Re: [Freesurfer] Reposting: Clusters by Multiple comparison
Hi Antonella, the right way to do it is to figure out what is going wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you send the log file? Should be permcsd.mri_glmfit-sim.log. If you need to run it for debugging purposes, you can run it with 10 iterations (change permcsd to permcsdtmp so you don't overwrite what is there). This should produce all the files, so if something is not there, it should be easy to track down why. doug Antonella Kis wrote: Dear Doug, When I run the: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space? Thank you. AK -- 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: 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.
Re: [Freesurfer] Reposting: Clusters by Multiple comparison
Hi Doug, Thank you very much for your help. I attached the log file. I can get the clusters summary if I run the mri_volcluster but it will give the correct clusters if I am not mentioning the --reg option? Also, when I am visualizing my clusters using tkmedit: tkmedit cvs_avg35 norm.mgz \ -ov /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh \ -seg /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh \ /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut \ -fthresh 0.2 -fmax 1 I can read the functional value for each cluster. What exactly this value represents? Is my FA value or -log10(p)? How can I get my FA values within each cluster in a table? Thank you so much. Antonella From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, February 8, 2012 11:37 AM Subject: Re: Reposting: Clusters by Multiple comparison Hi Antonella, the right way to do it is to figure out what is going wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you send the log file? Should be permcsd.mri_glmfit-sim.log. If you need to run it for debugging purposes, you can run it with 10 iterations (change permcsd to permcsdtmp so you don't overwrite what is there). This should produce all the files, so if something is not there, it should be easy to track down why. doug Antonella Kis wrote: Dear Doug, When I run the: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space? Thank you. AK -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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. permcsd.mri_glmfit-sim.log 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] Reposting: Clusters by Multiple comparison
Oh, ok, I remember this now. Yes, you can use your mri_volcluster command below the clusters. To get the table, run mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i fa.nii.gz --avgtwf fa.avg.dat --sum permcsd.sig.cluster.summary The fa.avg.dat will have a table of data. Each row will be a subject, each column a cluster (matching that found in permcsd.sig.cluster.summary) doug Antonella Kis wrote: Hi Doug, Thank you very much for your help. I attached the log file. I can get the clusters summary if I run the mri_volcluster but it will give the correct clusters if I am not mentioning the --reg option? Also, when I am visualizing my clusters using tkmedit: tkmedit cvs_avg35 norm.mgz \ -ov /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh \ -seg /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh \ /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut \ -fthresh 0.2 -fmax 1 I can read the functional value for each cluster. What exactly this value represents? Is my FA value or -log10(p)? How can I get my FA values within each cluster in a table? Thank you so much. Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, February 8, 2012 11:37 AM *Subject:* Re: Reposting: Clusters by Multiple comparison Hi Antonella, the right way to do it is to figure out what is going wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you send the log file? Should be permcsd.mri_glmfit-sim.log. If you need to run it for debugging purposes, you can run it with 10 iterations (change permcsd to permcsdtmp so you don't overwrite what is there). This should produce all the files, so if something is not there, it should be easy to track down why. doug Antonella Kis wrote: Dear Doug, When I run the: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space? Thank you. AK -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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 gr...@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
Re: [Freesurfer] Reposting: Clusters by Multiple comparison
What I have listed as fa.nii.gz should be the same file that you passed to mri_glmfit with the --y option. doug Antonella Kis wrote: Dear Doug, THANKS SO MUCH for your help. My last questions is: I suppose the --i fa.nii.gz is an input file. What should be my input in thi scase if for each subject I have different fa values and gor the mri_glmfit I used the GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz which is the concanetated masked file resampled to the CVS space. Should I use this file or what exactly for the fa.nii.gz? Also will mri_volcluster but it will give the correct clusters if I am not mentioning the --reg option? MAny thanks and have a great day! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, February 8, 2012 1:50 PM *Subject:* Re: Reposting: Clusters by Multiple comparison Oh, ok, I remember this now. Yes, you can use your mri_volcluster command below the clusters. To get the table, run mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i fa.nii.gz --avgtwf fa.avg.dat --sum permcsd.sig.cluster.summary The fa.avg.dat will have a table of data. Each row will be a subject, each column a cluster (matching that found in permcsd.sig.cluster.summary) doug Antonella Kis wrote: Hi Doug, Thank you very much for your help. I attached the log file. I can get the clusters summary if I run the mri_volcluster but it will give the correct clusters if I am not mentioning the --reg option? Also, when I am visualizing my clusters using tkmedit: tkmedit cvs_avg35 norm.mgz \ -ov /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh \ -seg /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh \ /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.lut \ -fthresh 0.2 -fmax 1 I can read the functional value for each cluster. What exactly this value represents? Is my FA value or -log10(p)? How can I get my FA values within each cluster in a table? Thank you so much. Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, February 8, 2012 11:37 AM *Subject:* Re: Reposting: Clusters by Multiple comparison Hi Antonella, the right way to do it is to figure out what is going wrong with mri_glmfit-sim. Did it obviously fail in some way? Can you send the log file? Should be permcsd.mri_glmfit-sim.log. If you need to run it for debugging purposes, you can run it with 10 iterations (change permcsd to permcsdtmp so you don't overwrite what is there). This should produce all the files, so if something is not there, it should be easy to track down why. doug Antonella Kis wrote: Dear Doug, When I run the: mri_glmfit-sim \ --glmdir GroupAnalysis_pos.glmdir \ --sim perm 1 3 permcsd \ --sim-sign pos \ --cwpvalthresh .05 I am not getting my clusters file permcsd.sig.cluster.mgh with the clusters summary so as you recommended I am running the mri_volcluster --in Group_Analysis.glmdir/contrast/sig.mgh --mask Group_Analysis.glmdir/mask.mgh --no-fixmni --cwsig Group_Analysis.glmdir/contrast/permcsd.sig.cluster.mgh --sum Group_Analysis.glmdir/contrast/permcsd.sig.cluster.summary --ocn Group_Analysis.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 norm.mgz --csdpdf Group_Analysis.glmdir/contrast/permcsd.pdf.dat --csd Group_Analysis.glmdir/csd/permcsd.j001-contrast.csd --vwsig Group_Analysis.glmdir/contrast/permcsd.sig.voxel.mgh My question is: it is OK if I am not mentioning any registration or what should I input under --reg while I running the mri_volcluster if my for DTI preprocessing I used the dt_recon which computes for each subject an fa.nii and register.dat using the Talairach registration and later I registered all my subjects on the CVS space? Thank you. AK -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:
