Re: [Freesurfer] R: Re: FDR map: hide very little cluster
just use the FDR thresholded input and set --thmin to 0.5 On 01/25/2016 11:21 AM, std...@virgilio.it wrote: > Thanks. But I do not know how I can obtain a corrected sig.nii.gz. > In this way I have obtained only summary.txt. > If I add --vwsig vwsig cds file is request. > > Stefano > > Messaggio originale > Da: Douglas Greve > Data: 25-gen-2016 17.10 > A: > Ogg: Re: [Freesurfer] FDR map: hide very little cluster > > Use the --minarea option to mri_surfcluster (not the CSD). > > On 1/25/16 10:39 AM, std...@virgilio.it wrote: >> Hi list, >> please, could you help me because from several days I'm trying to have a >> solution. >> I have performed a seed-based fcMRI analysis by FAST. >> After mri_glmfit, I have obtained a sig.nii.gz which contains >> uncorrected results.I have corrected by FDR using the graphical interface >> provided in tksurfur. The FDR corrected contains some very small areas >> (<5-10 voxels) which I would like to hide in order to present a more clear >> map. How is possible to do it?I have tried with mri_surfcluster. To have >> vwsig.nii.gz I should have a CSD file. But this file >> could be also produced when FDR correction is applied? I'm very confused. >> Thank you very much for your work. >> Kind regards. >> Stefano >> >> >> ___ >> 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 -- 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 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 Partners Compliance HelpLine at http://www.partners.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.
[Freesurfer] R: Re: FDR map: hide very little cluster
Thanks. But I do not know how I can obtain a corrected sig.nii.gz.In this way I have obtained only summary.txt.If I add --vwsig vwsig cds file is request. Stefano Messaggio originale Da: Douglas Greve Data: 25-gen-2016 17.10 A: Ogg: Re: [Freesurfer] FDR map: hide very little cluster Use the --minarea option to mri_surfcluster (not the CSD). On 1/25/16 10:39 AM, std...@virgilio.it wrote: Hi list, please, could you help me because from several days I'm trying to have a solution.I have performed a seed-based fcMRI analysis by FAST. After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file could be also produced when FDR correction is applied? I'm very confused. Thank you very much for your work. Kind regards. Stefano ___ 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 Partners Compliance HelpLine at http://www.partners.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.
[Freesurfer] R: Re: FDR map: hide very little cluster
Please could you suggest me an example of command line.I'm trying from several day without results.Thank you very much. Stefano Messaggio originale Da: Douglas Greve Data: 25-gen-2016 17.10 A: Ogg: Re: [Freesurfer] FDR map: hide very little cluster Use the --minarea option to mri_surfcluster (not the CSD). On 1/25/16 10:39 AM, std...@virgilio.it wrote: Hi list, please, could you help me because from several days I'm trying to have a solution.I have performed a seed-based fcMRI analysis by FAST. After mri_glmfit, I have obtained a sig.nii.gz which contains uncorrected results.I have corrected by FDR using the graphical interface provided in tksurfur. The FDR corrected contains some very small areas (<5-10 voxels) which I would like to hide in order to present a more clear map. How is possible to do it?I have tried with mri_surfcluster. To have vwsig.nii.gz I should have a CSD file. But this file could be also produced when FDR correction is applied? I'm very confused. Thank you very much for your work. Kind regards. Stefano ___ 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 Partners Compliance HelpLine at http://www.partners.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.
