Re: [Freesurfer] Using a cluster as an ROI for further analysis

[Ting Li]

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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   MNIZCWPCWPLow
CWPHi   NVtxsWghtVtx   Annot

   1   -4.773   53922   1279.30-32.98.5   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  wrote:
> 
> mri_segstats --i P2P3.stack.mgh --seg ocn.mgh --id N --avgwf 
> P2P3.means-in-clusterN.dat

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Re: [Freesurfer] Using a cluster as an ROI for further analysis

[Ting Li]

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Hi Douglas,

You instruction works perfect. Thanks a lot.

Regards,
Ting
> On Aug 14, 2018, at 11:01 AM, Ting Li  wrote:
> 
> 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 > > 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 >> > 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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>>> 
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> 

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Re: [Freesurfer] Using a cluster as an ROI for further analysis

[Martin Juneja]

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Dear Bruce and Doug,

Thank you so much. Its working perfectly fine.

Best,
MJ

On Tue, Aug 14, 2018 at 8:51 AM, Douglas Greve 
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  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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>
>
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Re: [Freesurfer] Using a cluster as an ROI for further analysis

[Ting Li]

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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  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 > > 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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>> 
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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
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> properly
> dispose of the e-mail.

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Re: [Freesurfer] Using a cluster as an ROI for further analysis

[Douglas Greve]

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 > 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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Re: [Freesurfer] Using a cluster as an ROI for further analysis

[Bruce Fischl]

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:



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  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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Re: [Freesurfer] Using a cluster as an ROI for further analysis

[Martin Juneja]

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  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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