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 ================================================
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
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
_______________________________________________ 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.
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
can you send the full terminal output?
On 10/11/2012 11:56 AM, Jacobs H (NP) wrote:
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
That's all I have :):
Thickness_GLM_qcache.csh --target fsaverage --fwhm 20 --slope dods --contrast contrast_1_-1.mat --glm_dir /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR --fsgd_dir /Volumes/HEIDI2/comparingTrioHybrid/FSGD --fsgd fsgd.Hybridversustrio_fsgd.txt contrast_1_-1.mat argv: Subscript out of range. Parse arguments done... Slope: dods Contrast File: contrast_1_-1.mat FSGD File(s): fsgd.Hybridversustrio_fsgd.txt parse and check arguments done. FSGD for this GLM is: fsgd.Hybridversustrio_fsgd.txt Subjects to be included in this GLM are: T001 H001 mris_preproc --target fsaverage --hemi lh --s T001 --s H001 --cache-in thickness.fwhm20.fsaverage --out /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/lh.Hybridversustrio_fsgd.sm20.mgh nsubjects = 2 tmpdir is /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/tmp.mris_preproc.3120 /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR Thu Oct 11 18:01:52 CEST 2012 /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR --target fsaverage --hemi lh --s T001 --s H001 --cache-in thickness.fwhm20.fsaverage --out /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/lh.Hybridversustrio_fsgd.sm20.mgh Darwin medmac47.ime.kfa-juelich.de 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Volumes/HEIDI2/comparingTrioHybrid tmpdir is /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/tmp.mris_preproc.3120 Src lh sphere.reg Trg lh sphere.reg \n\n --------------------------------------------------- #@# 1/2 T001 Thu Oct 11 18:01:52 CEST 2012 -------------- \n\n --------------------------------------------------- #@# 2/2 H001 Thu Oct 11 18:01:52 CEST 2012 -------------- \n\n ----------------------- mri_concat /Volumes/HEIDI2/comparingTrioHybrid/T001/surf/lh.thickness.fwhm20.fsaverage.mgh /Volumes/HEIDI2/comparingTrioHybrid/H001/surf/lh.thickness.fwhm20.fsaverage.mgh --o /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/lh.Hybridversustrio_fsgd.sm20.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/lh.Hybridversustrio_fsgd.sm20.mgh \n\n Cleaning up ----------------------- rm -r /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/tmp.mris_preproc.3120 Thu Oct 11 18:01:52 CEST 2012 mris_preproc done 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 gdfReadHeader: reading /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt INFO: ignoring tag Measurement WARNING: gdfReadV1: no variables on 'Variables' line found INFO: gd2mtx_method is dods Reading source surface /Volumes/HEIDI2/comparingTrioHybrid/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR cmdline 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/GLM_DIR/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 Creating output directory lh.Hybridversustrio_fsgd.dods.20.glmdir Loading y from /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/lh.Hybridversustrio_fsgd.sm20.mgh INFO: gd2mtx_method is dods Saving design matrix to lh.Hybridversustrio_fsgd.dods.20.glmdir/Xg.dat Matrix condition is 1 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 149955 voxels in mask Saving mask to lh.Hybridversustrio_fsgd.dods.20.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74612.965197 DOF = 0 ERROR: DOF = 0 mris_preproc --target fsaverage --hemi rh --s T001 --s H001 --cache-in thickness.fwhm20.fsaverage --out /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/rh.Hybridversustrio_fsgd.sm20.mgh nsubjects = 2 tmpdir is /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/tmp.mris_preproc.3222 /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR Thu Oct 11 18:01:55 CEST 2012 /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR --target fsaverage --hemi rh --s T001 --s H001 --cache-in thickness.fwhm20.fsaverage --out /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/rh.Hybridversustrio_fsgd.sm20.mgh Darwin medmac47.ime.kfa-juelich.de 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Volumes/HEIDI2/comparingTrioHybrid tmpdir is /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/tmp.mris_preproc.3222 Src rh sphere.reg Trg rh sphere.reg \n\n --------------------------------------------------- #@# 1/2 T001 Thu Oct 11 18:01:55 CEST 2012 -------------- \n\n --------------------------------------------------- #@# 2/2 H001 Thu Oct 11 18:01:55 CEST 2012 -------------- \n\n ----------------------- mri_concat /Volumes/HEIDI2/comparingTrioHybrid/T001/surf/rh.thickness.fwhm20.fsaverage.mgh /Volumes/HEIDI2/comparingTrioHybrid/H001/surf/rh.thickness.fwhm20.fsaverage.mgh --o /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/rh.Hybridversustrio_fsgd.sm20.