[Freesurfer] amount of manual corrections in 5.1 related to aparc+aseg?

Dear FreeSurfers, I'm working on a structural dataset and after running recon-all -all, I had to correct all cases (32 so far) from minimum pial/wm corrections to massive pial corrections (only three cases needed control points). Mostly, the corrections were needed due to remaining

[Freesurfer] Lateral ventricles not filled entirely

within the ventricles..in the tutorial is written that one should handle this in a described way but I was wondering if this is necessary when recon3 was sucessful without any errors. Does anyone have experience with that? (see attached picture) Thanks a lot, Dorit Kliemann Bild 6.png

[Freesurfer] again: qdec error

Dear all, I wanted to open qdec for the first time and experienced an error that was posted some days ago... ( RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow ; Juranek, Jenifer ) ERROR: In /usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 219

[Freesurfer] amygdala nuclear subregions

Hi Heidi, segmentation of amygdalar subregions is currently not yet implemented in FreeSurfer, but we are working on including this feature soon. Best, Dorit - Message: 9 Date: Fri, 8 Jan 2016 13:21:48 + From: "Jacobs H (NP)"

Re: [Freesurfer] Amygdala subfields

Hi Sascha, yes, we have developed an amygdala nuclei atlas similar to the hippocampal subfields . Its currently being tested and to be implemented (hopefully) soon. Stay tuned. Dorit > From: "sf" > Subject: [Freesurfer] Amygdala subfields > Date: 31 October 2016 at

Re: [Freesurfer] Amygdala subfields

to clarify: the amygdala subregion atlas is built and will be released early 2017. Dorit On Oct 31, 2016, at 11:46 AM, Dorit Kliemann <do...@mit.edu> wrote: > Hi Sascha, > yes, we have developed an amygdala nuclei atlas similar to the hippocampal > subfields . Its current

[Freesurfer] bbregister issues with ?h.only

Hi, I’m having some troubles with using bbregister on hemispherectomy brains (i.e only one hemisphere; data is successfully processed with recon-all dev version - thanks to Bruce). I use bbregister to create a register.dat for the functional (preprocessed with fmriprep and registered -but

[Freesurfer] annotation to volume with custom color scheme (Yeo parcellations)

Hi, I’m trying to use the Yeo2011 annotations to create individual volume masks in subject space. I first use mri_surf2surf to map the annotations from fsaverage to individual subjects: mri_surf2surf --srcsubject fsaverage --trgsubject subject --hemi rh --sval-annot

Re: [Freesurfer] annotation to volume with custom color scheme (Yeo parcellations)

ops. I guess that should have been obvious to me! Thanks! Dorit smime.p7s Description: S/MIME cryptographic signature ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

[Freesurfer] getting h/o atlas into individual surface (and then volume) space

Hi, I’m trying to get an atlas (Harvard/Oxford sub) into individual space via surface registration. Motivation is to replicate a finding in volume space (functional data) in a normal population with that atlas in a lesion data set where transformation to template volume space is not feasible.