hi doug i think i have actually already done what you suggest as my bold directory consists of all the retinotopy runs (in subdirs 001-010). this is the 'ls' of the bold directory:
001/ 003/ 005/ 007/ 009/ register.dat same-sess-reg.dat seq.info 002/ 004/ 006/ 008/ 010/ rtopy/ scripts/ i ran the motion correction from the study directory as: >mc-sess -sf sessid -df sesspar and it completed successfully. -so will that have aligned all the runs together? if so, what can explain the fact that the field sign map is not continuous when overlaid on the cortex and shows gaps in the blue/yellow colouring? thanks! jane In message <[EMAIL PROTECTED]> Doug Greve <[EMAIL PROTECTED]> writes: > > You can try putting all the runs into a single bold directory. The > motion correction will (do it's best to) align them. > > doug > > > > > > > Jane Aspell wrote: > > >Hi > > > >My question was asked last year by Tommi Raij (see email pasted below) but I > >couldn't find a reply to it in the archives. I am analysing retinotopy data > >that was collected over several sessions but I cannot see how to register > >scans from multiple sessions together, and to the subject's anatomical scan. > >Although Fs-Fast appears to combine the data from multiple sessions during > >the > >retinotopy analysis it only seems to be possible to use one registration > >file > >(register.dat) when overlaying the results onto the anatomical. I would have > >thought that registering scans from multiple sessions together would be a > >feature that many people would require. Is there anyway to do it? Tommi > >gives > >some possible methods in his email below. > >When I do try and overlay my data onto a surface I see 'gaps' in the > >blue/yellow colouring of the fieldsign map overlaid onto the cortical > >surface. > >I wonder if this could be due to the inaccuracy of the registration given > >that > >I only used the register.dat from the registration of the first session. > >hope that makes sense! > >i'd be grateful for any help with this! > > > >Jane > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
