yes and yes
On 12/07/2017 02:23 PM, Taylor, Johnmark wrote: > Thanks once again for all the help on this. I am running the GLM in > native space, typically so that I can get the beta values to use in an > MVPA analysis. So it sounds like if you specify per-run > motion-correction and registration, and don't tell it to resample to > anything (e.g., the MNI brain or the surface), then there's no > guarantee that the voxels will properly line up if you want to do, for > instance, a single-subject GLM in the subject's native space? So in > this case, per-session motion correction would be better so that all > the functional volumes in the session are registered properly? > > > > Thank you, this is very helpful! A few quick followup questions: > > > > 1) If you don't specifically tell preproc-sess what space to resample > > too (e.g., by using the "-surface" or "-mni305" flags), does it > > automatically resample to the subject's anatomical volume, then? > I don't think it will do anything if you don't specify > > > > 2) If fmc.nii.gz is already registered to the subject's volume, then > > how come a registration file has to be specified when visualizing GLM > > results using tksurfer? If fmc.nii.gz is already resampled to > > anatomical space, then surely any GLM contrasts should be as well, no? > fmc is not registered to the anatomical, it is registered to the > template. The template is registered to the anat through the > registration file. The data are still in the native functional space. > > > > 3) If per-run motion correction and registration is specified in > > pre-proc sess, then there will be a different functional-->structural > > transformation for each run, correct? > Correct > > If this is the case, then when visualizing session-wide GLM results > > using tksurfer, which registration file should be specified when > > loading up the overlay, since there'll be a different registration > > file for each run? > In what space are you doing the GLM? Usually, the raw data are resampled > onto the surface (eg, fmc.fsaverage.lh.sm05.nii.gz), and the GLM is done > in this spae.so no registration is needed. > > > > Apologies for these (probably basic) questions, I just want to make > > sure I am crystal-clear on what preproc-sess is doing. > > > > Cheers, and many thanks, > > > > JohnMark > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
