Hi Bryan,

Re: 1a) Did you run the case all the way through recon-all? Even if the skullstripping looks poor, it's possible that the surfaces will turn out ok and might only require some pial edits. Otherwise, this site has some helpful info on rerunning the skullstripping step: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview

Re: 1b) If you are referring to voxels located in dura being labelled as cerebral cortex in the aseg then this can be ignored. The cerebral cortex labeled voxels are not used to calculate the morphometry stats. https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats

Re: 3) You probably just need to adjust the contrast and brightness, using the window and level sliders on the left in freeview.

Re: 4) Could you send a snapshot (or two) of that?

-Louis

On Thu, 26 Jun 2014, Martin Reuter wrote:

Hi Bryan,

I can answer the longitudinal question (2), the rest is about cross sectional editing and can probably better be answered by someone else.

So yes, I would run the base and check brainmask and surfaces there before going too deep into editing the cross.

Best Martin

Sent via my smartphone, please excuse brevity.

-------- Original message -------- From: "Chiu, Bryan (PHTH)" Date:06/26/2014 8:06 PM (GMT+01:00) To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal preprocessing troubleshooting

Hi all, I have a set of data with ~75 subjects with up to 4 timepoints of scans. The structure of the data indicates that it would be best processed using a longitudinal design.

I have recon-all most of the scans. There are a few scans that I am worried about and wondering how to treat each case. I do one sanity check with freeview using a modified version of bert's command:  "freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red"

1a) Skull strip or underanalysis errors: I have attached one screenshot of a very severe case of an underanalysis. How should I treat this case? I have recently read about Editing a Recon in Freeview, but I'm not sure how to proceed with this.

b) Skull strip errors -- Some scans have a very small amount of cerebral cortex labelling into the dura mater/ skull. Does this warrant the manual removal via freeview of the skull?

2. Since I am running this through the longitudinal processing, could I be able to skip #1 hoping that the

averaging of the timepoints into a 'base' will remove these issues?

3. I have 2 brains that are completely whited out in Freeview (see attached). However the analysis went through

and it looks good to me. Opening the raw Nifti file in mricroGL does not show this at all. What is going on and should I be concerned?

4. I have 2 other brains that failed the recon-all. One of them is a Talairach fail and the other one failed

mri_watershed. Looking at these brains in mricroGL shows a dark shadow being cast over the brain running diagonally from the front of the head to the back. I think this is the root of the problem. Is there a way to fix this or should I consider these scans problematic and exclude them?

Regards,

• Bryan