Thanks Douglas. I am not sure that I understand. Will you please review the
commands below?
I believe I need to complete something like:
mri_surfcluster --in ${qdecoutputfolder}/cache.th40.abs.sig.masked.mgh
--fdr 0.05 --mask ${qdecoutputfolder}/mask.mgh --csd
/usr/local/freesurfer/average/mult-comp-cor/rh/cortex/fwhm25/abs/th40/mc-z.csd
--surf pial --ocn ${qdecoutputfolder}/
Which puts out a *.w file, a COR-00#, and COR.info, but I am not sure which
file I should supply to -- seg
mri_segstats --seg ?? --i y.mgh --avgfw ${nameoftextoutput} --exludeid 0
Could I supply the ocn file from the mri_glmfit-sim?
On Mon, Jan 23, 2017 at 7:10 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> It is probably better to work with the y.mgh file that qdec produces. It
> is in fsaverage space. If you create an ocn file with mri_surfcluster, you
> can feed that as the --seg to mri_segstats (along with --i y.mgh), spec the
> output with --avgwf to get a matrix of nsubjects by nclusters (make sure
> to also include --exludeid 0)
>
>
> On 01/23/2017 08:00 PM, Katherine Damme wrote:
>
>> Thank you so much!
>>
>> This got me to the stage of having separate labels for each significant
>> cluster, but I would like to extract the values from each subject to look
>> at the raw data.
>>
>> Do I have to use mri_label2label to move the label into each individual's
>> space?
>>
>> Can I use aparcstats2table to get a table of the individual values of the
>> label?
>> (It seems that this is set up for the segmentation data)
>>
>> Thank you again!
>>
>>
>> On Mon, Jan 23, 2017 at 11:44 AM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> Try mri_surfcluster. Run it with --help to get usage. You can set the
>> threshold with --fdr. Make sure to use the --mask option passing
>> it the
>> mask.mgh from the qdec output
>>
>>
>> On 01/22/2017 07:56 PM, Katherine Damme wrote:
>> > Hello Everyone,
>> >
>> > Is there a way to extract the significant clusters as masks from
>> > significant group comparisons using qdec?
>> >
>> > All I can seem to find is mri_glmfit-sim which doesn't quite
>> > replicate the QDEC FDR 0.05 output and doesn't seem to make anything
>> > that I could extract as a label, or hand drawing an ROI.
>> >
>> > I am working with a longitudinal model of cortical thickness, and
>> > would like to extract the average thickness of each significant
>> > cluster to understand the change in thickness.
>> >
>> > Thank you.
>> >
>> > Kate Damme
>> >
>> >
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>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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