Re: [Freesurfer] REPOST: QDEC analysis
That's what I feared. But ok, I'll try that. Thank you! - Ursprüngliche Mail - Von: "mreuter" <mreu...@nmr.mgh.harvard.edu> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Gesendet: Freitag, 8. April 2016 14:55:42 Betreff: Re: [Freesurfer] REPOST: QDEC analysis Hi Clara, I think the message is correct and Qdec can only do 2 levels. Qdec is rather limited. You need to use mri_glmfit for that. Best, Martin On 04/08/2016 08:14 AM, Clara Kühn wrote: > Dear FreeSurfer experts, > > I am trying to analyze some single time points of my longitudinal data in > QDEC. I have 3 groups and created a file for the discrete factor "group" with > three levels (1,2 and 3). I have done the same for gender (with 2 levels). > The analysis with gender works just fine but when I try to use group as a > factor I get an error message that factor 1 must have 2 levels: > > SUBJECTS_DIR is '/scr/etsch2/kids/ct' > ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels > ninputs = 72 > Checking inputs > nframestot = 72 > Allocing output > Done allocing > nframes = 72 > Writing to /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh > gdfReadHeader: reading > /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd > INFO: gd2mtx_method is dods > Reading source surface /scr/etsch2/kids/ct/87kids_template/surf/lh.white > ERROR: no contrasts specified. > Error in Analyze: command failed: mri_glmfit --y > /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh --fsgd > /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd dods --glmdir > /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1 --surf 87kids_template lh > > In the tutorial it doesn't state that QDEC has to have discrete factors with > 2 levels only. > Am I doing something wrong or is there a work-around for that? > > Cheers, Clara > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] REPOST: QDEC analysis
Hi Clara, I think the message is correct and Qdec can only do 2 levels. Qdec is rather limited. You need to use mri_glmfit for that. Best, Martin On 04/08/2016 08:14 AM, Clara Kühn wrote: > Dear FreeSurfer experts, > > I am trying to analyze some single time points of my longitudinal data in > QDEC. I have 3 groups and created a file for the discrete factor "group" with > three levels (1,2 and 3). I have done the same for gender (with 2 levels). > The analysis with gender works just fine but when I try to use group as a > factor I get an error message that factor 1 must have 2 levels: > > SUBJECTS_DIR is '/scr/etsch2/kids/ct' > ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels > ninputs = 72 > Checking inputs > nframestot = 72 > Allocing output > Done allocing > nframes = 72 > Writing to /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh > gdfReadHeader: reading > /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd > INFO: gd2mtx_method is dods > Reading source surface /scr/etsch2/kids/ct/87kids_template/surf/lh.white > ERROR: no contrasts specified. > Error in Analyze: command failed: mri_glmfit --y > /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh --fsgd > /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd dods --glmdir > /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1 --surf 87kids_template lh > > In the tutorial it doesn't state that QDEC has to have discrete factors with > 2 levels only. > Am I doing something wrong or is there a work-around for that? > > Cheers, Clara > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu ___ 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] REPOST: QDEC analysis
Dear FreeSurfer experts, I am trying to analyze some single time points of my longitudinal data in QDEC. I have 3 groups and created a file for the discrete factor "group" with three levels (1,2 and 3). I have done the same for gender (with 2 levels). The analysis with gender works just fine but when I try to use group as a factor I get an error message that factor 1 must have 2 levels: SUBJECTS_DIR is '/scr/etsch2/kids/ct' ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 72 Checking inputs nframestot = 72 Allocing output Done allocing nframes = 72 Writing to /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh gdfReadHeader: reading /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd INFO: gd2mtx_method is dods Reading source surface /scr/etsch2/kids/ct/87kids_template/surf/lh.white ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh --fsgd /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd dods --glmdir /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1 --surf 87kids_template lh In the tutorial it doesn't state that QDEC has to have discrete factors with 2 levels only. Am I doing something wrong or is there a work-around for that? Cheers, Clara ___ 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.
