Yes, method #1 will work better. doug On 12/04/2012 06:22 PM, Susan Alice McLaughlin wrote: > Hi Doug, > > Thanks for your helpful answer (below) with respect to the use of > mri_segstats on functional activation in subject-specific ROIS. > > I have a follow-up question, however, regarding the initial creation > of the ROIs. I am basing my ROIs on the Desikan-Killiany atlas, either > using existing labels in the atlas or sometimes splitting them into > anterior and posterior. I tried making the ROis 2 different ways, and > found I got different results. > > 1) If I make an ROI by selecting or drawing D-K atlas regions on > fsaverage, then morph it to each individual’s surface with: > > mri_label2label --srcsubject fsaverage --srclabel > /Applications/freesurfer/subjects/fsaverage/label/[ROIname].label > --trgsubject [subj] --trglabel > /Applications/freesurfer/subjects/[subj]/label/[ROIname].label > --regmethod surface --hemi lh > > and then – to go from the surface (.label) to the volume (.nii): > > mri_label2vol --temp example_func.nii.gz --reg > reg/freesurfer/anat2exf.register.dat --proj frac 0 1 .1 --hemi lh > --label /Applications/freesurfer/subjects/1012/label/[ROIname].label > --subject [subj] --o [output name].nii > > then I get a fully contiguous region when I view the ROI on the > individual’s surface or more total voxels when I look at a summary of > the ROI characteristics using mri_segstats. > > 2) If I instead make the ROI using: > > aseg2feat –feat [subj].feat --aseg aparc+aseg > > and then > > fslmaths [subj].feat/reg/freesurfer/aparc+aseg.nii.gz –thr [label # > of pertinent region] –uthr [label # of pertinent region] > [subj].feat/reg/freesurfer/[ROIname].nii.gz > > then I get a chopped up, non-contiguous region with fewer total voxels. > > My plan therefore is to use Method #1 above, but I want to make sure > this is OK: that I'm not somehow including spurious voxels that have > somehow been incorrectly generated by going from surface to volume. Am > I OK with Method #1 above? > > Thanks again, > > > Susan McLaughlin > Doctoral Candidate > SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) > Dept. of Speech and Hearing Sciences > University of Washington > > > On Mon, 26 Nov 2012, Douglas Greve wrote: > >> >> 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 >> >
-- 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
