldevilla - 2017-01-25 19:02:45 +0100
(In reply to Arjen Stolk from comment #3) thank you Gianni! Gratings from Barcelona
Arjen Stolk - 2017-01-25 19:08:33 +0100
Thanks, pal. p.s. we are writing up an intracranial data analysis guideline. Will send you a copy when finished, if interested.
Diego Lozano Soldevilla - 2017-01-25 19:13:29 +0100
(In reply to Arjen Stolk from comment #5) Sure! Thank you very much! Best wishes ;)
Robert Oostenveld - 2019-08-10 12:34:22 +0200
This closes a whole series of bugs that have been resolved (either FIXED/WONTFIX/INVALID) for quite some time. If you disagree, please file a new issue on https://github.com/fieldtrip/fieldtrip/issues.