External Email - Use Caution
Dear Greve,
Please can you let me know if you got the two folders of data I sent you?
Best regards
Ileana Camerino
PhD candidate
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognition
Spinozabuilding
Room B02.25
Montessorilaan 3, 6525 HR Nijmegen
The Netherlands
Tel. +31-24 3612618
On 16/04/2019, 21:14, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Greve, Douglas N.,Ph.D." <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgr...@mgh.harvard.edu> wrote:
Unfortunately, it usually means that you need to go in and manually fix
the problems that you are seeing. Probably the best thing is to look at
the aseg.presurf.mgz to see how the WM lesions are getting labeled. You
may have to go in an label them manually. Can you upload a case or two
here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
On 4/16/19 11:05 AM, Camerino, .I.L. (Ileana) wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
>
> I am running recon all from the terminal of a linux machine:
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.
>
>
> I tried recon all on an image dataset of small vessel disease
> patients. I tried the command on several subjects and I got the same
> outcome: a soft fallure.
>
> Please, find the recon all log in the attachment.
>
> Even though in the "recon all.log": it says: recon-all -s sub025
> finished without errors, after checking the pial and white matter
> segmentations, very clear misplacement failures and part of dura mater
> are present (see attachment: segmenation misplacement and dura).
>
>
> I am also wandering how to avoid that white matter lesions are taken
> into the aseg segmentation?
>
>
> I checked the documentation and this kind of errors is not mentioned
> anywhere. Can be the case, that this error is due to the fact that
> these are clinical images? Can this problem be fixed?
>
>
> For sake of curiosity, I tried the recon all command on another
> dataset (stroke) and with these data I got an hard failure.
>
> recon all exited with errors:
>
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> ***FAILED*** (p=0.0573, pval=0.0034 < threshold=0.0050). (see second
> recon all o35403143 with errors)
>
>
> Please, can anyone give me some ideas how to fix both errors?
>
> Thank you in advance
>
> Ileana
>
>
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