If you want to apply etiv correction when extracting the cortical volume with
mris_preproc, just add --etiv to the command
On 12/14/2020 9:59 AM, Sara Lyn wrote:
External Email - Use Caution
Hi
Thank you for your response. How do I correct this extracted volume for
intracranial volume (etiv)?
Thank you
Sara
On Sun, Dec 13, 2020 at 12:30 PM Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
When you run the thickness analysis with multiple comparisons correction
(mri_glmfit-sim), it will create "ocn" files. These will be clusters of the
significant areas. You can use this to extract other information. If you want
volume, then run mris_preproc using the --meas volume flag, the apply the ocn
to this file using mri_segstats using the --avgwf and --accumulate flags (and
--exclude 0). This will give you a nsubjects-by-nclusters text file where each
entry is the volume for that subject/cluster
On 12/8/2020 10:48 AM, Sara Lyn wrote:
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Hi Joceyln,
I'm not trying to run a new group analysis but want to extract volume values
from significant thickness ROIs obtained from a thickness group analysis.
Thank you
Sara
On Tue, Dec 8, 2020 at 10:38 AM Mora, Jocelyn S.
<jsm...@mgh.harvard.edu<mailto:jsm...@mgh.harvard.edu>> wrote:
Hi Sara,
You may want to try --meas volume in place of --meas thickness when running
mris_preproc.
I would also recommend looking at our ROI
Analysis<https://secure-web.cisco.com/1g2kRJfau7HjSgmWu9k1y2XTwIMcBGIA-XwH0H7VI8zAxTQzb4aOSMDp6R8Jfi0Po3NMRSG9C0LtNtm6-woQEgwl-cwbWL8_TXyPMqoIvev2Gk5xKmwgW8IuFaQjw69Y3FCuRKwDVHOMSTjPP3MAi29ARxwq_LRpLO7bxtHZW1jAyuRNtrmD4erpddTzuHg3F62ADZRqOYBLyWHlzBBPqp7yCdVoH4o7Gia01u1hT-aoNc8JHUlKMud7cMQz4MsOZAOv64wbXgkh8bAUP0bhvAg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FAnatomicalROIV6.0>
tutorial and Volumetric Group
Analysis<https://secure-web.cisco.com/1tHYiEwJMSx00y8RdQYJIg0nUV5bkFIzrk567zMxayemPQ09G48rqDnWqw4E6yrlMBJLktsyeyMdqA8GdbPJDzXQF7xx_UyMd7vKwH4Re9TF4tJdv1FaNzemfK7i5QI7Psfkt891h5PytK7i7KSod464UAFFriIC4NrIYk_lzZGh6ljc-y-Q3jIxXf0RbP6lDllgUJaJ3XS9i_BCSUoZAUhpAyzrfLoi1XWxtXjxQl_iCBoocEJOpE_SFyFHLaZYUyWgGShrqcIZTYr-w7rqWSQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FVolumetricGroupAnalysis%3Fhighlight%3D%2528thickness%2529%257C%2528volume%2529%257C%2528measure%2529>
tutorial. Please let us know if you are still having trouble.
Cheers,
Jocelyn
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Sara Lyn <saralyn...@gmail.com<mailto:saralyn...@gmail.com>>
Sent: Monday, December 7, 2020 10:43 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] group analyses
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Hi FS developers,
I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte carlo)
for a surface based thickness group analysis. I am trying to extract volume
measures from the same significant thickness ROIs. Is there any way to do this?
Thank you!
Sara
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