[Freesurfer] Research Engineer position in Neuroimaging (Madrid, Spain)

*Research Engineer position in Neuroimaging at the *“Biomedical Imaging and Instrumentation Group (BiiG) ”, Madrid. The BiiG is a research organization located in Madrid (Spain) and affiliated with the “Instituto de Investigación Sanitaria Gregorio Marañón” a

[Freesurfer] Fwd: nu_correct failure

-- Forwarded message -- From: miracle ozzoude Date: Thu, Sep 21, 2017 at 11:20 AM Subject: nu_correct failure To: Douglas N Greve Hello expert, I ran several subjects on FS v6 and they failed on the same stage (mri_nu_correct.mni and nu_correct). How can I solve this problem?

Re: [Freesurfer] lobes volume (WM and GM)

Hi Douglas: I am looking for that paper, but I couldn't found it... Which is it ? Sincerely, Gonzalo Rojas Costa Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170

Re: [Freesurfer] curvature

Hi Heidi it's hard to say which one should be used - that is really dependent on your biological hypothesis. The "index" calculations are from David Van Essen paper. Sorry, I don't have the ref handy. The "integrated rectified" ones are just taking the absolute value of each, then summing them

Re: [Freesurfer] lobes volume (WM and GM)

https://www.ncbi.nlm.nih.gov/pubmed/19027860 On 09/22/2017 10:11 AM, Gonzalo Rojas Costa wrote: > Hi Douglas: > >I am looking for that paper, but I couldn't found it... Which is it ? > >Sincerely, > > > Gonzalo Rojas Costa > Gonzalo Rojas Costa > Laboratory for Advanced Medical Image Proc

[Freesurfer] longtitudinal pipeline

Hello Freesurfer, For the longitudinal pipeline, the website/ recon-all -help suggested that I calculate the different on the results from the longitudinal command (e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were named 0001a.long.0001.longbase and 0001b.long.0001.longbase

[Freesurfer] Error in segmentHA_T1

Dear Experts, I recently installed Freesurfer development version (dated Sept. 16, 2017) on a Mac Sierra (10.12.6). When trying to run segmentHA_T1.sh I encounter a java problem: "JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/lib

[Freesurfer] Problem with New Hippocampus/Amygdala Segmentation

Hi Freesurfer Experts, I'm trying to run the new version 6.0 hippocampus/amygdala segmentation procedure (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) on data from subjects with whom I have already completed recon-all. I have downloaded the newest development version (and licens

Re: [Freesurfer] sim-sign abs/ cluster summary results confirmation

I forgot to send the cluster summary sheet. Here is it. # Input lh.stroke.fsgd.glmdir/contrast/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # annot aparc # SUBJECTS_DIR /Users/CT/Documents/stroke # SearchSpace_mm2 65416.6 # SearchSpace_vtx 149953 # Bonf

[Freesurfer] bad midline cut

Dear all, Here is my question again. Somehow, it didn't appear on the Freesurfer forum. I'm resending it without the attachments. > I've a subject, where the midline cut is bad (see the attached pictures), > therefore the segmented left lateral ventricle also includes considerable > number of vo