Re: [Freesurfer] glmfit error on v5.1
Can you send the matrix that it creates? On 12/02/2013 06:09 AM, Gabriel Gonzalez Escamilla wrote: Dear Freesurfer experts, Sorry for the inconvenience but I posted this message last week, but I did not receive any answer. I really need to keep going on with my analyses. I have runned the following command line: mri_glmfit --surf PLI_MCI_sample7_avg lh --C /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/contrast_withinE4_neg.mat --fsgd /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/lh.cortex_AVGthickness_APOB_fsgd.txt dods --label /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/label/lh.cortex.label --y /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/lh.thickness_s12mm.mgh --no-prune --glmdir /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/resultsthickness_cortex_s12mm_BiomrkrsWithin/lh.cortex_AVGthickness_APOB_contrast_withinE4_neg/ which is always prompts the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.75146e+07 Possible problem with experimental design I'm sending attached the fsgd.txt and contras.mat files used in case you need them Does anyone knows what's wrong with my design? Many thanks in advanced, Gabriel. ___ 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 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] glmfit error on v5.1
There you are!Hope it helps- Mensaje original -De: Douglas N Greve gr...@nmr.mgh.harvard.eduFecha: Lunes, 2 de Diciembre de 2013, 5:09 pmAsunto: Re: [Freesurfer] glmfit error on v5.1A: freesurfer@nmr.mgh.harvard.edu Can you send the matrix that it creates? On 12/02/2013 06:09 AM, Gabriel Gonzalez Escamilla wrote: Dear Freesurfer experts, Sorry for the inconvenience but I posted this message last week, but I did not receive any answer. I really need to keep going on with my analyses.I have runned the following command line: mri_glmfit --surf PLI_MCI_sample7_avg lh --C/root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/contrast_withinE4_neg.mat --fsgd/root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/lh.cortex_AVGthickness_APOB_fsgd.txt dods --label/root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/label/lh.cortex.label --y/root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/lh.thickness_s12mm.mgh --no-prune --glmdir/root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/resultsthickness_cortex_s12mm_BiomrkrsWithin/lh.cortex_AVGthickness_APOB_contrast_withinE4_neg/ which is always prompts the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.75146e+07 Possible problem with experimental designI'm sending attached the fsgd.txt and contras.mat files used in case you need themDoes anyone knows what's wrong with my design?Many thanks in advanced, Gabriel.___ 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 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. font size="3"--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font Xg.dat Description: Binary data ___ 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] glmfit error on v5.1
The problem is in the noE4female group. You only have 3 subjects and the zAPOB and thickness are nearly equal and opposite in sign. The correlation between these two regressors exceeds .96. This is probably spurious, but it is killing the design matrix. doug On 12/02/2013 11:44 AM, Gabriel Gonzalez Escamilla wrote: There you are! Hope it helps - Mensaje original - De: Douglas N Greve gr...@nmr.mgh.harvard.edu Fecha: Lunes, 2 de Diciembre de 2013, 5:09 pm Asunto: Re: [Freesurfer] glmfit error on v5.1 A: freesurfer@nmr.mgh.harvard.edu Can you send the matrix that it creates? On 12/02/2013 06:09 AM, Gabriel Gonzalez Escamilla wrote: Dear Freesurfer experts, Sorry for the inconvenience but I posted this message last week, but I did not receive any answer. I really need to keep going on with my analyses. I have runned the following command line: mri_glmfit --surf PLI_MCI_sample7_avg lh --C /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/contrast_withinE4_neg.mat --fsgd /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/glm_files/lh.cortex_AVGthickness_APOB_fsgd.txt dods --label /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/label/lh.cortex.label --y /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/lh.thickness_s12mm.mgh --no-prune --glmdir /root/trabajo/freesurfer/subjects/PLI_MCI_sample7_avg/stats_MRI_PET_Biomarkers/resultsthickness_cortex_s12mm_BiomrkrsWithin/lh.cortex_AVGthickness_APOB_contrast_withinE4_neg/ which is always prompts the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.75146e+07 Possible problem with experimental design I'm sending attached the fsgd.txt and contras.mat files used in case you need them Does anyone knows what's wrong with my design? Many thanks in advanced, Gabriel. ___ 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 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. font size=3--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font -- 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
