Re: [Freesurfer] FS-FAST: cluster size from 1st level analysis

[Keri Woods]

External Email - Use Caution

Thanks.

On Tue, Oct 15, 2019 at 5:00 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Correct
>
> On 10/15/2019 9:38 AM, Keri Woods wrote:
>
> External Email - Use Caution
> Hi Doug
>
> Thank you very much for the very helpful reply! It worked perfectly and
> was exactly what I needed. I assume that these are the clusters after
> cluster-level correction for multiple comparison since --csd is used?
>
> Thanks,
> Keri
>
> On Tue, Oct 15, 2019 at 4:17 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Sorry for the delay ...
>>
>> First, run selxavg3-sess with -fwhm ( you might need to delete the
>> bold/analysis folder to get it to re-run).
>>
>> cd session/bold/analyis
>> There will be a filed called fwhm.dat. Look in that. Depending upon how
>> much you smoothed it might be something like 10.395. This is the FWHM in
>> mm. Next, you can run something like the following command
>>
>> mri_surfcluster --in contrast/sig.nii.gz --hemi lh --csd
>> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhmXX/abs/thTT/mc-z.cdf
>> --mask mask.nii.gz --sum contrast.sum.dat --oannot ./lh.contrast.annot
>> --thmin T --sign abs --subject fsaverage --cwpvalthresh .05
>>
>> Note that the subject must be fsaverage because the tables were computed
>> with fsaverage. Above, fwhmXX would be fwhm11 (because the FWHM is 10.395,
>> but round up to 11). TT refers to the cluster forming threshold (eg, p<.001
>> would be 30), and so --thmin T would be 3. "abs" in the path to the CSD
>> file indicates that you want to use an unsigned (absolute) value; you can
>> also use pos and neg. --cwpvalthresh .05 means to filter out any clusters
>> that are not significant at p=0.05. The cluster table will be in
>> contrast.sum.dat
>>
>> doug
>>
>>
>> On 10/3/2019 7:52 AM, Keri Woods wrote:
>>
>> External Email - Use Caution
>> Hi
>>
>> From the 1st level analysis of an fMRI study I'm trying to extract the
>> size of the clusters of activation from each subject, but don't know how to
>> go about this. I know that for the group analysis you can get the cluster
>> sizes from the output from mri_glm-sim. Is there a way to run the multiple
>> comparison correction on the first level analysis in order to get this
>> table? Or is there another way of getting the cluster sizes?
>>
>> Any help would be much appreciated.
>>
>> Thank you,
>> Keri
>>
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>>
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Re: [Freesurfer] FS-FAST: cluster size from 1st level analysis

[Greve, Douglas N.,Ph.D.]

Correct

On 10/15/2019 9:38 AM, Keri Woods wrote:

External Email - Use Caution

Hi Doug

Thank you very much for the very helpful reply! It worked perfectly and was 
exactly what I needed. I assume that these are the clusters after cluster-level 
correction for multiple comparison since --csd is used?

Thanks,
Keri

On Tue, Oct 15, 2019 at 4:17 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Sorry for the delay ...

First, run selxavg3-sess with -fwhm ( you might need to delete the 
bold/analysis folder to get it to re-run).

cd session/bold/analyis
There will be a filed called fwhm.dat. Look in that. Depending upon how much 
you smoothed it might be something like 10.395. This is the FWHM in mm. Next, 
you can run something like the following command

mri_surfcluster --in contrast/sig.nii.gz --hemi lh --csd 
$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhmXX/abs/thTT/mc-z.cdf
 --mask mask.nii.gz --sum contrast.sum.dat --oannot ./lh.contrast.annot --thmin 
T --sign abs --subject fsaverage --cwpvalthresh .05

Note that the subject must be fsaverage because the tables were computed with 
fsaverage. Above, fwhmXX would be fwhm11 (because the FWHM is 10.395, but round 
up to 11). TT refers to the cluster forming threshold (eg, p<.001 would be 30), 
and so --thmin T would be 3. "abs" in the path to the CSD file indicates that 
you want to use an unsigned (absolute) value; you can also use pos and neg. 
--cwpvalthresh .05 means to filter out any clusters that are not significant at 
p=0.05. The cluster table will be in contrast.sum.dat

doug


On 10/3/2019 7:52 AM, Keri Woods wrote:

External Email - Use Caution

Hi

From the 1st level analysis of an fMRI study I'm trying to extract the size of 
the clusters of activation from each subject, but don't know how to go about 
this. I know that for the group analysis you can get the cluster sizes from the 
output from mri_glm-sim. Is there a way to run the multiple comparison 
correction on the first level analysis in order to get this table? Or is there 
another way of getting the cluster sizes?

