[Freesurfer] cortical thickness value of each pixel
Hi, I want to calculate the global thickness statistics (mean +/- SD) for all my subjects. And, I could calculate the global thickness statistics by some information about cortical thickness values of each pixel. But I can’t find any files regarding cortical thickness values of each pixel. Could you suggest me how to calculate the global thickness statistics or tell me where to get the file regarding cortical thickness values of each pixel? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical thickness value of each pixel
Hi Feng-Xian, the ?h.thickness files in each subject's surf dir contain the vertex-wise thickness, and mris_anatomical_stats will compute the average. Make sure to give it -l ?h.cortex.label so it only computes them over the cortial region of the surface cheers, Bruce On Mon, 1 Jun 2009, Feng-Xian wrote: Hi, I want to calculate the global thickness statistics (mean +/- SD) for all my subjects. And, I could calculate the global thickness statistics by some information about cortical thickness values of each pixel. But I canÿÿt find any files regarding cortical thickness values of each pixel. Could you suggest me how to calculate the global thickness statistics or tell me where to get the file regarding cortical thickness values of each pixel? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical thickness value of each pixel
oops, I meant non cortical regions On Mon, 1 Jun 2009, Feng-Xian wrote: Hi, From your response, I thick that if I want to get the global thickness statistics (mean +/- SD) without any regions where the thickness is 0, I would consider these regions where the thickness is 0. But, I donÿÿt know what can I do? Would you teach me? First, I get the global thickness statistics with all regions by the following command: mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh And, I get the following information: table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 155006 103166 299737 2.608 1.022 0.121 0.041 2632 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_0 /surf/lh.white Then, I get the global thickness statistics with some regions where the thickness is 0 by the following command: mris_anatomical_stats -t subjid/label/lh.cortex.label -b subjid lh And, I get the following information: table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 155006 103166 0 0.000 0.0000.1210.0412632 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_ 0/surf/lh.white Thank you in advance! Feng-Xian On Mon, 1 Jun 2009 10:47:19 -0400 (EDT), Bruce Fischl wrote that's right, but it will average over the whole surface including e.g. the callosum where the thickness is 0. If you specify the ?h.cortex.label file it will exclude these regions Bruce On Mon, 1 Jun 2009, Feng-Xian wrote: Hi, From your suggestion, I get the global thickness statistics (mean +/- SD) by the following command: mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh Then, I get the following information: table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 155006 103166 299737 2.608 1.022 0.121 0.041 2632 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_0 /surf/lh.white So, I think 2.608 1.022 is the global thickness statistics (mean +/- SD) for this subject. Do I have something wrong? Thank you in advance! Feng-Xian On Mon, 1 Jun 2009 07:29:46 -0400 (EDT), Bruce Fischl wrote Hi Feng-Xian, the ?h.thickness files in each subject's surf dir contain the vertex- wise thickness, and mris_anatomical_stats will compute the average. Make sure to give it -l ?h.cortex.label so it only computes them over the cortial region of the surface cheers, Bruce On Mon, 1 Jun 2009, Feng-Xian wrote: Hi, I want to calculate the global thickness statistics (mean +/- SD) for all my subjects. And, I could calculate the global thickness statistics by some information about cortical thickness values of each pixel. But I canÿÿt find any files regarding cortical thickness values of each pixel. Could you suggest me how to calculate the global thickness statistics or tell me where to get the file regarding cortical thickness values of each pixel? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical thickness value of each pixel
use -l lh.cortex.label or rh.cortex.label to exclude the non-zero regions On Mon, 1 Jun 2009, Feng-Xian wrote: Hi, From your response, I thick that if I want to get the global thickness statistics (mean +/- SD) without any regions where the thickness is 0, I would consider these regions where the thickness is 0. But, I donÿÿt know what can I do? Would you teach me? First, I get the global thickness statistics with all regions by the following command: mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh And, I get the following information: table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 155006 103166 299737 2.608 1.022 0.121 0.041 2632 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_0 /surf/lh.white Then, I get the global thickness statistics with some regions where the thickness is 0 by the following command: mris_anatomical_stats -t subjid/label/lh.cortex.label -b subjid lh And, I get the following information: table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 155006 103166 0 0.000 0.0000.1210.0412632 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_ 0/surf/lh.white Thank you in advance! Feng-Xian On Mon, 1 Jun 2009 10:47:19 -0400 (EDT), Bruce Fischl wrote that's right, but it will average over the whole surface including e.g. the callosum where the thickness is 0. If you specify the ?h.cortex.label file it will exclude these regions Bruce On Mon, 1 Jun 2009, Feng-Xian wrote: Hi, From your suggestion, I get the global thickness statistics (mean +/- SD) by the following command: mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh Then, I get the following information: table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 155006 103166 299737 2.608 1.022 0.121 0.041 2632 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_0 /surf/lh.white So, I think 2.608 1.022 is the global thickness statistics (mean +/- SD) for this subject. Do I have something wrong? Thank you in advance! Feng-Xian On Mon, 1 Jun 2009 07:29:46 -0400 (EDT), Bruce Fischl wrote Hi Feng-Xian, the ?h.thickness files in each subject's surf dir contain the vertex- wise thickness, and mris_anatomical_stats will compute the average. Make sure to give it -l ?h.cortex.label so it only computes them over the cortial region of the surface cheers, Bruce On Mon, 1 Jun 2009, Feng-Xian wrote: Hi, I want to calculate the global thickness statistics (mean +/- SD) for all my subjects. And, I could calculate the global thickness statistics by some information about cortical thickness values of each pixel. But I canÿÿt find any files regarding cortical thickness values of each pixel. Could you suggest me how to calculate the global thickness statistics or tell me where to get the file regarding cortical thickness values of each pixel? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical thickness value of each pixel
If you simply want some stats on the 'lh.thickness' and 'rh.thickness' files, you can also try: $mris_calc lh.thickness stats $mris_calc rh.thickness stats Feng-Xian wrote: Hi, I want to calculate the global thickness statistics (mean +/- SD) for all my subjects. And, I could calculate the global thickness statistics by some information about cortical thickness values of each pixel. But I can’t find any files regarding cortical thickness values of each pixel. Could you suggest me how to calculate the global thickness statistics or tell me where to get the file regarding cortical thickness values of each pixel? Thank you in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
