you would report .03 doug
On 05/30/2013 05:10 PM, Fotiadis, Panagiotis wrote: > 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 > > -- 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.
