On 9/3/2021 9:28 AM, Junyeon Won wrote:
External Email - Use Caution
Dear Freesurfer experts,
Could I have a couple of questions regarding visualization?
1) I found significant clusters on the right hemisphere volume after
glm_fit and cluster correction. I would like to extract the volume
from this cluster for each participant. According to the freeview
instruction (*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization
<https://secure-web.cisco.com/1WRlFruYs_qR7muzrjF79S4e7sBuB1ehkXj2GwiMajz3IASfPmkzmB1E9T4PPZ9dGT0v66A85cj7byX3PHhDPOXrhW46SQ_ZutKLBQsOvH5WBf3dWkxI5M9_t6mCRrQUudNcGLBjUaPrbcUrKd9l45cn8VrR6OXtlrnBeIiPbgQtRJ0deryLhIl4ot4RSJW9IfRtLC6Xm7alFOXsoSqXTg6uXojnBCQzywngH29JWvYoN8FPlkjofsoLxolH1lDVkctDODNOugoBF2_Vja_-TQg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FVisualization>),
the FSGD file (y.fsgd) should be loaded and select a point by clicking
on the parametric map at that vertex to generate a plot for a
particular vertex. I tried this but I am wondering if the mean value
from the cluster can be extracted for each participant. I want to
extract the values from each participant not just view the values
through the FSGD file for further analysis.
You would not use freeview in this way. Is this a surface-based or
volume-based anlaysis? If surface-based, do you mean you want to
cortical volume of your significant area? If so, you can run
preproc-sess with the same options you used for thickness, but --meas
volume instead. You can then compute the volume for each subject with
mri_segstats --seg ocn.mgz --i lh.volume.mgz --excludeid 0 --avgwf table.dat
table.dat will be a number-of-subject by number-of-clusters table.
2) Could you please let me know if it is possible to show the p-value
numbers on the color scale?
what p-value? can you be more specific?
Best,
JW
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Mass General Brigham
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If
the e-mail was sent to you in error but does not contain patient information,
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
