Re: [Freesurfer] PetSurfer: Other quantification algorithms?

Hi Doug, Sure, I hope these links help: https://www.ncbi.nlm.nih.gov/pubmed/17204713 https://www.nature.com/articles/npjschz201631 Indeed, such a functionality in PetSurfer will be much appreciated

Re: [Freesurfer] Tracula

Hi Nicole – You can skip the eddy current correction, check the TRACULA tutorial for how to do so. BET thresholds don’t matter here, because TRACULA will make a brain mask out of the freesurfer segmentation and use it to mask your DWIs. Best, a.y From: mailto:freesurfer-boun...@nmr.mgh.harva

Re: [Freesurfer] PetSurfer: Other quantification algorithms?

That would be a great thing to do if I could find the time/funding to do it:). I have not used that method. Can you send a paper? Maybe it is not too hard. On 01/25/2018 06:37 PM, Elijah Mak wrote: > Dear Doug, > > In addition to the MRTM approaches, I was wondering if you have any plans to >

[Freesurfer] PetSurfer: Other quantification algorithms?

Dear Doug, In addition to the MRTM approaches, I was wondering if you have any plans to implement other algorithms in PetSurfer, such as supervised cluster analysis for extracting reference tissue activity? I am working with [11C]PK11195 PET data (neuroinflammation), for which there is no suita

[Freesurfer] Fwd: OHBM Call for Nominations

Forwarded Message Subject:OHBM Call for Nominations Date: Thu, 25 Jan 2018 16:15:20 -0600 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu Organization for Human Brain Mapping

[Freesurfer] Tracula

Hi all, I have previously run full diffusion preprocessing using FSL and would like to now use tracula to construct the paths. Is it possible to input my already processed data into the tracula pipeline for just the path reconstruction and stats steps? I have already run recon-all too. Or perhap

Re: [Freesurfer] New hippocampal subfields

Hi Eugeno, I am hitting the same error as described in this post, but using a Dev El Capitan version. Here is my error output: [arkadiysnewimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] arkadiy% segmentHA_T1.sh SILVA053 # #@

Re: [Freesurfer] resting state motion censoring

Yes,you need a time point exclusion file (-tpexclude filename option to mkanalysis-sess). Run mkanalysis with -help to get more info on how to create it. On 01/25/2018 04:43 PM, Adam Martersteck wrote: > Hi Freesurer experts, > > I’m looking to censor (drop volumes) from my resting state fMRI ti

[Freesurfer] resting state motion censoring

Hi Freesurer experts, I’m looking to censor (drop volumes) from my resting state fMRI time series that violate a predetermined motion and signal threshold (FD and DVARS). I've already determined which volumes violate X and Y criteria. Is there a way to to tell FS to "ignore" these time points in

Re: [Freesurfer] aparcstat2table with new destrieux atlas

Hi Lisa, Have you tried using the --parc flag to specify the parcellation atlas you want? Run aparcstats2table --help for more information. Best Emma From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lisa Delalande Sent: Thursday, January 25,

[Freesurfer] aparcstat2table with new destrieux atlas

Dear FreeSurfer expert, I would like to use the new destrieux atlas for extracting anatomical data with the aparcstat2table command. Is that possible ? If yes can you give me the command ? Or give me some references that can help me ? Thanks in advance Best regards Lisa

[Freesurfer] strange output from lme analysis - Max r value=inf

Dear all I am using the lme toolbox to perform a longitudinal comparison of cortical thickness among 4 patient groups. Following the lme tutorial, I concatenated all files and I built a design matrix with following columns: -one column for intercept (all ones) -one column for time -four columns