Re: [Freesurfer] FW: Permutation output

Hi Doug, I am attaching the permutation log file. Thanks! Pablo Date: Mon, 17 Aug 2015 11:15:14 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: Permutation output Can you send me the log file from the glmdir folder? The

Re: [Freesurfer] Trakula

Hi Anastasia, Please find attached the trac-all.log file. Thank you very much for your help. Bahram 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote:

[Freesurfer] control points from cross transferred to long

Hi, On this page https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits it mentions it is recommended to check if all CPs are accurately placed in the long. I was wondering what is the best way to do this? I know I can type in the RAS coordinates from the control.dat file and check

Re: [Freesurfer] license error

Hello, You say the .license file is in your applications folder but it's supposed to be located in your /Applications/freesurfer folder. If /Applications/freesurfer/.license does exist on your machine, than please make absolutely sure it exactly matches the email sent to you after you

[Freesurfer] license error

Hi, I just installed freesurfer on my computer and included the license.txt film in the applications folder but when I tried to use the tkmedit bert orig.mgz to test the installation I received a message saying that ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If

Re: [Freesurfer] control points from cross transferred to long

In the dev version of freeview, you can go to File -Load Point set, and choose the control point file (shoulb be subject/tmp/control.dat) This allows you to flip through the points by entering the control point number or using an arrow to go to the next/previous control point in the file.

[Freesurfer] Using FreeSurfer Suggested Morphometry Sequences

Hi all, We have recently installed the FreeSurfer suggested morphometry sequences on our Siemens Verio 3T. Specifically, the multiecho MPRAGE (MEMPRAGE), and multiecho FLASH (MEFLASH). Our goal is to get the best FreeSurfer reconstruction results possible for use with fMRI surface analyses,

[Freesurfer] fast_selxavg3 ( ) failed\n

Hi - I've encountered an error in step 8 of the functional connectivity analysis. here is some of the information requested with errors: FREESURFER_HOME: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin

Re: [Freesurfer] control points from cross transferred to long

Hi P, if you want to investigate the control.dat file you can do so with freeview (File- Load Point Set and choose the control.dat file). In the dev version of Freeview there is an option to select a cp number or move through the list with arrows. In the stable version, there is no box, but

Re: [Freesurfer] Using FreeSurfer Suggested Morphometry Sequences

no, there is a post-hoc recon-all target you can use. -T2 or -T2pial or something. Sorry, I don't remember, maybe someone else can fill in the details Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi Bruce, Thanks so much! We do have a bandwidth matched T2-space. So should that be fed into

Re: [Freesurfer] Using FreeSurfer Suggested Morphometry Sequences

Hi Bruce, Thanks so much! We do have a bandwidth matched T2-space. So should that be fed into recon-all at the same time as the MEMPRAGE as a second series? best, John On 8/18/15, at Tue,Aug 18 - 8:32:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi John the MEFLASH never

Re: [Freesurfer] Using FreeSurfer Suggested Morphometry Sequences

Hi John the MEFLASH never achieved as good cortical contrast as the memprage, so for cotical stuff we still recomment memprage. And yes, feeding the RMS to recon-all will be fine. If you can get a readout/bandwidth matched T2-space or FLAIR that can be a pretty big help as well for avoiding

[Freesurfer] Query about transformations in the recon-all

Dear Freesurfer experts, I have some questions in the recon-all. After reading online manual and discussing with the experts in the maillist, I have known all the recon-all procedures performed in the individual native space. However, I very confuse that there are many transformations in the

Re: [Freesurfer] Query about transformations in the recon-all

Hi Feng we compute many transforms for many reasons. The em reg is computed once in the image with skull to help with skull stripping, then again to the GCA atlas to initialize the nonlinear transform for computing the aseg segmentation. cheers Bruce On Tue, 18 Aug 2015, chenhf_uestc

Re: [Freesurfer] Permutation output

The log file ends abruptly. Try the following mri_glmfit-sim --debug --glmdir rh_sulc_fwhm25 --sim perm 5000 1.3 perm.neg.13 --sim-sign neg | tee doug.log and send me doug.log doug On 08/11/2015 07:02 AM, pablo najt wrote: Thanks. Sorry but I am not being able to figure it out yet.

Re: [Freesurfer] Query about transformations in the recon-all

Hi, Bruce Thanks for your reply. Another question is What is talairach transformation procedure (This computes the affine transform from the orig volume to the MNI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer script called talairach). Why I need