Re: [Freesurfer] absolute value of effect size
You can do it to the sig file (the p-value already assumes a two-sided test). Why do you want to do it with the ces and cesvar files? If you are planning to use the abs(ces) for a higher level analysis then you need to be very careful as you can get some unintended effects doug On 01/07/2014 03:46 PM, SHAHIN NASR wrote: Hi, I have two related questions. I have two conditions (e.g. C1 and C2) and I want to generate a map that shows all voxels that can differentiate C1 from C2 _irrespective_ of whether C1C2 or C1C2. I think it can be done easily by: mris_calc -o sig.nii abs_sig.nii abs If I am right, then: 1) Can I apply the same command to ces.nii file to have the absolute value of the effect size (i.e. abs(C1-C2 effect size)) or should I consider other factors? 2) Do I need to apply the same routine to cesvar? Thanks -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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.
Re: [Freesurfer] absolute value of effect size
Several potential problems. It makes the statistics non-gaussian and the abs(ces) becomes noise dependent (and so there will be a noise dependent bias). This makes interpretation more difficult (eg, is a difference between groups a difference in ces or a difference in noise?). The non-gaussianity could be addressed with a permutation test. doug On 01/08/2014 07:11 PM, sha...@nmr.mgh.harvard.edu wrote: Exactly! I need ces and cesvar files for a second order analysis. More specifically, I need to subtract this absolute map from another map. Would you be more specific about what I should check when I am doing this second order analysis? You can do it to the sig file (the p-value already assumes a two-sided test). Why do you want to do it with the ces and cesvar files? If you are planning to use the abs(ces) for a higher level analysis then you need to be very careful as you can get some unintended effects doug On 01/07/2014 03:46 PM, SHAHIN NASR wrote: Hi, I have two related questions. I have two conditions (e.g. C1 and C2) and I want to generate a map that shows all voxels that can differentiate C1 from C2 _irrespective_ of whether C1C2 or C1C2. I think it can be done easily by: mris_calc -o sig.nii abs_sig.nii abs If I am right, then: 1) Can I apply the same command to ces.nii file to have the absolute value of the effect size (i.e. abs(C1-C2 effect size)) or should I consider other factors? 2) Do I need to apply the same routine to cesvar? Thanks -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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.
[Freesurfer] absolute value of effect size
Hi, I have two related questions. I have two conditions (e.g. C1 and C2) and I want to generate a map that shows all voxels that can differentiate C1 from C2 *irrespective* of whether C1C2 or C1C2. I think it can be done easily by: mris_calc -o sig.nii abs_sig.nii abs If I am right, then: 1) Can I apply the same command to ces.nii file to have the absolute value of the effect size (i.e. abs(C1-C2 effect size)) or should I consider other factors? 2) Do I need to apply the same routine to cesvar? Thanks -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list 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.
