mri_binarize --i HC.43.rh/v1.slope/results.ocn.mgh --match 1 --o
cluster1mask.mgh
You can concatenate all your subjects together in fsaverage space
(mris_preprpoc), optionally smooth it, then
mri_segstats ---i yourstackallsubjects.mgh --excludeid 0 --seg
HC.43.rh/v1.slope/results.ocn.mgh --avgwf ocn.avgwf.dat
ocn.avgwf.dat will be a text file with number of rows = number of
subjects in the stack, and number of columns equal to the number of clusters
On 04/09/2017 12:01 PM, lindsay hanford wrote:
> Hello Freesurfer Developers,
>
> The main point of my post is to determine whether its possible to
> create a mask from a cluster ID run using a subset of the sample, and
> then use that mask to extract cortical thickness values from a model
> run with the full sample.
>
> I am running a pretty basic cortical thickness- behavioural
> correlation analysis with two groups using fsgd. Because I have a
> relatively small sample size (just over 40 participants in each group)
> I wanted to restrict my analysis to only regions that showed a
> relationship within the HC group. I ran the model using mri_glmfit:
>
> mri_glmfit --y HC.43.rh.10.mgh --fsgd Behav.fsgd --C v1.slope.mtx
> --surf fsaverage rh --cortex --glmdir MCCB.HC.43.rh
>
> Behav.fsgd setup:
> GroupDescriptorFile 1
> Title MaineffectofGroup
> Class HC
> Variables BehavMC
> Input 128 HC -5
> Input 132 HC 8
> Input 192 HC -10
> Input 193 HC -6
> ...
>
> v1.slope.mtx:
> 0 1
>
> *quick side question - in the past I was curious to see if this could
> test positive and negative relationships. I tried two different
> contrasts: 0 1 and 0 -1 to test the positive and negative
> relationships, respectively, however the results were the direct
> inverse of each other... it didn't show negative slope relationships.
> I am curious if its possible to test for negative relationships in
> freesurfer? How would you set up that contrast?
>
> next, I used mri_surfcluster to generate image and table files:
> mri_surfcluster --in HC.43.rh/v1.slope/sig.mgh --subject fsaverage
> --hemi rh --surf pial --annot aparc --thmin 2 --ocn
> HC.43.rh/v1.slope/results.ocn.mgh --sum HC.43.rh/v1.slope/results.sum.txt
>
> my results.sum.txt file shows a number of clusters
> ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZNVtxs Annot
>13.719 163035270.33 57.7 -34.6 -21.5 234
> inferiortemporal
>23.499 22608217.35 33.2 -48.2 -15.1 230 fusiform
>33.1702804 93.01 42.1 22.1 23.9 132
> rostralmiddlefrontal
>
> Would it be possible to create a mask defined by say "ClusterNo 1"?
>
> Once the mask is created, I want to use it to extract the cortical
> thickness values for all participants (including those that weren't
> used to create the mask).. Is this possible? Can that be done using
> mri_segstats?
>
> Let me know if you require any other details.
> Freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
>
> Thank you in advance,
>
>
> Lindsay
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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