[Freesurfer] Post-Doctoral position in brain imaging and computational morphometry – University of Geneva

Post-Doctoral applications are invited in the newly established Brain and Language Lab at the Department of Clinical Neuroscience at the University of Geneva, in collaboration with the Swiss Institute of Technology (EPFL) in Lausanne, Switzerland. Projects will include the development of new

Re: [Freesurfer] Chunks of missing WM

We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are considered. Emily On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt whats...@umich.edu wrote: OK will do... I'll upload both versions, before

[Freesurfer] Beta maps

Dear FreeSurfer List, How can I visualise the beta maps ? previously there is a mail about this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02048.html The /average7/ subject is missing in FreeSurfer 5.1, so I guess using /fsaverage/ is the same, but that command shows no

Re: [Freesurfer] Beta maps

that command is correct. you might try adjusting the threshold doug On 12/14/2012 12:04 PM, Alex Hanganu wrote: Dear FreeSurfer List, How can I visualise the beta maps ? previously there is a mail about this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02048.html The

Re: [Freesurfer] Chunks of missing WM

Emily, This is good news, can I find or download this revised version somewhere? jon On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote: We ran into this issue frequently and found that it was resolved by using the revised recon -all script that alters the stage where control points are

Re: [Freesurfer] Chunks of missing WM

I think Emily is talking about this one: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/ a. Le 14/12/2012 12:59 PM, Jonathan Holt a écrit : Emily, This is good news, can I find or download this revised version somewhere? jon On Dec 14, 2012, at 11:37 AM, Emily

Re: [Freesurfer] tksurfer - view only clusters from a certain nr of voxels

Hi Alex, you can't do that with tksurfer. You will have to run mri_surfcluster to create a new overlay with clusters smaller than 50 removed. doug ps. Please send emails to the FS list and not directly to me. thanks! On 12/14/2012 02:17 PM, Alex Hanganu wrote: Dear Douglas, I am using

Re: [Freesurfer] tksurfer - view only clusters from a certain nr of voxels

Thanks Douglas ! OK !! Alex. Le 14/12/2012 2:27 PM, Douglas N Greve a écrit : Hi Alex, you can't do that with tksurfer. You will have to run mri_surfcluster to create a new overlay with clusters smaller than 50 removed. doug ps. Please send emails to the FS list and not directly to me.

Re: [Freesurfer] Interpretation of voxel values in TRACULA path.pd images

Hi Anastasia, Just follow up on this thread.. If 5000 samples were used for each voxel, how can I normalize the intensity of path.pd volumes to a sum of 1 ? Also what thresholding value was chosen to calculate the tract volume, shown in the pathstats.overall.txt ? Thanks. ping On Fri, Nov 9,

[Freesurfer] regarding use-mritotal

Hi, this link: http://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 discusses a solution to bad talairach.xfm transforms, the -use-mritotal flag. this link: http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV mentions that the talairach.xfm is used to calculate the total intracranial volume. is using

[Freesurfer] Contents of SUBJECTS_DIR

Hello everyone, I'm following the group analysis tutorial, but have difficulty getting all files in the right folders. I have my tutorial data set in * /media/Dell/_FS/buckner_data/* (a folder that is shared in my VirtualBox), and my original subjects folder in the default path of *

Re: [Freesurfer] Contents of SUBJECTS_DIR

Hi Tudor, you can create a symbolic link to fsaverage rather than copying it. doug On 12/14/2012 04:18 PM, Tudor Popescu wrote: Hello everyone, I'm following the group analysis tutorial, but have difficulty getting all files in the right folders. I have my tutorial data set in

Re: [Freesurfer] Chunks of missing WM

it doesn't, although the 5.2 mri_normalize should help as well cheers Bruce On Fri, 14 Dec 2012, Jonathan Holt wrote: OK this is great. Does this require the latest version of Freesurfer? I see recon-all v 5.2, we're running Freesurfer 5.0.0 for reference On Dec 14, 2012, at 1:16 PM, Alex

Re: [Freesurfer] Contents of SUBJECTS_DIR

On 12/14/2012 04:51 PM, Tudor Popescu wrote: Thanks Doug! I tried figuring out how to create symlinks manually (as I think recon-all has already been run in the case of the group analysis tutorial, therefore they were not generated automatically) but could not find anything helpful on the

[Freesurfer] ooops deleted fsaverage

do I need to download the whole freesurfer package again to get it? - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the