Hi Doug,
This is from the log file:
mri_glmfit --y lh.Hybridversustrio_fsgd.sm20.mgh --fsgd /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt dods --glmdir lh.Hybridversustrio_fsgd.dods.20.glmdir --surf fsaverage lh --C /Volumes/HEIDI2/comparingTrioHybrid/GLM_CONTRAST.MAT/contrast_1_-1.mat sysname Darwin hostname medmac47.ime.kfa-juelich.de machine x86_64 user hjacobs FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Volumes/HEIDI2/comparingTrioHybrid/THICKNESS_GLM/lh.Hybridversustrio_fsgd.sm20.mgh logyflag 0 usedti 0 FSGD /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt labelmask /Volumes/HEIDI2/comparingTrioHybrid/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.Hybridversustrio_fsgd.dods.20.glmdir IllCondOK 0 DoFFx 0
Heidi
================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl
Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================ ________________________________________ Van: Douglas N Greve [greve@nmr.mgh.harvard.edu] Verzonden: donderdag 11 oktober 2012 17:52 Aan: Jacobs H (NP) CC: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] basic comparison
what's your command line and resulting terminal output?
On 10/11/2012 11:49 AM, Jacobs H (NP) wrote:
Hi Doug,
Thanks for your help. I just ran the mri_glmfit the way you suggested. But FreeSurfer does not provide me a contrast directory and no gamma.mgh. It only gives me a mask.mgh, Xg.dat and the mri_glmfit.log?
Any ideas what might have gone wrong?
Thanks! Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl
Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================ ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Douglas N Greve [greve@nmr.mgh.harvard.edu] Verzonden: donderdag 11 oktober 2012 17:35 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] basic comparison
Hi Heidi, the easiest way is probably to do the analysis with mri_glmfit specifying that each subject is it's own group and a contrast to compute the difference between the groups.The gamma.mgh in the contrast directory will be the thickness difference between the two subjects. There will be a sig.mgh there as well, but, as you mention, you will not be able to get reasonable p-values out because of not enough DOF. doug
On 10/11/2012 08:31 AM, Jacobs H (NP) wrote:
Hi FreeSurfers,
I am preparing a simple presentation, to show some basic stuff in my lab and therefore I would like to compare the cortical thickness of two subjects. Is there a way to do this? For the GLM, I probably have not enough degrees of freedom? Is there a way that I could subtract the two thickness overlays?
Thanks Heidi
================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs@maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl
Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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