Hi Heidi,
You can use mri_segstats on the surface. You can either use the --label option or, if you have a lot of labels, you can merge them into an annotation with mris_label2annot and then use the --annot option to extract from all at once (values are extracted from each region separately; this just might save some time/typing).
Note that the file you're extracting from (the one after the --i flag) must be stored as a surface.
Best, Mike
On Mon, Aug 16, 2010 at 10:46 AM, freesurfer-request@nmr.mgh.harvard.eduwrote:
Hi,
Last year, I have been working for four months with David Salat and so, I have learnt a lot, including the dt_recon command. From David, I also learnt to use mri_segstats command in order to get minimum p-values for each label in my volume. However, now I have performed cortical thickness analyses. Based on the results on the inflated surface, I created labels and deprojected them to native space, to get the statistics. Now, I also would like to have the minimum p-value of each label in the cortical thickness analyses. However, the mri_segstats command is not suitable for surfaces. Do you have any idea how I can extract these minimim p-values?
Thank you very much.
Best Heidi.
*Heidi Jacobs * *PhD student Faculty of Health, Medicine and Life Sciences* *School for Mental Health and Neurosciences* *Alzheimer Center Limburg* *Division Cognitive Neuropsychiatry and Clinical Neurosciences* *h.jacobs@np.unimaas.nl *www.maastrichtuniversity.nl
Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 126 F +31 43 38 84 092
*Please consider your environmental responsibility before printing this e-mail.*
Mike is correct. Thanks Mike!
doug
Michael Waskom wrote:
Hi Heidi,
You can use mri_segstats on the surface. You can either use the --label option or, if you have a lot of labels, you can merge them into an annotation with mris_label2annot and then use the --annot option to extract from all at once (values are extracted from each region separately; this just might save some time/typing).
Note that the file you're extracting from (the one after the --i flag) must be stored as a surface.
Best, Mike
On Mon, Aug 16, 2010 at 10:46 AM, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Hi, Last year, I have been working for four months with David Salat and so, I have learnt a lot, including the dt_recon command. From David, I also learnt to use mri_segstats command in order to get minimum p-values for each label in my volume. However, now I have performed cortical thickness analyses. Based on the results on the inflated surface, I created labels and deprojected them to native space, to get the statistics. Now, I also would like to have the minimum p-value of each label in the cortical thickness analyses. However, the mri_segstats command is not suitable for surfaces. Do you have any idea how I can extract these minimim p-values? Thank you very much. Best Heidi. * * *Heidi Jacobs * /PhD student Faculty of Health, Medicine and Life Sciences/ /School for Mental Health and Neurosciences/ /Alzheimer Center Limburg/ /Division Cognitive Neuropsychiatry and Clinical Neurosciences/ _h.jacobs@np.unimaas.nl <mailto:h.jacobs@np.unimaas.nl> _www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 126 F +31 43 38 84 092 *Please consider your environmental responsibility before printing this e-mail.*
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Michael Waskom