There should be a .log file created by mris_preproc. Is that good enough? Also, when you run mri_sestats you can add "--id 1" and it will only report the results for things inside your mask. doug
Marco Loggia, PhD wrote: > Thank you so much Michael for clarifying this. > > Final, related question: is there a way to retrieve the name/paths of > the files concatenated with mris_preproc to create the .mgh file > mentioned below? I usually have everything logged, but was wondering > if there was something like a flag for mri_info to directly find this > information. > > Marco > > On Mar 1, 2012, at 1:18 AM, Michael Waskom wrote: > >> Hi Marco, >> >> The columns correspond to the integer IDs in the --seg image, so >> assuming you passed in a binary mask the first column is mean over >> everything that isn't your ROI and the second column is the mean in >> your ROI. >> >> Cheers, >> Michael >> >> On Wed, Feb 29, 2012 at 10:56 AM, Marco Loggia >> <ma...@nmr.mgh.harvard.edu <mailto:ma...@nmr.mgh.harvard.edu>> wrote: >> >> Dear all, >> >> Given a series of fsaverage-registered rCBF maps, I am trying to >> extract >> the average rCBF value from one specific region. This region, >> which was a >> significant cluster from a volumetric (fsl) analysis, was >> binarized and >> then converted to surface. >> >> When I run mri_segstats with the --avgwf I obtain two columns. >> Can you >> please remind me which one is the average extracted from that >> ROI, and >> what is the other column? >> >> Thanks! >> Marco >> >> >> >> >> mri_vol2surf --mov >> >> DMN_s1_RS1_correlates_with_ASL1_rating.gfeat/cope1.feat/cluster_mask_zstat1.nii.gz >> --mni152reg --hemi rh --o >> >> /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF/rh.RS1_correlates_ASL1.mgz >> >> >> >> cd >> >> /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF >> >> for f in `ls *.mgz` ; do >> >> mri_segstats --seg $f --in >> >> /homes/14/marco/cluster_6/lbp/lbp_freesurfer_ASL/patients+controls/analyses/rh.lbp+ctrl.session1.asl2-asl1_projfrac-max_nopaired-diff_sm7_03mm_OCT18.mgh >> --avgwf "$f"_RH_nopaired_diff.txt >> done >> >> >> nedit rh.RS1_correlates_ASL1.mgz_RH_nopaired_diff.txt & >> >> 38.2811 47.6476 >> 40.3997 36.0856 >> 42.6304 46.2465 >> 44.4789 36.7066 >> 69.2376 51.4098 >> 66.0043 47.2098 >> 34.5957 40.3854 >> 36.8976 42.2028 >> 38.2475 35.875 >> 39.9503 37.0186 >> 35.1582 36.6949 >> 35.1924 38.874 >> 43.4415 36.2505 >> 43.3516 34.5041 >> 58.3073 50.3295 >> 61.8703 60.8415 >> 61.1754 51.3476 >> 47.9508 51.594 >> 51.5809 48.2985 >> 49.6545 50.974 >> 62.9431 72.1211 >> 54.0272 55.7234 >> 35.0701 34.5995 >> 37.9241 35.3844 >> 37.2277 42.3105 >> 38.2136 46.7896 >> 45.0951 51.9831 >> 45.4391 51.6242 >> 46.2971 47.5424 >> 44.3713 41.1725 >> 37.4132 36.1166 >> 36.7285 39.2947 >> 44.0285 46.501 >> 45.4698 50.5906 >> 51.0392 48.2324 >> 55.0885 50.9392 >> 66.7224 67.7807 >> 64.8932 68.5847 >> 45.5101 45.6065 >> 46.7002 45.232 >> 40.6324 48.9768 >> 44.3654 45.9017 >> 39.4908 32.8936 >> 39.5983 36.4909 >> 55.9295 59.1527 >> 55.6738 55.7016 >> 44.7433 50.9412 >> 42.6953 50.0857 >> 42.4522 48.7366 >> 43.5595 42.3424 >> 43.9283 36.5026 >> 41.9838 36.8662 >> 39.9873 44.505 >> 43.442 49.2243 >> 57.6304 55.5628 >> 53.3496 49.4215 >> 43.2505 42.5797 >> 43.5452 42.0694 >> 50.4555 47.993 >> 49.8977 49.6568 >> 41.5077 42.8473 >> 40.2357 42.3246 >> 40.3846 39.1473 >> 38.7073 41.502 >> >> >> >> ______________________ >> >> Marco L. Loggia, PhD >> Postdoctoral Fellow, Mass General Hospital & Brigham and Women's >> Hospital >> Harvard Medical School >> >> Psychiatric Neuroimaging Research Program >> CNY Building 120, suite 100 >> Charlestown, Massachusetts 02129 >> Phone: (617) 643-7267 >> Fax: (617) 643-7340 >> ma...@nmr.mgh.harvard.edu <mailto:ma...@nmr.mgh.harvard.edu> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto: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. >> >> > > ______________________________ > > Marco L. Loggia, PhD > Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital > Harvard Medical School > > Massachusetts General Hospital > 120 Second Avenue, Charlestown, MA 02129 > Phone: (617) 643-7267 > Fax: (617) 643-7340 > ma...@nmr.mgh.harvard.edu <mailto:ma...@nmr.mgh.harvard.edu> > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
