[Freesurfer] register data to the surface
Hi! I successfully run the preprocessing on some polarangle data (preproc-sess -sf seesid -surface self lhrh -fwhm 5). Now I would like to do the subtraction between some runs and then to visualize this subtraction on the surface (so without to analyze the data with Fourier analysis). Does anybody know how to do that? Thanks! Francesca ___ 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.
Re: [Freesurfer] register data to the surface
Hi Francesca, can you be more specific about what you want to do? If you just want to subtract the raw data between runs, you can use fscalc. doug francesca strappini wrote: > Hi! I successfully run the preprocessing on some polarangle data > (preproc-sess -sf seesid -surface self lhrh -fwhm 5). > Now I would like to do the subtraction between some runs and then to > visualize this subtraction on the surface (so without to analyze the > data with Fourier analysis). > Does anybody know how to do that? > > Thanks! > > Francesca > ___ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] register data to the surface
Sorry, I try to be more specific. I would like to be able to take the volume-to-surface transformation calculated on one set of functional data, and apply that transformation to another set of functional data (the subtraction) of the same subject. This will allow me to display arbitrary functional values on a surface. Thanks! Francesca ___ 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.
Re: [Freesurfer] register data to the surface
You can use bbregister to compute the transformation for each run based on the middle time point of that run (and assuming you've motion corrected the run), then use mri_vol2surf to resample any data set aligned with the middle time point to the subject's surface or the fsaverage surface. You can do that for each run separately, then use fscalc to compute the difference. doug francesca strappini wrote: > Sorry, I try to be more specific. > I would like to be able to take the volume-to-surface transformation > calculated on one set of functional data, and apply that > transformation to another set of functional data (the subtraction) of > the same subject. This will allow me to display arbitrary functional > values on a surface. > > Thanks! > > Francesca > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] register data to the surface
Thanks a lot! I tried the registration with bbregister but unfortunately when I checked the result the functional volume was very distant from the target. Could I tried something else to improve the registration? I typed: bbregister --s subject --mov name_file.nii --reg register.dat --init-fsl --bold Thanks again! Francesca ___ 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.
Re: [Freesurfer] register data to the surface
It was probably the initialization that failed. To test this, run fslregister (very similar command line to bbregister). If that does not look good, then it is an init problem. If these were acquired in the same session, then you can try using --init-header. If you have spm installed, you can try --init-spm. The spm solution requires that SPM be set up properly for this program, which is not always so easy. It also requires matlab. doug francesca strappini wrote: > Thanks a lot! > I tried the registration with bbregister but unfortunately when I > checked the result the functional volume was very distant from the > target. > Could I tried something else to improve the registration? > > I typed: > > bbregister --s subject --mov name_file.nii --reg register.dat > --init-fsl --bold > > > Thanks again! > > Francesca -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] register data to the surface
This is not the correct procedure. Try looking at the multi-modal integration tutorial on our web site. Basically you should not register the difference image. Instead, register the middle time point of the raw data of the fMRI to the anatomical. Motion correct the time series to the middle time point. When you analyze the data in whatever way you are using, analyze the motion corrected data. You can then use the registration computed from the raw data for anything derived from the motion corrected data. doug francesca strappini wrote: > Yes, It's a whole brain acquisition and the functional and the > anatomical data come from the same subject. > I try to explain all the story. I acquired 12 runs of polarangle per > subject in two different days. I have 3 conditions and 4 runs for > every condition. In each day the subjects did all the conditions (6 > runs per day). > I calculated a sort of subtraction between these conditions, > unfortunately it's not a simple subtraction and for this reason I > didn't use fscalc. What I tried to do is to register this subtraction > to the surface but the process failed probably because the result of > the subtraction is as very small activation only in the occipital > cortex (in fact the conditions are slightly different). > Do you think that is there something else that I can try? > > Thanks! > > > Francesca > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