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/rh.Hybridversustrio_fsgd.sm20.mgh \n\n Cleaning up ----------------------- rm -r /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/tmp.mris_preproc.3222 Thu Oct 11 18:01:55 CEST 2012 mris_preproc done mri_glmfit --y rh.Hybridversustrio_fsgd.sm20.mgh --fsgd /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt dods --glmdir rh.Hybridversustrio_fsgd.dods.20.glmdir --surf fsaverage rh --C /Volumes/HEIDI2/comparingTrioHybrid/GLM_CONTRAST.MAT/contrast_1_-1.mat gdfReadHeader: reading /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt INFO: ignoring tag Measurement WARNING: gdfReadV1: no variables on 'Variables' line found INFO: gd2mtx_method is dods Reading source surface /Volumes/HEIDI2/comparingTrioHybrid/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566
$Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR cmdline mri_glmfit --y rh.Hybridversustrio_fsgd.sm20.mgh --fsgd /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt dods --glmdir rh.Hybridversustrio_fsgd.dods.20.glmdir --surf fsaverage rh --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/GLM_DIR/rh.Hybridversustrio_fsgd.sm20.mgh logyflag 0 usedti 0 FSGD /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt labelmask /Volumes/HEIDI2/comparingTrioHybrid/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.Hybridversustrio_fsgd.dods.20.glmdir IllCondOK 0 DoFFx 0 Creating output directory rh.Hybridversustrio_fsgd.dods.20.glmdir Loading y from /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/rh.Hybridversustrio_fsgd.sm20.mgh INFO: gd2mtx_method is dods Saving design matrix to rh.Hybridversustrio_fsgd.dods.20.glmdir/Xg.dat Matrix condition is 1 Found 149926 points in label. Pruning voxels by thr: 0.000000 Found 149926 voxels in mask Saving mask to rh.Hybridversustrio_fsgd.dods.20.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74490.928733 DOF = 0 ERROR: DOF = 0 [medmac47:/Volumes/HEIDI2/comparingTrioHybrid] hjacobs%
================================================ 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 17:57 Aan: Jacobs H (NP) CC: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] basic comparison
can you send the full terminal output?
On 10/11/2012 11:56 AM, Jacobs H (NP) wrote:
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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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Yea, it won't allow DOF=0. Instead, you can just take the difference with
mri_concat --paired-diff rh.Hybridversustrio_fsgd.sm20.mgh --o diff.mgh doug
On 10/11/2012 12:02 PM, Jacobs H (NP) wrote:
That's all I have :):
Thickness_GLM_qcache.csh --target fsaverage --fwhm 20 --slope dods --contrast contrast_1_-1.mat --glm_dir /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR --fsgd_dir /Volumes/HEIDI2/comparingTrioHybrid/FSGD --fsgd fsgd.Hybridversustrio_fsgd.txt contrast_1_-1.mat argv: Subscript out of range. Parse arguments done... Slope: dods Contrast File: contrast_1_-1.mat FSGD File(s): fsgd.Hybridversustrio_fsgd.txt parse and check arguments done. FSGD for this GLM is: fsgd.Hybridversustrio_fsgd.txt Subjects to be included in this GLM are: T001 H001 mris_preproc --target fsaverage --hemi lh --s T001 --s H001 --cache-in thickness.fwhm20.fsaverage --out /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/lh.Hybridversustrio_fsgd.sm20.mgh nsubjects = 2 tmpdir is /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/tmp.mris_preproc.3120 /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR Thu Oct 11 18:01:52 CEST 2012 /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR --target fsaverage --hemi lh --s T001 --s H001 --cache-in thickness.fwhm20.fsaverage --out /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/lh.Hybridversustrio_fsgd.sm20.mgh Darwin medmac47.ime.kfa-juelich.de 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Volumes/HEIDI2/comparingTrioHybrid tmpdir is /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/tmp.mris_preproc.3120 Src lh sphere.reg Trg lh sphere.reg \n\n
#@# 1/2 T001 Thu Oct 11 18:01:52 CEST 2012 -------------- \n\n
#@# 2/2 H001 Thu Oct 11 18:01:52 CEST 2012 -------------- \n\n
mri_concat /Volumes/HEIDI2/comparingTrioHybrid/T001/surf/lh.thickness.fwhm20.fsaverage.mgh /Volumes/HEIDI2/comparingTrioHybrid/H001/surf/lh.thickness.fwhm20.fsaverage.mgh --o /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/lh.Hybridversustrio_fsgd.sm20.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/lh.Hybridversustrio_fsgd.sm20.mgh \n\n Cleaning up
