[Freesurfer] postdoctoral fellowship in developmental cognitive neuroscience

$50K plus benefits postdoc in Miami, FL, two years. Please take a look! http://myweb.fiu.edu/adick/post-doctoral-fellow-positions/ -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Florida International U

[Freesurfer] Postdoctoral Position: Developmental Neuroimaging

The Program for Translational Research on Adversity and Neurodevelopment (P-TRAN) at The Pennsylvania State University is seeking a qualified postdoctoral researcher with expertise in human brain imaging, specifically magnetic resonance imaging (MRI)) with children and adolescents. This position i

Re: [Freesurfer] mris_decimate missing for Mac

Hi Paula, thanks for pointing this out. It looks like there's an issue with the libs required to build mris_decimate on the current mac build machine. I’ll sort this out, but for now, you can just download and copy ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/OSX/mris_decima

[Freesurfer] Qdec for Brodmann Areas

Dear Freesurfer experts, I would like to use "Qdec" tool to study the volume/cortical thickness of one region (Perirhinal) belonging to the Brodmann areas. As I understand Qdec load only the aparc and aseg stat lists. I am wondering if we could realty to do that with "Qdec"? Any suggestion/advi

Re: [Freesurfer] Recons for Allen Brain Institute T1 images with v5.3 online

Fantastic, thank you! On 30 October 2017 at 10:03, Bruce Fischl wrote: > thanks Mel! > Bruce > > On Mon, 30 Oct 2017, Melanie Ganz wrote: > > >> Hi, >> >> >> >> So here’s the Wiki page for the human Allen brain data recons: >> https://surfer.nmr.mgh.harvard.edu/fswiki/AllenBrainAtlas >> >> Right

Re: [Freesurfer] Recons for Allen Brain Institute T1 images with v5.3 online

Dear Zheng, Sean had asked for help in performing FreeSurfer recons of the human data from the Allan brain institute. We have already done this and QC’ed it, hence I uploaded it to share with everyone. You can see the thread of our previous discussion here: https://www.mail-archive.com/freesurfer@

Re: [Freesurfer] Registration

Hi Nazanin the nonlinear registration is actually to our segmentation atlas (*.gca). I guess you could try using something else, but you should extract a mean intensity image from the gca as a target, not the MNI305. You can do this with: mri_convert -nth 0 .gca mean_gca.mgz FYI, this: mri

Re: [Freesurfer] Recons for Allen Brain Institute T1 images with v5.3 online

thanks Mel! Bruce On Mon, 30 Oct 2017, Melanie Ganz wrote: Hi,   So here’s the Wiki page for the human Allen brain data recons: https://surfer.nmr.mgh.harvard.edu/fswiki/AllenBrainAtlas Right now there’s only the v5.3 recons, but the v6 recons are coming asap.   Cheers, Melanie

Re: [Freesurfer] dmrirc_v1

Hi - It's hard to tell from the screenshot. Can you please send your entire log file from scripts/trac-all.log? The error seems to be related to the gradient table, so if you can also send that and the b-value table, that'd be great. Best, a.y From: freesurfer

Re: [Freesurfer] Fwd: cortical/subcortical volume based analysis

Hello Bruce, I am still waiting on your response or Lilla's. Thank you. Best, Paul On Wed, Oct 18, 2017 at 8:20 PM, Bruce Fischl wrote: > Hi Paul > > I was waiting for Lilla to respond :) > Bruce > > On Wed, 18 Oct 2017, miracle ozzoude wrote: > > Hello Bruce, >> >> I wasn't sure if you answer

[Freesurfer] Registration

Dear Experts, In the volume-based stream, if I'm right the FreeSurfer does two registration with MNI305 ,one affine and one nonlinear , is it possible to perform the nonlinear registration somewhere else and then use the result in FreeSurfer and run the rest of the analysis ? thank's alot for you

Re: [Freesurfer] Recons for Allen Brain Institute T1 images with v5.3 online

Hi Melanie, I don't understand what you mean. Could you tell me what I am going to do to solve my problem? Thanks, Zheng At 2017-10-30 16:33:02, "Melanie Ganz" wrote: Hi, So here’s the Wiki page for the human Allen brain data recons: https://surfer.nmr.mgh.harvard.edu/fswiki

[Freesurfer] Recons for Allen Brain Institute T1 images with v5.3 online

Hi, So here’s the Wiki page for the human Allen brain data recons: https://surfer.nmr.mgh.harvard.edu/fswiki/AllenBrainAtlas Right now there’s only the v5.3 recons, but the v6 recons are coming asap. Cheers, Melanie ___ Freesurfer mailing list

[Freesurfer] Qdec result

Dear experts I'm using Qdec. I want to check regions where age and thickness are correlated, and regions where the thickness-age correlation differ between genotype(Hetero or WT). When I choose "genotype(Hetero or WT)" as Fixed factors and "age" as Continuous variables, I can choice the result

[Freesurfer] mris_decimate missing for Mac

Hello FreeSurfer Developers, I am using the development version of FreeSurfer, both for Mac and Linux. I have noticed that mris_decimate is not included in the package for Mac, but it does exist for Linux. I would like to know what will happen with it? Will it be included in the Mac package so