[Freesurfer] design is ill-conditioned

External Email - Use Caution Dear experts, I’m running into an error when running selxavg3. It says the design is ill-conditioned. I’m a bit stuck, because the same pipeline works in most subjects, but not all. Also, if I exchange the functional scan (f.nii.gz) with a scan from

[Freesurfer] Postdoc available at the Central Institute of Mental Health

External Email - Use Caution The Central Institute of Mental Health (CIMH) stands for cutting-edge international research and groundbreaking treatment concepts in psychiatry, psychotherapy, child and adolescent psychiatry, psychosomatics and addiction medicine. The Department of

[Freesurfer] small volume correction in native space

External Email - Use Caution Dear experts, I'm running an analysis on sensory mapping. It's a simple event-related design and my analysis stream seems to work fine. I need to analyze all the data in single subject space, because I'd like to calculate surface distances later (us

[Freesurfer] 1) single subject surface activation in volume space and 2) small volume correction

External Email - Use Caution Dear experts, I'm running a sensory mapping experiment, which I would like to analyse in single subject space. Everything seems to be working fine (see code excerpt below). Now I'd like to do two additional things: 1) show the surface results

Re: [Freesurfer] changing label outlines in tksurfer

x27;t support tksurfer anymore, and changing label color/outline color is trivial using freeview. cheers Bruce On Sun, 8 Jul 2018, Loeffler, Martin wrote: > > External Email - Use Caution > > Dear experts, > >   > > I’m visualizing a 1st level sig-map tog

[Freesurfer] changing label outlines in tksurfer

External Email - Use Caution Dear experts, I’m visualizing a 1st level sig-map together with two specific label files using tksurfer (Freesurfer version 6.0). I’ve extracted those labels before using mri_annotation2label. I would like to change the colours of the label outlines.

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

eesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Loeffler, Martin mailto:martin.loeff...@zi-mannheim.de>> Sent: Tuesday, December 12, 2017 11:57:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst Dea

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

2017, Loeffler, Martin wrote: > Dear Bruce, > > thanks for the quick reply! You are right, of course. I do find errors in > lh.inflated.nofix. > I have attached a screenshot of the biggest errors I found.. > Can you maybe guide me a little how to fix the issue? Do I just cancel t

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

ofix and/or the ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find defect 9 cheers Bruce On Mon, 11 Dec 2017, Loeffler, Martin wrote: > > Dear FreeSurfer team, > > > > For a case report I’m running recon-all on a patient with a giant arachnoid > cyst in the left

[Freesurfer] CORRECTING DEFECT recon-all giant cyst

Dear FreeSurfer team, For a case report I'm running recon-all on a patient with a giant arachnoid cyst in the left hemisphere. It gets stuck at this point (last message): CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849) XL defect detected... It is stuck here since a whole day now,