[Freesurfer] Voxel dimensions and final recon

External Email - Use Caution Dear Freesurfer, I'm enquiring about the known effect that pixel spacing has on the reconstructions and final volume estimates produces by Freesurfer. Specifically, is there a range of pixel spacing values that are necessary for accuracy? Secondly,

Re: [Freesurfer] [EXTERNAL] Re: create ctab from annot

External Email - Use Caution Hi Bruce, Yes, we are trying to replicate a recent publication on morphometric similarity networks and are using this subParcellation script (https://github.com/RafaelRomeroGarcia/subParcellation ). Cheers, Steph -Original Message- From:

Re: [Freesurfer] create ctab from annot

External Email - Use Caution Hi Douglas, I followed your advice doing the following: mri_annotation2label \ --subject fsaverage \ --hemi lh \ --annotation new.aparc \ --outdir ./label_new However, that results only in the single labels. I couldn'

[Freesurfer] PNM Gui

Hello FS team, When I try to run Physiological Noise Modeling through the PNM GUI, I get an error message saying that I don't have permission to run the script "_pnm_stage3." Do you know how I may remedy this? Thanks, Steven -- Steven L. Meisler, M.S.E. Clinical Research Coor

[Freesurfer] Postdoc openings on the Connectome 2.0 project

https://www.ismrm.org/jobs/j06670.pdf The Connectome 2.0 Project is a new BRAIN initiative-funded effort at the Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School. Building on our experience designing the first Connectome scanner, we

Re: [Freesurfer] Voxel dimensions and final recon

Hi Michael by default we resample everything to 1mm isotropic. Different parts of our analysis are susceptible to changes in voxel size in different ways. I expect the volume stream resulting in the aseg is ok with relatively coarse voxels, but the surface stream will start to fail catastrophi

Re: [Freesurfer] create ctab from annot

Just add --ctab colortable On 12/4/18 9:32 AM, Winkelbeiner, Stephanie A wrote: > External Email - Use Caution > > Hi Douglas, > > I followed your advice doing the following: > > mri_annotation2label \ > --subject fsaverage \ > --hemi lh \ > --annotation new.aparc \ >

Re: [Freesurfer] create ctab from annot

External Email - Use Caution Oh! I thought with that flag I have to provide a colortable. That worked perfectly now!! Thanks so much! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Dougla

[Freesurfer] Direction of significant group comparison

External Email - Use Caution Dear FreeSurfer experts, I am running whole-brain based group comparisons of cortical measures between a patient group and a control group using glm-fit and Monte-Carlo correction for multiple comparisons. It works fine but I am not sure where to fi

[Freesurfer] Extracting ROI from atlases

External Email - Use Caution Hello, Is there a command to extract ROIs from atlases (ex. desikan) in nifti file formats? Thank you so much in advance for your time. Best, Da-Yea -- Disclaimer: The materials

[Freesurfer] Help with Data

External Email - Use Caution Dear Help Desk - I have a few basic questions about freesurfer. I am retired military bomb technician working on a blast TBI initiative and not a research so please bear with me. We are looking at a long term study of bomb technicians and I am curi

[Freesurfer] problem with mri_label2vol

External Email - Use Caution Hello FreeSurfer Developers, I am trying to bring functional ROIs defined in a different program into FreeSurfer, so that I can dilate them into the white matter with –proj abs, but I am running into a problem I was hoping you could help me with. He

[Freesurfer] Fwd: fcseedcor output

External Email - Use Caution Dear freesurfer experts, I want to calculate corrolation between two seeds with freesurfer-linux-centos6_x86_64_stable_pub-v6 .after using fcseed-config and fseed-sess , I used fcseedcor. the command that I trying to run is as follow: fcseedcor

[Freesurfer] Registering Anatomical Parcellation to DWI

External Email - Use Caution Dear FreeSurfer experts, I have a parcellation and a whole brain white matter files which are the outputs of FreeSurfer. I want to register them to my DWI. I mean I want my parcellation and white matter to be in the physical space of my DWI. Can Free

[Freesurfer] Necessity of Matlab for Using FsFast

External Email - Use Caution Dear experts, Is it necessary to install Matlab to use FsFast for functional connectivity? Thanks in advance Best Maedeh,___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.