Hi Chris, you're almost there. There are a few mods I'd make to your stream:
1. You can run preproc-sess -s subXX -fsd rest -surface self lhrh -fwhm 0 (without the -mni305 since you are working in the subject's anatomy) 2. mri_segstats \ --annot subXX lh myaparcPXXXXXX \ --i $FUNCTIONALS_DIR/subXX/rest/001/fmcpr.lh.self.nii.gz \ --sum lh_1_16.sum.txt \ --avgwf lh_1_16.wav.txt So you pass mri_segstats the surface data and the annotation doug On 12/04/2012 11:11 AM, Chris McNorgan wrote: > Hi all. I have a question regarding the use of freesurfer + fs-fast > preprocessing to apply the Lausanne 2008 parcellation scheme to some > structural data, and then extract from those ~1000 ROIs the average > time series from a 4D resting state functional run. > > I'm posting what I have carried out so far, both to verify that I > haven't missed anything important, but also because I have seen > evidence within this and other mailing lists that others are > interested in doing something similar. This thread may then answer > their questions as well. > > Structural and functional data is in $SUBJECTS_DIR/sub00?/mri and > $FUNC_DIR/sub00?/rest, respectively > For each subject: > > * I carried out recon-all -autorecon1, -autorecon2, -autorecon 3, > checking data quality in between > * inspected ?h.aparc.annot, possibly made minor edits ( > https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit) > * used cmtk.Parcellate() with the Lausanne 2008 scheme ( > https://groups.google.com/forum/#!topic/cmtk-users/k_o3s8Yy2jQ) > <https://groups.google.com/forum/#%21topic/cmtk-users/k_o3s8Yy2jQ> > * This created a number of .label files and some .annot files, > notably ?h.myaparcP*.annot, which have sub-parcellations of the > 1-16, 17-28 and 29-36 regions indicated in the ?h.aparc.annot > files (I'm not entirely clear why they couldn't just go into a > single .annot file) > * Converted the .annot files to surface space using mri_aparc2aseg > --subXX --annot myaparcPXXXXXX which generated > myaparcPXXXXX+aseg.mgz (3 files total, as each of three sets of lh > and rh annot files describe both hemispheres in a single file) > * ran each of the functional runs through: > preproc-sess -s subXX -fsd rest -surface self lhrh -mni305 -fwhm 0 > > That brings me to my question. I have my functional data: > $FUNC_DIR/subXX/rest/001/fmcpr.siemens.sm0.mni305.2mm.nii.gz (I also > have 2 fmcpr.siemens.sm0.self.?h.nii.gz files, but they didn't work > either) > > I want to pull the average timeseries data for the functional data out > of the ROIs defined in myaparcP1_17+aseg.mgz (and similarly for the > other two myaparcP*.mgz files) > > I tried > mri_segstats \ > --seg $SUBJECTS_DIR/subXX/mri/myaparcP1_16+aseg.mgz \ > --i $FUNCTIONALS_DIR/subXX/rest/001/fmcpr.siemens.sm0.mni305.2mm.nii.gz \ > --annot subXX lh lh.myaparcP1_16.annot \ > --sum lh_1_16.sum.txt \ > --avgwf lh_1_16.wav.txt > > However, this gave me the following output: > > sysname Linux > hostname Sage > machine x86_64 > user chris > Loading /home/chris/resting/anat/subXX/mri/myaparcP1_16+aseg.mgz > Loading > /home/chris/resting/func/subXX/rest/001/fmcpr.siemens.sm0.mni305.2mm.nii.gz > ERROR: dimension mismatch between input volume and seg > input 76 76 93 > seg 256 256 256 > > I then tried resampling my resting state data with mri_vol2vol using > my func data as the --mov parameter, and my myaparc files as the > --targ parameter, and used tkregister2 on the resampled volume. > mri_segstats just hung when I ran it on the resampled volume; by the > next morning nothing had been written to either text output file. > > I can open my ?h surface files in tksurfer, and then load in the > appropriate timecourse > ($FUNCTIONALS_DIR/subXX/rest/001/fmcpr.siemens.sm0.self.?h.nii.gz) and > when I do so, I can click on various vertices and see timecourse > plots. And I can paint my surfaces with .annot files that define my > ROIs. So it seems I should be able to get these timecourse data from > ROIs in surface space without making a thousand individual ROIs in > volumetric space (my guess is I'd use flsmaths on my myaparc files to > do this). But I am not clear if mri_segstats can be used in this way, > or if indeed it is the appropriate tool. > > Any assistance to get me through this last step would be appreciated. > > Thanks > > > _______________________________________________ > 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.
