Hi Susan, ok, I see what you are doing now. Let's do it this way: 1. First transfer your label to the volume: mri_label2vol --temp example_func.nii --reg anat2exf.register.dat --proj 0 1 .1 --hemi lh --label lh.your.label --o yourlabel.func.nii
2. Then run segstats: mri_segstats --i cope2.nii --seg yourlabel.func.nii --mask zstat1.nii --maskthresh 2 --masksign abs --o sum.dat The cope and the zstat are now volumes. doug On 11/26/12 8:26 PM, Susan Alice McLaughlin wrote: > Hi Doug, > > Thanks for the quick answer. Sorry to be dense, but does this need > somewhere to include registration matrix, anat2exf.register.dat, to > register to the subject's surface? > > And at this point in the analysis, the feat folder does not include > copes and zstats separated out by hemisphere, although there are > zstat[#].surf.lh.w and .rh.w files in the main feat folder. > > Again, sorry for my limited understanding of file structure. > > Susan > > > On Mon, 26 Nov 2012, Douglas N Greve wrote: > >> Hi Susan, you can't use func2roi-sess. You'll have to put together some >> commands, but it should not be too hard, something like >> >> mri_segstats --i lh.cope2.nii --slabel subjectname lh your.label --mask >> lh.zstat1.nii --maskthresh 2 --masksign abs --o sum.dat >> >> where zstat1 is your all/nothing contrast sampled onto the surface and >> cope2 is some other contrast sampled on the surface. >> You can do this for each subject, then run asegstats2table giving it >> paths to all of your sum.dat files >> >> doug >> >> >> >> >> On 11/26/2012 07:01 PM, Susan Alice McLaughlin wrote: >>> Hi, >>> >>> I am hoping do a surface-based functional ROI analysis on >>> subject-specific ROIs that are both defined structurally and are >>> masked by an all/nothing functional contrast. func2roi-sess seems >>> perfect for this except that my data are not in an FS-FAST >>> data/analysis structure, but are instead pre-processed and >>> preliminarily analyzed using FSL and mapped to the surface using >>> reg-feat2anat. >>> >>> Is there any way to pass my original analysis into func2roi-sess? I >>> tried using: >>> >>> func2roi-sess -roidef LH_ant_STG_soundthresh2 -analysis >>> 1012_Run4_featFULLrev.feat/stats/zstat4.nii.gz -anatlabel lh_ant_STG >>> -maskcontrast 1012_Run4_featFULLrev/stats/zstat16.nii.gz >>> -maskthreshold 2 -s 1012 -d >>> >>> but get "ERROR: cannot find any sessions." >>> >>> Or is there another tool more appropriate for what I am trying to >>> do? I am looking at mri_segstats, but my hand-drawn ROIs (drawn on >>> fsaverage in tksurfer and morphed to each subject using >>> label_2_label) are in .label format and are on the surface. >>> >>> Thanks in advance for and advice or suggestions. >>> >>> Susan McLaughlin >>> Doctoral Candidate >>> SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) >>> Dept. of Speech and Hearing Sciences >>> University of Washington >>> >>> >>> _______________________________________________ >>> 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 >> 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. 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. >> >> > > Susan McLaughlin > Doctoral Candidate > SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) > Dept. of Speech and Hearing Sciences > University of Washington > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
