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. 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@nmr.mgh.harvard.edu
-
Douglas N Greve