Hi David, please post to the list ... answers below
On 11/13/2017 01:48 PM, David Beeler wrote: > Hi Doug, really helpful thanks! > So if I want all the motion corrected functional data across runs to be > aligned with a downsampled version of my anatomical, is it better to run > preproc-sess with -per-session or should I do -per-run and then map each > functional to anatomical without resampling using: > mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg \ --o > fmcpr.new.vox2ras.nii.gz --no-resample > and then run selxavg3-sess on the fmcpr.new.vox2ras.nii.gz in each run > folder? I've heard motion correction with -per-run is better but I > don't understand why... can you explain? Oh, if you want to do it that way, then you would not use the --no-resample (that just changes the geometry in the header). per-run registers and resamples to the middle time point, meaning that there is generally less interpolation. You should add --fstarg orig.mgz This will have it sample into the 1mm orig space. This will create a very largefile. If you want to downsample the anat, you can run mri_convert --downsample 2 2 2 orig.mgz orig.ds2.mgz and then --fstarg orig.ds2.mgz > Further, I don't get how selxavg3-sess chooses its input. If I first > do preproc-sess with -per-run, do my transformation to downsampled > anatomical space (as described above), and then run selxavg3-sess with > the -no-preproc flag, what volume will selxavg3-sess use by default? I > assume it will search the run folders for fmcpr.nii.gz (because using > f.nii.gz would defeat the purpose of doing motion correction in the > first place), but is there a flag I could use to tell selxavg3-sess to > use my transformed fmcpr.new.vox2ras.nii.gz as input instead? Should I > just rename fmcpr.new.vox2ras.nii.gz to fmcpr.nii.gz and then > selxavg3-sess will take it automatically? When you create your analysis, you should put -funcstem fmcpr.new.vox2ras > Thanks again! > David > PS is this the correct way to respond to threads on this mailing list > so that the thread is maintained? > On 11/8/17 5:57 PM, David Beeler wrote: > > Hi freesurfer people, > > I'm trying to understand preprocessing a little better, especially > registration of functional data to anatomical space. I am > currently running everything in the volume, doing motion > correction per-run and then pooling all the runs in the session > together for the first level analysis.As far as I can tell, > running preproc-sess with -per-run takes the rawfunctional data > (f.nii.gz), pulls out the middle timepoint and calls it > template.nii.gz, bbregisters func to anat and creates a > register.dof6.lta file in each of the functional run folders, > transforms the aparc+aseg from the subject's mri folder and > binarizes it into a brainmask (brain.nii.gz), and runs mc-afni > using f.nii.gz as the input vol and template.nii.gz as the > template vol to create the motion corrected volume (fmcpr.nii.gz). > Is this correct? > > yes > > Then when I run selxavg3-sess it somehow mri_converts an > intermediary motion corrected volume from the mc-afni command > above (eg <run#>/tmp.mc-afni2.20097/outvol.nii.gz) into an > fmc.nii.gz file in each run folder. Are these fmc.nii.gz's > supposed to be coregistered between runs? (i.e. if the subject > moved a bunch between two of the runs, would those two volumes be > aligned at all?). How do these files work? > > Not with -per-run. per-run was designed with the idea that you would > beresampling to some common space (eg, surface or mni305 or cvs), and > then running sexlavg3-sess on that data. If you want all the > fmc.nii.gz to be in the same space, then use -per-session. > > At the end I have an analysis directory with my betas, sigmaps, > etc. What functional volume is everything registered to? Is the > transform between this functional volume and anatomical space the > register.dof6.lta file located in the session directory? > > Thanks for bearing with me! > -David > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. 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