rm -r /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/tmp.mris_preproc.3120 Thu Oct 11 18:01:52 CEST 2012 mris_preproc done 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 gdfReadHeader: reading /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt INFO: ignoring tag Measurement WARNING: gdfReadV1: no variables on 'Variables' line found INFO: gd2mtx_method is dods Reading source surface /Volumes/HEIDI2/comparingTrioHybrid/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR cmdline 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/GLM_DIR/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 Creating output directory lh.Hybridversustrio_fsgd.dods.20.glmdir Loading y from /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/lh.Hybridversustrio_fsgd.sm20.mgh INFO: gd2mtx_method is dods Saving design matrix to lh.Hybridversustrio_fsgd.dods.20.glmdir/Xg.dat Matrix condition is 1 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 149955 voxels in mask Saving mask to lh.Hybridversustrio_fsgd.dods.20.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74612.965197 DOF = 0 ERROR: DOF = 0 mris_preproc --target fsaverage --hemi rh --s T001 --s H001 --cache-in thickness.fwhm20.fsaverage --out /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/rh.Hybridversustrio_fsgd.sm20.mgh nsubjects = 2 tmpdir is /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/tmp.mris_preproc.3222 /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR Thu Oct 11 18:01:55 CEST 2012 /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR --target fsaverage --hemi rh --s T001 --s H001 --cache-in thickness.fwhm20.fsaverage --out /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/rh.Hybridversustrio_fsgd.sm20.mgh Darwin medmac47.ime.kfa-juelich.de 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Volumes/HEIDI2/comparingTrioHybrid tmpdir is /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/tmp.mris_preproc.3222 Src rh sphere.reg Trg rh sphere.reg \n\n
#@# 1/2 T001 Thu Oct 11 18:01:55 CEST 2012 -------------- \n\n
#@# 2/2 H001 Thu Oct 11 18:01:55 CEST 2012 -------------- \n\n
mri_concat /Volumes/HEIDI2/comparingTrioHybrid/T001/surf/rh.thickness.fwhm20.fsaverage.mgh /Volumes/HEIDI2/comparingTrioHybrid/H001/surf/rh.thickness.fwhm20.fsaverage.mgh --o /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/rh.Hybridversustrio_fsgd.sm20.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/rh.Hybridversustrio_fsgd.sm20.mgh \n\n Cleaning up
rm -r /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/tmp.mris_preproc.3222 Thu Oct 11 18:01:55 CEST 2012 mris_preproc done mri_glmfit --y rh.Hybridversustrio_fsgd.sm20.mgh --fsgd /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt dods --glmdir rh.Hybridversustrio_fsgd.dods.20.glmdir --surf fsaverage rh --C /Volumes/HEIDI2/comparingTrioHybrid/GLM_CONTRAST.MAT/contrast_1_-1.mat gdfReadHeader: reading /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt INFO: ignoring tag Measurement WARNING: gdfReadV1: no variables on 'Variables' line found INFO: gd2mtx_method is dods Reading source surface /Volumes/HEIDI2/comparingTrioHybrid/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566
$Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR cmdline mri_glmfit --y rh.Hybridversustrio_fsgd.sm20.mgh --fsgd /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt dods --glmdir rh.Hybridversustrio_fsgd.dods.20.glmdir --surf fsaverage rh --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/GLM_DIR/rh.Hybridversustrio_fsgd.sm20.mgh logyflag 0 usedti 0 FSGD /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt labelmask /Volumes/HEIDI2/comparingTrioHybrid/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.Hybridversustrio_fsgd.dods.20.glmdir IllCondOK 0 DoFFx 0 Creating output directory rh.Hybridversustrio_fsgd.dods.20.glmdir Loading y from /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR/rh.Hybridversustrio_fsgd.sm20.mgh INFO: gd2mtx_method is dods Saving design matrix to rh.Hybridversustrio_fsgd.dods.20.glmdir/Xg.dat Matrix condition is 1 Found 149926 points in label. Pruning voxels by thr: 0.000000 Found 149926 voxels in mask Saving mask to rh.Hybridversustrio_fsgd.dods.20.glmdir/mask.mgh Reshaping mriglm->mask... search space = 74490.928733 DOF = 0 ERROR: DOF = 0 [medmac47:/Volumes/HEIDI2/comparingTrioHybrid] hjacobs%
================================================ 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 17:57 Aan: Jacobs H (NP) CC: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] basic comparison
can you send the full terminal output?
On 10/11/2012 11:56 AM, Jacobs H (NP) wrote:
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Jacobs H (NP)