Sorry for the follow up email. If for instance I want to see any clusters that have a p value of 0.05 or less, I need to set the cluster wise p value in the mri_glmfit-sim command to 0.025 (to account for the correction over the two hemispheres). Then, suppose that a cluster is shown in the summary that has a p value of 0.015. Is that its actual p value, or is its actual p value (that is the value reported to the paper) 0.03?
Thanks, Panos ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis Sent: Thursday, May 30, 2013 4:50 PM To: Douglas N Greve Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error Great, thanks! Panos ________________________________________ From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 4:47 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error yes On 05/30/2013 04:43 PM, Fotiadis, Panagiotis wrote: > Great, thanks!! > > In addition, since I am applying the mri_glmfit (and mri_glmfit-sim) analysis > on each hemisphere separately (lh.******.glmfit and rh.******.glmfit) do I > still need to apply the correction over the two hemispheres (that is divide > by 2 the cluster wise threshold since in FS 5.0.0 the --2spaces flag does not > apply)? > > Best, > Panos > ________________________________________ > From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] > Sent: Thursday, May 30, 2013 4:29 PM > To: Fotiadis, Panagiotis > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Correction for multiple comparisons error > > This is a problem with version 5.0 when you set the clusterwise pvalue > to something close to 1. I re-rand it with .995 and it work. This is > fixed in 5.3 > doug > > > On 05/30/2013 04:23 PM, Fotiadis, Panagiotis wrote: >> Definitely, just uploaded it! >> >> Panos >> ________________________________________ >> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] >> Sent: Thursday, May 30, 2013 4:10 PM >> To: Fotiadis, Panagiotis >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Correction for multiple comparisons error >> >> hmm, can't tell from that what is going on. Can you tar up >> lh.Diseased_gender_age.glmdir and drop it to me at our file drop (URL at >> the end of this email)? >> doug >> >> On 05/30/2013 03:57 PM, Fotiadis, Panagiotis wrote: >>> Hey Doug, >>> >>> Of course, I attached it in txt format in this email! >>> >>> Best, >>> Panos >>> >>> >>> ________________________________________ >>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] >>> Sent: Thursday, May 30, 2013 2:55 PM >>> To: Fotiadis, Panagiotis >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Correction for multiple comparisons error >>> >>> Can you send me the terminal output in a text file? A word doc is very >>> inconvenient:). >>> doug >>> >>> On 05/28/2013 01:38 PM, Fotiadis, Panagiotis wrote: >>>> Hi Doug, >>>> >>>> 1) My cmd line is: >>>> >>>> mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd >>>> Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C >>>> CAA_male-vs-female.mtx --C CAA-vs-Control_age_slope.mtx --C >>>> CAA-vs-Control.mtx --C Males-vs-Females_age_slope.mtx --C >>>> Males-vs-Females.mtx --surf fsaverage lh --cortex --glmdir >>>> lh.Diseased_gender_age.glmdir >>>> >>>> 2) The FS version that I am using is the stable 5.0.0, >>>> >>>> 3) I have attached the full terminal output in this email. >>>> >>>> Thank you for your time! >>>> Panos >>>> ________________________________________ >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve >>>> [gr...@nmr.mgh.harvard.edu] >>>> Sent: Monday, May 27, 2013 10:08 PM >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] Correction for multiple comparisons error >>>> >>>> what is your cmd line? What version of FS are you using? What is the >>>> full terminal output? >>>> doug >>>> >>>> >>>> On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: >>>>> Hi! >>>>> >>>>> I have been running the mri_glmfit-sim command to do the correction for >>>>> multiple comparisons for my group analysis and for some voxel-based >>>>> thresholds (not all) there is an error that comes up when reading the >>>>> colortable from the annotation file: >>>>> >>>>> reading colortable from annotation file... >>>>> colortable with 35 entries read (originally >>>>> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) >>>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: >>>>> 0x0000000006e61230 *** >>>>> *** glibc detected *** mri_surfcluster: malloc(): memory corruption: >>>>> 0x0000000006e61230 *** >>>>> >>>>> and then it gets stuck. Do you happen to know what might be causing this >>>>> issue? >>>>> >>>>> Thank you for your time, >>>>> Panos >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> _______________________________________________ >>>> 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/ >>> >> -- >> 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/ >> >> >> > -- > 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/ > > > -- 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 _______________________________________________ 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 . 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