Jurgen, Both of these files were created with identical command lines. doug
Jürgen Hänggi wrote: > Hi Doug > > Attached are the two files generated from the same subject by using > mris_anatomical_stats, once without smoothing (rh.aparc.a2005s.stats) and > once with smoothing (rh.aparc.a2005s_with_smoothing.stats). > > But the same results appear. This is also the case if I first use > mri_smooth2smooth to smooth the area map first. > > I recognised that the volume or thickness information changed with > smoothing, but the area information remained the same for smoothed and > unsmoothed data. > > Thans > Jürgen > > > On [DATE], "Douglas N Greve" <[ADDRESS]> wrote: > > >> Can you send me the output stats file for both? >> >> Jürgen Hänggi wrote: >> >>> Hi Doug >>> >>> Yes, exactly that was the problem >>> >>> Thanks >>> Cheers >>> Jürgen >>> >>> >>> >>> >>> On [DATE], "Douglas N Greve" <[ADDRESS]> wrote: >>> >>> >>> >>>> Hi Jurgen, did you say that the results with the smoothing and without >>>> the smoothing are identical? Is that what the problem is? >>>> >>>> doug >>>> >>>> Jürgen Hänggi wrote: >>>> >>>> >>>>> Hi Doug >>>>> >>>>> Here is the output from the terminal when running mris_anatomical_stats. I >>>>> have run a loop, but show only the output of one subject. The smoothed >>>>> file >>>>> is rg.area_smooth.mgh and the output file is called like the old aparc >>>>> file >>>>> in order to be readable with aparcstats2table. >>>>> >>>>> foreach s ( biid_* ) >>>>> foreach? mris_anatomical_stats -a area_p01.annot -t rh.area_smooth.mgh -f >>>>> $s/stats/rh.aparc.a2005s.stats $s rh >>>>> foreach? end >>>>> computing statistics for each annotation in area_p01.annot. >>>>> using thickness file rh.area_smooth.mgh. >>>>> reading volume /Applications/freesurfer/subjects/biid_b101/mri/wm.mgz... >>>>> reading input surface >>>>> /Applications/freesurfer/subjects/biid_b101/surf/rh.white... >>>>> reading input pial surface >>>>> /Applications/freesurfer/subjects/biid_b101/surf/rh.pial... >>>>> reading input white surface >>>>> /Applications/freesurfer/subjects/biid_b101/surf/rh.white... >>>>> reading colortable from annotation file... >>>>> colortable with 14 entries read (originally none) >>>>> structure is "cluster-001" >>>>> number of vertices = 138 >>>>> total surface area = 88 mm^2 >>>>> total gray matter volume = 62 mm^3 >>>>> average cortical thickness = 0.663 mm +- 0.048 mm >>>>> average integrated rectified mean curvature = 0.188 >>>>> average integrated rectified Gaussian curvature = 0.065 >>>>> folding index = 5 >>>>> intrinsic curvature index = 0.4 >>>>> structure is "cluster-002" >>>>> number of vertices = 111 >>>>> total surface area = 84 mm^2 >>>>> total gray matter volume = 42 mm^3 >>>>> average cortical thickness = 0.751 mm +- 0.033 mm >>>>> average integrated rectified mean curvature = 0.129 >>>>> average integrated rectified Gaussian curvature = 0.020 >>>>> folding index = 1 >>>>> intrinsic curvature index = 0.1 >>>>> structure is "cluster-003" >>>>> number of vertices = 122 >>>>> total surface area = 75 mm^2 >>>>> total gray matter volume = 44 mm^3 >>>>> average cortical thickness = 0.671 mm +- 0.027 mm >>>>> average integrated rectified mean curvature = 0.098 >>>>> average integrated rectified Gaussian curvature = 0.021 >>>>> folding index = 0 >>>>> intrinsic curvature index = 0.1 >>>>> structure is "cluster-004" >>>>> number of vertices = 415 >>>>> total surface area = 269 mm^2 >>>>> total gray matter volume = 178 mm^3 >>>>> average cortical thickness = 0.690 mm +- 0.034 mm >>>>> average integrated rectified mean curvature = 0.132 >>>>> average integrated rectified Gaussian curvature = 0.033 >>>>> folding index = 4 >>>>> intrinsic curvature index = 0.6 >>>>> structure is "cluster-005" >>>>> number of vertices = 131 >>>>> total surface area = 76 mm^2 >>>>> total gray matter volume = 66 mm^3 >>>>> average cortical thickness = 0.671 mm +- 0.055 mm >>>>> average integrated rectified mean curvature = 0.106 >>>>> average integrated rectified Gaussian curvature = 0.031 >>>>> folding index = 2 >>>>> intrinsic curvature index = 0.2 >>>>> structure is "cluster-006" >>>>> number of vertices = 223 >>>>> total surface area = 145 mm^2 >>>>> total gray matter