Re: [Freesurfer] longitudinal spc over an ROI

[Martin Reuter]

Hi Rachel,

yes, there is a difference if you compute SPC of the average thickness in an 
ROI or if you average the SPC computed on a vertex level. 

For the second, you can use long_mris_surf to map your third group to fsaverage 
and compute SPC, there is an option to write out the stack, then using the 
label and that stack you can average the values inside the label. I would do 
that in Matlab (read the stack, read the label, select the vertices with that 
label and average). Maybe there are other tools for that. 

Best, Martin


> On Sep 16, 2016, at 5:05 PM, Rachel Romeo  wrote:
> 
> Hi,
> 
> I have 3 participant groups in my data set, all with 2 longitudinal time 
> points approximately evenly spaced. I've run everyone through the 
> longitudinal pipeline, and used the Monte Carlo simulation to find a cluster 
> that differs in SPC between groups 1 and 2. Now I want to calculate the 
> average SPC in that cluster for group 3, simply for qualitative reference. 
> 
> I've extracted the cluster to a label using mri_surfcluster, mapped that 
> label to each of the participants' surfaces using mri_label2label, and used 
> mris_anatomical_stats to extract the average thickness in the ROI, and then I 
> manually calculated SPC per subject. But, no matter whether I use 
> participants' CROSS or LONG surfaces, I can't replicate the average SPC 
> values in the "y.ocn.dat" file generated by the simulation.
> 
> My guess is that the difference arises because of the averaging -- I'm 
> averaging over thickness, and then calculating SPC, whereas I'm guessing that 
> the GLM calculates SPC per voxel, and then averages over the cluster. 
> 
> Is there a way I can extract the average SPC for group 3 over this ROI? 
> 
> Thanks,
> Rachel
> 
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[Freesurfer] longitudinal spc over an ROI

[Rachel Romeo]

Hi,

I have 3 participant groups in my data set, all with 2 longitudinal time
points approximately evenly spaced. I've run everyone through the
longitudinal pipeline, and used the Monte Carlo simulation to find a
cluster that differs in SPC between groups 1 and 2. Now I want to calculate
the average SPC in that cluster for group 3, simply for qualitative
reference.

I've extracted the cluster to a label using mri_surfcluster, mapped that
label to each of the participants' surfaces using mri_label2label, and used
mris_anatomical_stats to extract the average thickness in the ROI, and then
I manually calculated SPC per subject. But, no matter whether I use
participants' CROSS or LONG surfaces, I can't replicate the average SPC
values in the "y.ocn.dat" file generated by the simulation.

My guess is that the difference arises because of the averaging -- I'm
averaging over thickness, and then calculating SPC, whereas I'm guessing
that the GLM calculates SPC per voxel, and then averages over the cluster.

Is there a way I can extract the average SPC for group 3 over this ROI?

Thanks,
Rachel
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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.