Hi Doug, I determined that SPM does create a mean volume during motion correction. My question now is how do I incorporate several functional runs (each with a different "template" mean volume from motion correction) into a registration with the anatomical. I have statistical activation maps generated based on 4 functional runs, so eventually I would like to overlay this on the anatomical volume in Freesurfer and extract information from ROIs. If I were to use one of the "template" mean volumes (say from function run 1) to conduct the registration then I would be assuming that the subject did not move across the rest of the runs.
Your thoughts are greatly appreciated. Vanessa Palzes Research Assistant Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155 -----Original Message----- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 13, 2011 1:12 PM To: Palzes, Vanessa Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bert functional data set Hi Vanessa, you have to use some sort of template volume. I'm not sure what SPM uses as the motion correction template. It's probably the middle time point or the average across all time points. But it is using something. You need to find out what it is and use that. doug Palzes, Vanessa wrote: > Hi Doug, > > Thanks for your help. I also have a question regarding registering > multiple functional scans to the anatomical so that way I can overlay > activation T maps generated from SPM and extract ROI information. This > tutorial uses a motion correction template.nii file generated from > FS-FAST, and am wondering if there is any output (e.g. the realignment > parameters txt file) from SPM that can be used instead of a motion > correction template file. > > Thanks, > > Vanessa Palzes > Research Assistant > Brain Imaging & EEG Lab > San Francisco VA Medical Center > 4150 Clement Street > San Francisco, CA 94121 > Tel: 415-221-4810 ext. 6155 > > > -----Original Message----- > From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: Thursday, April 07, 2011 12:40 PM > To: Palzes, Vanessa > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] bert functional data set > > That tutorial is out of date. Try using the multimodal below. > > doug > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal > > Palzes, Vanessa wrote: > >> Hi, >> >> I'm trying to go through this tutorial: >> >> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AutomaticRegistratio > >> nSpm >> >> I have already downloaded/unpacked the >> buckner_data-tutorial-subjs.tar.gz, and also set up the correct >> SUBJECTS_DIR as: >> setenv TUTORIAL_DATA /Applications/freesurfer/subjects >> cd $TUTORIAL_DATA/buckner_data/tutorial_subjs >> setenv SUBJECTS_DIR ${PWD} >> >> But, when I try to run the following command, it tells me it cannot >> > find > >> bert-brf... >> >> spmregister --s bert-brf --mov f001.img --reg register.dat >> >> Any suggestions on how I can locate and use this tutorial data? >> >> Vanessa Palzes >> Research Assistant >> Brain Imaging & EEG Lab >> San Francisco VA Medical Center >> 4150 Clement Street >> San Francisco, CA 94121 >> Tel: 415-221-4810 ext. 6155 >> >> _______________________________________________ >> 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 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
