Great, thank you for your help!
Panos ________________________________________ From: Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 5:39 PM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@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 [greve@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 [greve@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 [greve@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 [greve@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,
- 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
The FS version that I am using is the stable 5.0.0,
I have attached the full terminal output in this email.
Thank you for your time! Panos ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@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 greve@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 greve@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 greve@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 greve@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 greve@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/