volume = 139 mm^3 >>>>> average cortical thickness = 0.665 mm +- 0.185 mm >>>>> average integrated rectified mean curvature = 0.146 >>>>> average integrated rectified Gaussian curvature = 0.073 >>>>> folding index = 3 >>>>> intrinsic curvature index = 0.6 >>>>> structure is "cluster-007" >>>>> number of vertices = 45 >>>>> total surface area = 37 mm^2 >>>>> total gray matter volume = 36 mm^3 >>>>> average cortical thickness = 0.780 mm +- 0.060 mm >>>>> average integrated rectified mean curvature = 0.138 >>>>> average integrated rectified Gaussian curvature = 0.048 >>>>> folding index = 1 >>>>> intrinsic curvature index = 0.0 >>>>> structure is "cluster-008" >>>>> number of vertices = 150 >>>>> total surface area = 81 mm^2 >>>>> total gray matter volume = 53 mm^3 >>>>> average cortical thickness = 0.578 mm +- 0.067 mm >>>>> average integrated rectified mean curvature = 0.142 >>>>> average integrated rectified Gaussian curvature = 0.081 >>>>> folding index = 10 >>>>> intrinsic curvature index = 0.8 >>>>> structure is "cluster-009" >>>>> number of vertices = 74 >>>>> total surface area = 51 mm^2 >>>>> total gray matter volume = 36 mm^3 >>>>> average cortical thickness = 0.719 mm +- 0.042 mm >>>>> average integrated rectified mean curvature = 0.169 >>>>> average integrated rectified Gaussian curvature = 0.052 >>>>> folding index = 1 >>>>> intrinsic curvature index = 0.1 >>>>> structure is "cluster-010" >>>>> number of vertices = 55 >>>>> total surface area = 31 mm^2 >>>>> total gray matter volume = 26 mm^3 >>>>> average cortical thickness = 0.631 mm +- 0.037 mm >>>>> average integrated rectified mean curvature = 0.153 >>>>> average integrated rectified Gaussian curvature = 0.090 >>>>> folding index = 2 >>>>> intrinsic curvature index = 0.2 >>>>> structure is "cluster-011" >>>>> number of vertices = 78 >>>>> total surface area = 45 mm^2 >>>>> total gray matter volume = 21 mm^3 >>>>> average cortical thickness = 0.662 mm +- 0.036 mm >>>>> average integrated rectified mean curvature = 0.113 >>>>> average integrated rectified Gaussian curvature = 0.017 >>>>> folding index = 1 >>>>> intrinsic curvature index = 0.1 >>>>> structure is "cluster-012" >>>>> number of vertices = 4 >>>>> total surface area = 4 mm^2 >>>>> total gray matter volume = 4 mm^3 >>>>> average cortical thickness = 0.824 mm +- 0.010 mm >>>>> average integrated rectified mean curvature = 0.052 >>>>> average integrated rectified Gaussian curvature = 0.003 >>>>> folding index = 0 >>>>> intrinsic curvature index = 0.0 >>>>> structure is "cluster13" >>>>> number of vertices = 8 >>>>> total surface area = 4 mm^2 >>>>> total gray matter volume = 3 mm^3 >>>>> average cortical thickness = 0.634 mm +- 0.021 mm >>>>> average integrated rectified mean curvature = 0.133 >>>>> average integrated rectified Gaussian curvature = 0.026 >>>>> folding index = 0 >>>>> intrinsic curvature index = 0.0 >>>>> computing statistics for each annotation in area_p01.annot. >>>>> using thickness file rh.area_smooth.mgh. >>>>> >>>>> Thanks >>>>> Cheers >>>>> Jürgen >>>>> >>>>> On [DATE], "Douglas N Greve" <[ADDRESS]> wrote: >>>>> >>>>> >>>>> >>>>> >>>>>> Juegen, can you send the full terminal output? Also, you can try >>>>>> explicitly smoothing the file with mri_surf2surf and then run anatomical >>>>>> stats on the smoothed file. >>>>>> doug >>>>>> >>>>>> Jürgen Hänggi wrote: >>>>>> >>>>>> >>>>>> >>>>>>> Dear FS experts >>>>>>> >>>>>>> I tried to read out in each subject the surface area values of some >>>>>>> clusters >>>>>>> derived from a group comparison. >>>>>>> For that purpose, I used mri_surf2surf and mris_anatomical_stats. >>>>>>> >>>>>>> Everything worked fine, but in some clusters the direction of the >>>>>>> effects >>>>>>> reversed. A first guess was that this might have to do with the >>>>>>> smoothing >>>>>>> that we applied to the group comparison. >>>>>>> >>>>>>> Therefore, I smoothed the individual area files to get the smoothed >>>>>>> surface >>>>>>> area in each subject using the following command: >>>>>>> >>>>>>> mris_anatomical_stats -a area_p01.annot -t rh.area -nsmooth 15 -f >>>>>>> $s/stats/rh.aparc.a2005s.stats $s rh >>>>>>> >>>>>>> But the surface area of this smoothed data gives the same values as the >>>>>>> unsmoothed data. >>>>>>> >>>>>>> Any idea what is wrong here? >>>>>>> >>>>>>> Thanks in advance >>>>>>> Regards >>>>>>> Jürgen >>>>>>> >>>>>>> PS: sorry for posting this message twice, but the first post did not >>>>>>> appeared in the archives >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>> --------------------------------------------------------------------------->> >>> >>> - >>> >>> >>>>>>> Jürgen Hänggi, Ph.D. >>>>>>> Division Neuropsychology >>>>>>> Institute of Psychology >>>>>>> University of Zurich >>>>>>> Binzmuehlestrasse 14, PO Box 25 >>>>>>> 8050 Zurich, Switzerland >>>>>>> 0041 44 635 73 97 (phone office) >>>>>>> 0041 76 445 86 84 (phone mobile) >>>>>>> 0041 44 635 74 09 (fax office) >>>>>>> BIN 4.D.04 (office room number) >>>>>>> j.haenggi[at]psychologie.uzh.ch (email) >>>>>>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>>>>>> http://www.juergenhaenggi.ch (private website) >>>>>>> >>>>>>> This e-mail (and any attachment/s) contains confidential and/or >>>>>>> privileged >>>>>>> information. If you are not the intended recipient (or have received >>>>>>> this >>>>>>> e-mail in error) please notify the sender immediately and destroy this >>>>>>> e-mail. Any unauthorised copying, disclosure or distribution of the >>>>>>> material in this e-mail is strictly forbidden. >>>>>>> >>>>>>> >>>>>>> >>> --------------------------------------------------------------------------->> >>> >>> - >>> >>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> > --------------------------------------------------------------------------->>>> > - > >>>>> Jürgen Hänggi, Ph.D. >>>>> Division Neuropsychology >>>>> Institute of Psychology >>>>> University of Zurich >>>>> Binzmuehlestrasse 14, PO Box 25 >>>>> 8050 Zurich, Switzerland >>>>> 0041 44 635 73 97 (phone office) >>>>> 0041 76 445 86 84 (phone mobile) >>>>> 0041 44 635 74 09 (fax office) >>>>> BIN 4.D.04 (office room number) >>>>> j.haenggi[at]psychologie.uzh.ch (email) >>>>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>>>> http://www.juergenhaenggi.ch (private website) >>>>> >>>>> This e-mail (and any attachment/s) contains confidential and/or privileged >>>>> information. If you are not the intended recipient (or have received this >>>>> e-mail in error) please notify the sender immediately and destroy this >>>>> e-mail. Any unauthorised copying, disclosure or distribution of the >>>>> material in this e-mail is strictly forbidden. >>>>> >>>>> > --------------------------------------------------------------------------->>>> > - > >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>> ---------------------------------------------------------------------------- >>> Jürgen Hänggi, Ph.D. >>> Division Neuropsychology >>> Institute of Psychology >>> University of Zurich >>> Binzmuehlestrasse 14, PO Box 25 >>> 8050 Zurich, Switzerland >>> 0041 44 635 73 97 (phone office) >>> 0041 76 445 86 84 (phone mobile) >>> 0041 44 635 74 09 (fax office) >>> BIN 4.D.04 (office room number) >>> j.haenggi[at]psychologie.uzh.ch (email) >>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>> http://www.juergenhaenggi.ch (private website) >>> >>> This e-mail (and any attachment/s) contains confidential and/or privileged >>> information. If you are not the intended recipient (or have received this >>> e-mail in error) please notify the sender immediately and destroy this >>> e-mail. Any unauthorised copying, disclosure or distribution of the >>> material in this e-mail is strictly forbidden. >>> ---------------------------------------------------------------------------- >>> >>> >>> >>> >>> >>> >>> > > > ---------------------------------------------------------------------------- > Jürgen Hänggi, Ph.D. > Division Neuropsychology > Institute of Psychology > University of Zurich > Binzmuehlestrasse 14, PO Box 25 > 8050 Zurich, Switzerland > 0041 44 635 73 97 (phone office) > 0041 76 445 86 84 (phone mobile) > 0041 44 635 74 09 (fax office) > BIN 4.D.04 (office room number) > j.haenggi[at]psychologie.uzh.ch (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > > This e-mail (and any attachment/s) contains confidential and/or privileged > information. 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