Any help would be much appreciated.

Thank you,
Keri



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Re: [Freesurfer] FS-FAST: cluster size from 1st level analysis

[Keri Woods]

External Email - Use Caution

Hi Doug

Thank you very much for the very helpful reply! It worked perfectly and was
exactly what I needed. I assume that these are the clusters after
cluster-level correction for multiple comparison since --csd is used?

Thanks,
Keri

On Tue, Oct 15, 2019 at 4:17 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Sorry for the delay ...
>
> First, run selxavg3-sess with -fwhm ( you might need to delete the
> bold/analysis folder to get it to re-run).
>
> cd session/bold/analyis
> There will be a filed called fwhm.dat. Look in that. Depending upon how
> much you smoothed it might be something like 10.395. This is the FWHM in
> mm. Next, you can run something like the following command
>
> mri_surfcluster --in contrast/sig.nii.gz --hemi lh --csd
> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhmXX/abs/thTT/mc-z.cdf
> --mask mask.nii.gz --sum contrast.sum.dat --oannot ./lh.contrast.annot
> --thmin T --sign abs --subject fsaverage --cwpvalthresh .05
>
> Note that the subject must be fsaverage because the tables were computed
> with fsaverage. Above, fwhmXX would be fwhm11 (because the FWHM is 10.395,
> but round up to 11). TT refers to the cluster forming threshold (eg, p<.001
> would be 30), and so --thmin T would be 3. "abs" in the path to the CSD
> file indicates that you want to use an unsigned (absolute) value; you can
> also use pos and neg. --cwpvalthresh .05 means to filter out any clusters
> that are not significant at p=0.05. The cluster table will be in
> contrast.sum.dat
>
> doug
>
>
> On 10/3/2019 7:52 AM, Keri Woods wrote:
>
> External Email - Use Caution
> Hi
>
> From the 1st level analysis of an fMRI study I'm trying to extract the
> size of the clusters of activation from each subject, but don't know how to
> go about this. I know that for the group analysis you can get the cluster
> sizes from the output from mri_glm-sim. Is there a way to run the multiple
> comparison correction on the first level analysis in order to get this
> table? Or is there another way of getting the cluster sizes?
>
> Any help would be much appreciated.
>
> Thank you,
> Keri
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] FS-FAST: cluster size from 1st level analysis

[Greve, Douglas N.,Ph.D.]

Sorry for the delay ...

First, run selxavg3-sess with -fwhm ( you might need to delete the 
bold/analysis folder to get it to re-run).

cd session/bold/analyis
There will be a filed called fwhm.dat. Look in that. Depending upon how much 
you smoothed it might be something like 10.395. This is the FWHM in mm. Next, 
you can run something like the following command

mri_surfcluster --in contrast/sig.nii.gz --hemi lh --csd 
$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhmXX/abs/thTT/mc-z.cdf
 --mask mask.nii.gz --sum contrast.sum.dat --oannot ./lh.contrast.annot --thmin 
T --sign abs --subject fsaverage --cwpvalthresh .05

Note that the subject must be fsaverage because the tables were computed with 
fsaverage. Above, fwhmXX would be fwhm11 (because the FWHM is 10.395, but round 
up to 11). TT refers to the cluster forming threshold (eg, p<.001 would be 30), 
and so --thmin T would be 3. "abs" in the path to the CSD file indicates that 
you want to use an unsigned (absolute) value; you can also use pos and neg. 
--cwpvalthresh .05 means to filter out any clusters that are not significant at 
p=0.05. The cluster table will be in contrast.sum.dat

doug


On 10/3/2019 7:52 AM, Keri Woods wrote:

External Email - Use Caution

Hi

From the 1st level analysis of an fMRI study I'm trying to extract the size of 
the clusters of activation from each subject, but don't know how to go about 
this. I know that for the group analysis you can get the cluster sizes from the 
output from mri_glm-sim. Is there a way to run the multiple comparison 
correction on the first level analysis in order to get this table? Or is there 
another way of getting the cluster sizes?

Any help would be much appreciated.

Thank you,
Keri



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[Freesurfer] FS-FAST: cluster size from 1st level analysis

[Keri Woods]

External Email - Use Caution

Hi

From the 1st level analysis of an fMRI study I'm trying to extract the size
of the clusters of activation from each subject, but don't know how to go
about this. I know that for the group analysis you can get the cluster
sizes from the output from mri_glm-sim. Is there a way to run the multiple
comparison correction on the first level analysis in order to get this
table? Or is there another way of getting the cluster sizes?

Any help would be much appreciated.

Thank you,
Keri
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