Hi Doug, We don't want to do ROIs because we're trying to get a thickness map of the entire subcortical region of the brain.
Prior to trying this, we ran a within subjects paired analysis that gave us thickness maps of cortical surface. We ran these commands to look at the thickness maps in each of our two groups: mris_preproc --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/15_ActiveFolate_PreAndPostPAIRED_Structural/LH/lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED_Structural.fsgd --paired-diff mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED_Structural.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx cd /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/15_ActiveFolate_PreAndPostPAIRED_Structural/LH mri_glmfit --glmdir lh.paired-diff.sm05 --y lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/15_ActiveFolate_PreAndPostPAIRED2_Structural.fsgd osgm (and then the same for our second group) And then we ran these commands to get a thickness map for the interaction between the two groups: mris_preproc --target fsaverage1 --hemi lh --meas thickness --out /cluster/roffman/users/Stable5_PerRun/Analyses_Patients/22_ActiveFolateAndPlacebo_PreAndPostPAIRED_Structural/LH/lh.paired-diff.thickness.mgh --fsgd /cluster/roffman/users/fsgd/22_ActiveFolateAndPlacebo_PreAndPostPAIRED_Structural.fsgd paired-diff mri_surf2surf --s fsaverage1 --hemi lh --fwhm 5 --sval lh.paired-diff.thickness.mgh --tval lh.paired-diff.thickness.sm05.mgh mri_glmfit --glmdir lh.paired-diff.sm05 --y lh.paired-diff.thickness.sm05.mgh --fsgd /cluster/roffman/users/fsgd/22_ActiveFolateAndPlacebo_PreAndPostPAIRED2_Structural.fsgd --C /cluster/roffman/users/fsgd/Top_Minus_Bottom.mtx Basically what we're wondering is if there's a way to do the same type of paired within subjects analyses on the same data that will instead generate volume thickness maps of the subcortical brain. I hope this clarifies my question a bit better, and if anyone has any ideas that'd be great! Thanks, Alex > Hi Alex, do you want to do it on an ROI basis? If so, you can use > asegstats2table to create a table of your subjects at the two time > points, then import this table into SPSS. Or you can run the table > through mri_glmfit to do the paired-t analysis. > doug > > On 07/24/2012 01:56 PM, Alexandra Tanner wrote: >> Hi Doug, >> >> Yes, sorry about that! I realized after I'd sent the email to you that I >> should've sent the email to the freesurfer list as well. >> >> We were hoping to look at volume in subcortical regions of the brain -- >> basal ganglia, hippocampus, amygdala, etc. Do know if there are commands >> to do the within subjects paired analysis this way? And if so, what they >> are? >> >> Thanks so much! >> Alex >> >>> Hi Alexandra, what structure are you looking to analyze? Ie, the volume >>> of what? The volume of cortex? >>> doug >>> ps. In the future, please post such questions to the freesurfer list as >>> it gives others the opportunity to answer and to learn. thanks! >>> >>> On 07/23/2012 12:03 PM, Alexandra Tanner wrote: >>>> Hi Mr. Greve, >>>> >>>> My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain >>>> Genomics Lab. I had a question regarding conducting volume analyses. >>>> On >>>> the freesurfer wiki there are commands that show how to conduct Paired >>>> Analyses to look at average surface, and I was curious if it was >>>> possible >>>> to do a paired analysis looking at volume instead. >>>> Any information you have would be very helpful. >>>> >>>> Thanks so much! >>>> >>>> Best, >>>> >>>> Alexandra Tanner >>>> Clinical Research Coordinator >>>> Laboratory for Brain Genomics >>>> Division of Psychiatric Neuroimaging >>>> Massachusetts General Hospital >>>> 149 13th Street >>>> Charlestown, MA 02129 >>>> (p) 617.643.3215 >>>> >>>> >>> -- >>> 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 >>> >>> >>> >> > > -- > 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.
