6 Sep
2021
6 Sep
'21
11:08 p.m.
On 9/6/2021 4:34 PM, Junyeon Won wrote:
External Email - Use Caution
Hi Douglas,
Really appreciate your help and sorry for the confusion due to unclear questions.
- Right, it was surface-based analysis. Below is the screenshot of
the significant result (right volume) I got after running mris_preproc, mris_glmfit, and mris_glmfit-sim.
image.png
In the summary file, this region is right superior frontal. Could you please confirm that mri_segstats command you suggested will allow me to get the value presented in the figure above for each subject?
There is not a significance for each subject (sig is a property of the group analysis).
- Sorry for the confusion. Would it be possible to show conventional
p-values (0.05, 0.01, or 0.001) in the color scale instead of 1.75 or -1.75 in the image above?
Not in freeview. If you need to make a figure, just grab the colorbar and put your own numbers in.
Best, JW
On Mon, Sep 6, 2021 at 1:18 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
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 <mailto: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/freesurfer <https://secure-web.cisco.com/1_mDdVUGQO4rycxR7MCJOaJoioJ206VoZs4slaKQsQvdQaonXQCWuzkn_a-fDJOLDJAcBkMI1in8K6RmVhdWKunJx298nNHdYeUQ8oCkK1KIYYvjKE2MrzePP4Umzm1VMPtPwepm4l1P1tpbJcz9JV8xP0iXuv84LjWGWePfQDDy_w-DGaH5FFVqn5se0CKUVaK5tVXAG3a6-280LeRPrZd5V_92C5z-pTsBU157W5i8GuYUAlMHzDObsS3p_ciOU/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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/freesurfer <https://secure-web.cisco.com/1_mDdVUGQO4rycxR7MCJOaJoioJ206VoZs4slaKQsQvdQaonXQCWuzkn_a-fDJOLDJAcBkMI1in8K6RmVhdWKunJx298nNHdYeUQ8oCkK1KIYYvjKE2MrzePP4Umzm1VMPtPwepm4l1P1tpbJcz9JV8xP0iXuv84LjWGWePfQDDy_w-DGaH5FFVqn5se0CKUVaK5tVXAG3a6-280LeRPrZd5V_92C5z-pTsBU157W5i8GuYUAlMHzDObsS3p_ciOU/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/1FBurCCNdVCYqDmSE0q-BLfHD0ZRZin2VQvOGmUXLeohH4J_ntE38OX3IvOgtPEGZd6A5831iIt_Et7utDb-ccP77nFzGpOGoOmbT8Xy3AB_Udtg1Dc38Hh0sCVrmBtS15B2xaSvd2KLw7mH8uPhafIdOmI6-Of6aq9Xe2nK9L7MQNxB99Ll-3yoUvA5EhM1iKVzMgZjkWJWy_RQYFawBSBnoSsOFv_4DyOeuivgzJlmddA8drLSGHznOVYb8ZtID/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.
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