[Freesurfer] Director Position, Center for Mind/Brain Sciences, University of Trento, Italy

Director, Center for Mind-Brain Sciences (CIMeC) : Trento, Italy http://www.nature.com/naturejobs/science/jobs/534333-director-center-for-mind-brain-sciences-cimec The University of Trento, Italy, invites expressions of interest from highly motivated scholars for the position of Director of

[Freesurfer] saving clusters in qdec

Hello, Is it possible to save a mask of significant clusters past a certain threshold, say 3.0, directly from the qdec interface? I want to save a few clusters, and then map them back to individual subject space. I see I can do this if I manually trace the cluster and save the ROI, but this not

Re: [Freesurfer] couple TRACULA questions

Hi Anastasia, Will the next version of TRACULA support the use of 'topup' and 'eddy' by any chance? thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine

[Freesurfer] 3 group comparison

Dear FS experts following to my query below I run into further errors. If anyone could advice it would be great help.Regards,Pablomri_glmfit \ --y lh.g3v0.thickness.10B.mgh \ --fsgd g3v0.fsgd dods\ --C HC-BD_fam.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.g3v0.glmdir? --y

Re: [Freesurfer] convert FS volume in scanner space

Thanks for your reply. I tried mri_convert with -rt interpolate (resulting in trilinear interpolation), however, the results were partially prone to artifacts and different from those I get with mir_vol2vol (but in dicom space). Is there a way using mir_vol2vol with results in dicom space, or

[Freesurfer] wm- volume limitations

Freesurfer provides ctx- and wm- volumes on either side of the white labelled sheet, all for a particular cortical region. What is the idea which is used to limit the extent of the wm- volume which is adjacent to a particular ctx- volume? Is it as simple as a maximum distance normal to the

Re: [Freesurfer] Repost: What algorithm does mri_label2label use?

Yes, it is the same as surf2surf with nnf doug On 07/07/2015 05:05 PM, Caspar M. Schwiedrzik wrote: Hi! We are using mri_label2label to map functionally defined ROIs from one anatomy to another (within subjects), using --regmethod surface. We were wondering which algorithm mri_label2label

Re: [Freesurfer] convert FS volume in scanner space

I think you meant you want nearest neighbor interpolation, not trilinear, since you are mapping labels. Try using -rt nearest insted On Wed, 8 Jul 2015, von Polier, Georg wrote: Thanks for your reply. I tried mri_convert with -rt interpolate (resulting in trilinear interpolation), however,

[Freesurfer] 3 Group comparison

Dear FS experts,I am trying to run a 3 group comparison with FS.I have run preproc ( script from ENIGMA Cortical protocol) on my first fsgd file. As I have three groups I have prepared my second fsgd file as g3v0.fsgd and all my desired contrasts, rather than using QDEC. I run this second stage

Re: [Freesurfer] wm- volume limitations

the wmparc gets the cortical parcellation of the closest cortical parcellation (not necessarily normal to the surface). I think it has to be within 5mm of cortex or else it gets Unsegmented White Matter. The method is described here http://www.ncbi.nlm.nih.gov/pubmed/19027860 On 7/7/15

Re: [Freesurfer] convert FS volume in scanner space

what was your vol2vol command line? What wiki page were you referencing? What was the problem with the coordinates? On 7/7/15 8:11 PM, Bruce Fischl wrote: I think you meant you want nearest neighbor interpolation, not trilinear, since you are mapping labels. Try using -rt nearest insted On

Re: [Freesurfer] Reconstructing surfaces

Hi Andre those are options to recon-all, so you would run: recon-all -autorecon-pial ... where ... means the rest of the normal argument (e.g. -s subject id) For the 2nd question, we write summary statistics into each subject's stats dir, so look in there for data you can iport into excel.

[Freesurfer] Reconstructing surfaces

Hello, I'm new to Freesurfer and DOS and have been navgating my way through it using the online resources. However, I have a couple of questions: 1) I have a set of MRIs processed and I've manually adjusted areas where the pial surfaces were taking in dura. I've been trying to reconstruct

Re: [Freesurfer] Reconstructing surfaces

Hi Bruce, Thanks for the reply. I'm still having some confusion. The steps I would take are as follows? 1. Run Command. 2. Type: recon-all -autorecon-pial -s subject id ? - what am I typing inside the ? is it the name of the brain volume I edited? I've been looking for a tutorial online

[Freesurfer] Repost: What algorithm does mri_label2label use?

Hi! We are using mri_label2label to map functionally defined ROIs from one anatomy to another (within subjects), using --regmethod surface. We were wondering which algorithm mri_label2label uses to map the labels? Is it using mri_surf2surf, and if so, which mapmethod is it using? Thanks, Caspar

Re: [Freesurfer] Reconstructing surfaces

Hi Andre, We have a Freesurfer tutorial available here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial There you can find talks going over the basics of Freesurfer, and tutorials where you can practice running the commands. Also, we have a YouTube channel if you would prefer to watch

[Freesurfer] Computing SA from an older FS version

Dear FreeSurfer-experts, In 2012 I used a (currently outdated) version of FreeSurfer to analyze my data on an external server and wrote an article about our findings. Now the reviewers asked us to recalculate surface area using the pial surface, instead of the WM/GM boundary. I found the