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:
External Email - Use Caution
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. <JSMORA@mgh.harvard.edumailto:JSMORA@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 Analysishttps://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 Analysishttps://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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sara Lyn <saralyn543@gmail.commailto:saralyn543@gmail.com> Sent: Monday, December 7, 2020 10:43 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] group analyses
External Email - Use Caution
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1R7gYfs8YU2juqb8rGfBqpwv3CspfKQQgYn6WAikOwc_TDtnxjDjMy1r78KDcMil_IHVde58fWtF5nHDeV6y8sFImL3Jlld9a57iSW_DaW4BFEV6cg_YjqRNhnbaF-4ZaZFCs50k7MRt2-YvVF4mZuaP6kh5g9RnM5y_TMYZJm0LyS8ruzjLF6IgU9yMOHVXmVHUWva7T8KfHrZiljMRns81fwr4TsXqvlnzXZDMISe0Rk2ANRklyDOi8QKTcN8ierog6gWIQQPYLNQce_Kn_gw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer