If there are no CSF voxels in the native functional space, there are a couple of things to do. (1) don't use a CSF regressor for any of your subjects, or (2) change the fill threshold for all subjects. The default is .95, meaning a voxel has to be at least 95% CSF for it to be classified as CSF in the seed.
doug On 10/30/2015 02:42 PM, std...@virgilio.it wrote: > Yes, the ventricle is very small. > The segmentation in aparc and aseg is nice. > How can I do to analyze this subject? I need to include it in the > analysis. > Many thanks, > > > Stefano > > ----Messaggio originale---- > Da: gr...@nmr.mgh.harvard.edu > Data: 30-ott-2015 16.03 > A: <freesurfer@nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] error vcsf.config > > That means it could not find any CSF voxels. Try checking the > registration. It could also be that this is a subject with really > small ventricles. > > On 10/30/15 3:57 AM, std...@virgilio.it wrote: >> >> Hi list, >> >> >> During fcseed-sess -s subj -cfg vcsf.config >> >> >> a subject produces the follow error. >> >> I have rerun recon-all, cheched aparc+aseg with tkmedit. They >> seem to be ok. >> >> Why this error is produced? >> >> >> Thanks >> >> >> >> Stefano >> >> >> >> Creating output directory >> >> /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm >> >> Loading y from >> /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz >> >> Saving design matrix to >> >> /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/Xg.dat >> >> Normalized matrix condition is 61.5872 >> >> Matrix condition is 1e+08 >> >> Pruning voxels by thr: 0.000000 >> >> Found 0 voxels in mask >> >> Saving mask to >> >> /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/mask.mgh >> >> search space = 0.000000 >> >> DOF = 297 >> >> Starting fit and test >> >> Fit completed in 0.0008 minutes >> >> Computing temporal AR1 >> >> Writing results >> >> Computing FSNR >> >> mean >> >> maxvox sig=0 F=0 at index 0 0 0 seed=1446518089 >> >> linear >> >> maxvox sig=0 F=0 at index 0 0 0 seed=1446518089 >> >> quad >> >> maxvox sig=0 F=0 at index 0 0 0 seed=1446518089 >> >> Computing PCA (300) >> >> ERROR: no voxels in mask >> >> >> >> _______________________________________________ >> 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.
