Re: [Freesurfer] R: Re: error vcsf.config

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, stdp82@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: greve@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, stdp82@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



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