[Freesurfer] Reading values from overlays with PETcoreg

Dear Freesurfer experts! I am currently working on PET analysis using FS I coregistered my PET with the processed MR using bbregister, transfered it to a surface using mri_vol2surf and now createt an overlay in freeview with the lh.inflated and used the labels from the lh.aparc.a2009s.annot

[Freesurfer] amygdala nuclear subregions

URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160108/65569d25/attachment-0001.html -- smime.p7s Description: S/MIME cryptographic signature ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu ht

Re: [Freesurfer] Gray Matter Errors, Ignored Areas

see: http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Fri, 8 Jan 2016, Julio Alberto González Torre wrote: Where could I upload it? 2016-01-07 14:44 GMT+01:00 Bruce Fischl : Hi Julio it's hard to tell why this is happening, but if you

[Freesurfer] transform statistical map in MNI to surface

Hi Experts, I have statistical map in MNI space and I want to view it using tksurfer how can i transform this map to a surface ?     Bests, John  ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] transform statistical map in MNI to surface

If it is in mni152 space, then you can run recon-all on the mni152 T1 map, then use mri_vol2surf with --regheader to map the volume tothe surface, then use tksurfer or freeview to view the resulting map On 01/08/2016 12:49 PM, John Anderson wrote: > Hi Experts, > I have statistical map in MNI

Re: [Freesurfer] transform statistical map in MNI to surface

Thanks Bruce,  if my statistical map "stat1.nii.gz"  is in MNI152 standard space what are the command lines that I need ( or if possible any link to wiki) Thanks a lot!     John  Sent: Friday, January 08, 2016 at 2:49 PM From: "Bruce Fischl" To: "Freesurfer

[Freesurfer] Postdoctoral positions available -- San Diego

The Brain Development Imaging Laboratory (BDIL) at the Dept.of Psychology, San Diego State University (SDSU), is offering 1-2 postdoctoralpositions in diffusion-weighted and other anatomical MRI techniques. Job Description Post-doctoral positions will be supported by several newlyfunded NIH

Re: [Freesurfer] transform statistical map in MNI to surface

you wouldn't run it on the stats map - you would run it on the T1-weighted MNI152 volume On Fri, 8 Jan 2016, John Anderson wrote: Thanks you Doug, Kindly how can I run recon-all on the statistical map ? my statistical map is an output of TBSS analysis   Bests, John    Sent: Friday, January

Re: [Freesurfer] transform statistical map in MNI to surface

Thanks you Doug, Kindly how can I run recon-all on the statistical map ? my statistical map is an output of TBSS analysis   Bests, John    Sent: Friday, January 08, 2016 at 1:41 PM From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer]

Re: [Freesurfer] transform statistical map in MNI to surface

Hi John you would run recon-all on the MNI 152 T1 image (NOT your map), then use mri_vol2surf to map the stats map onto the resulting surfaces. Note that this won't give you great results as a bunch of your clusters will probably not be near the cortical surface (since in general subjects

[Freesurfer] About the pdf_gamma function in fsfast's toolbox

Hi,   I’m working on some fMRI data processing these days. In order to construct a HRF, I find this Matlab function in fsfast. But after some careful comparison, it seems that the gamma pdf in this function is not consistent with FSL’s version, and differs from the standard gamma pdf. So

[Freesurfer] amygdala nuclear subregions

Dear FreeSurfer developers, In the FreeSurferColorLut file I see labels for the subregions of the amygdala. Is it possible to extract the volumes for these regions? And how can I do this? I don't see them in the aseg or aparc stat files. Many thanks! Heidi

[Freesurfer] R: R: Re: FDR correction

Hi list, I have resolved my issue on the previous point 2 by downloading matlab file on: https://sites.google.com/site/kittipat/mvpa-for-brain- fmri/convert_matlab_nifti after the command that you suggest: fdrthresh = fast_fdrthresh(p,0.05); the script produce p=0.053 Therefore, coming back to

Re: [Freesurfer] Gray Matter Errors, Ignored Areas

Where could I upload it? 2016-01-07 14:44 GMT+01:00 Bruce Fischl : > Hi Julio > > it's hard to tell why this is happening, but if you upload the entire > subject directory and give us the coordinates of the inaccuracy we will > take a look > > cheers > Bruce > On Thu,

Re: [Freesurfer] malloc error with mri_glmfit-sim

Dear FreeSurfer experts, I am getting the same error with malloc(): memory corruption on mri_segstats invoked within mri_glmfit-sim. Apart from Frances, the process continues forever without any output after error message (i.e. without "Writing to..." and "Abort..." line). My commandline is:

Re: [Freesurfer] malloc error with mri_glmfit-sim

Can you test whether it works on non-ubuntu platforms? I also have another program that is better for monte carlo simulations referenced here https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo On 01/08/2016 12:02 PM, Antonin Skoch wrote: > Dear FreeSurfer experts, > > I am