Just reposting a message not answered yet.
Many thanks!
Pablo
From: pablonajt@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Tue, 6 Oct 2015 14:39:13 +0000
Subject: Re: [Freesurfer] percent difference adjust to results {Disarmed}
_______________________________________________ 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.
From: pablonajt@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Tue, 6 Oct 2015 14:39:13 +0000
Subject: Re: [Freesurfer] percent difference adjust to results {Disarmed}
Hello Doug,
Group.mean.mgh doesn't look negative see when opening with tksurfer, below. 
I re-run the computation to make sure. When I opened the pctdiff and increased the minimum threshold from 3 to 4 and above the colour maps changed from light blue to yellow. 
Date: Mon, 5 Oct 2015 19:28:06 -0400
From: greve@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] percent difference adjust to results {Disarmed}
It looks like the pctdiff changed sign which would happen if group.mean.mgh had negatives. Does it?
_______________________________________________ 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.
I re-run the computation to make sure. When I opened the pctdiff and increased the minimum threshold from 3 to 4 and above the colour maps changed from light blue to yellow.
Pctdiff with threshold 3
With threshold 4
Could you advice which would be the right setup and also how do I figure it out how much percent difference in the cluster of my results below, please?
Date: Mon, 5 Oct 2015 19:28:06 -0400
From: greve@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] percent difference adjust to results {Disarmed}
It looks like the pctdiff changed sign which would happen if group.mean.mgh had negatives. Does it?
On 10/3/15 2:38 AM, pablo najt wrote:
Hi my message was lost in the long correspondences. Would anyone advice about below, please?Thank you.Pablo
From: pablonajt@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Thu, 1 Oct 2015 11:47:10 +0000
Subject: [Freesurfer] percent difference adjust to results {Disarmed}
Dear FS expertsI have a query about how can I make that the percent difference results matches the same clusters of my output from my main glm analysis.I run a glm analysis g4v1 (Male_Pt, Male_HC, Fem_Pt, Fem_HC) with Age and sex as covariates.My contrasts are as follow-0.5 0.5 -0.5 0.5 0 0 0 0This contrast is meant to test "is there a difference between HC and PT controlling for age and sex.
I separately run contrast of PT agains "0"0.5 0 0.5 0 0 0 0 0and HC against "0"0 0.5 0 0.5 0 0 0 0
calculated percent difference as followsfscalc Pt_group/gamma.mgh add HCgroup/gamma.mgh div 2 -o group.mean.mghThen computed the percent difference: fscalc HCgroup/gamma.mgh sub Pt_group/gamma.mgh div group.mean.mgh mul 100 -o pctdiff.mgh
Now when I open my results from the first contrast above and the pctdiff.mgh separately, I am not quite sure they match. How could I adjust the min and saturation values to make them match and show how much percent difference is between the groups in the cluster shown in the main contrast. I have embedded the two results and parameters to give you an idea of how I am setting this up and if there is anything I can tune to improve visualisation.Thank you very much in advance.Pablo
results from main contrast
pctdiff
_______________________________________________ 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.
_______________________________________________ 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 . 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.
_______________________________________________ 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.