Hi Martin

create a label for X1, then use mri_label2label to map it to each of your subjects in P2 and P3

cheers Bruce On Mon, 13 Aug 2018, Martin Juneja wrote:

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For instance, if there is any way to extract spatial location of cluster X1 and use this location to extract thickness values of all the subjects from P2 and P3, that way I can perform two-sample t-test. I am not sure if that's feasible and if so, then how can we do that?

On Mon, Aug 13, 2018 at 7:04 PM, Martin Juneja mj70481@gmail.com wrote: Hi experts, I found a cluster X1, which showed significant difference in cortical thickness between two groups C1 and P1, determined using mris_preproc, mri_surf2surf and mri_glmfit commands.

I am interested in determining if the same cluster X1 has significantly different cortical thickness group between two other groups P2 and P3.

I would really appreciate if you could please give me the step-by-step guidance how this can be done.

Thanks.

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Hi experts,

I have a significant cortical thickness cluster and want the cluster thickness information in every subjects. How should I do it? Thanks.

Ting

On Aug 14, 2018, at 10:51 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:

First, run mris_preproc and mri_surf2surf commands as before to create a stack of P2 and P3. If you ran mri_glmfit-sim on P1, then you will have an "ocn" output file. You can run mri_segstats --i P2P3.stack.mgh --seg ocn.mgh --id N --avgwf P2P3.means-in-clusterN.dat where N is the number of your cluster P2P3.means-in-clusterN.dat will have a row for each subject in the stack, the value will be the mean in cluster N

On 8/13/18 11:48 PM, Martin Juneja wrote:

...

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For instance, if there is any way to extract spatial location of cluster X1 and use this location to extract thickness values of all the subjects from P2 and P3, that way I can perform two-sample t-test. I am not sure if that's feasible and if so, then how can we do that?

On Mon, Aug 13, 2018 at 7:04 PM, Martin Juneja <mj70481@gmail.com mailto:mj70481@gmail.com> wrote: Hi experts,

I found a cluster X1, which showed significant difference in cortical thickness between two groups C1 and P1, determined using mris_preproc, mri_surf2surf and mri_glmfit commands.

I am interested in determining if the same cluster X1 has significantly different cortical thickness group between two other groups P2 and P3.

I would really appreciate if you could please give me the step-by-step guidance how this can be done.

Thanks.

---

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Hi experts,

How to create the stack of P2P3.stack.mgh after mris_preproc and mir_surf2surf? Great thanks.

Regards, Ting

On Aug 14, 2018, at 10:51 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:

First, run mris_preproc and mri_surf2surf commands as before to create a stack of P2 and P3. If you ran mri_glmfit-sim on P1, then you will have an "ocn" output file. You can run mri_segstats --i P2P3.stack.mgh --seg ocn.mgh --id N --avgwf P2P3.means-in-clusterN.dat where N is the number of your cluster P2P3.means-in-clusterN.dat will have a row for each subject in the stack, the value will be the mean in cluster N

On 8/13/18 11:48 PM, Martin Juneja wrote:

...

    External Email - Use Caution        

For instance, if there is any way to extract spatial location of cluster X1 and use this location to extract thickness values of all the subjects from P2 and P3, that way I can perform two-sample t-test. I am not sure if that's feasible and if so, then how can we do that?

On Mon, Aug 13, 2018 at 7:04 PM, Martin Juneja <mj70481@gmail.com mailto:mj70481@gmail.com> wrote: Hi experts,

I found a cluster X1, which showed significant difference in cortical thickness between two groups C1 and P1, determined using mris_preproc, mri_surf2surf and mri_glmfit commands.

I am interested in determining if the same cluster X1 has significantly different cortical thickness group between two other groups P2 and P3.

I would really appreciate if you could please give me the step-by-step guidance how this can be done.

Thanks.

---

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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.

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Hi experts,

I have extracted the area of the significant cluster with the command like the following: mri_segstats --i mgh/lh.volume.all.mgh --seg glmdir_az_vz/lh.volume.all.glmdir/av-group2-vs-group2/cache.th20.neg.sig.ocn.mgh --id 1 --sumwf group1_group2_volume_l.sum-clusters.dat

When I use a t-test for these two group summarized area value, the p value is 0.1398. I did the same process for other significant clusters. However, it is the only one without significant p-value. The detail of the cluster information is listed below.

# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot

1 -4.773 53922 1279.30 -32.9 8.5 55.3 0.00300 0.00200 0.00400 2126 -5375.69 caudalmiddlefrontal

Could you give me some ideas where I should find the reason? Thanks a lot!

Regards, Ting

On Aug 14, 2018, at 10:51 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:

mri_segstats --i P2P3.stack.mgh --seg ocn.mgh --id N --avgwf P2P3.means-in-clusterN.dat