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 TalZ NVtxs Annot 1 3.719 163035 270.33 57.7 -34.6 -21.5 234 inferiortemporal 2 3.499 22608 217.35 33.2 -48.2 -15.1 230 fusiform 3 3.170 2804 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
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 TalZ NVtxs Annot 1 3.719 163035 270.33 57.7 -34.6 -21.5 234 inferiortemporal 2 3.499 22608 217.35 33.2 -48.2 -15.1 230 fusiform 3 3.170 2804 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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lindsay hanford