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
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
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-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
Hey Doug,
I was wondering whether you had a chance to give this a look!
Thanks again, Panos ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis Sent: Tuesday, May 28, 2013 1:38 PM To: Douglas Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons error
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-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
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
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/
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/
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/
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/
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/
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/
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/
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
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
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/
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Fotiadis, Panagiotis