Re: [Freesurfer] CSF segmentation and cortical ribbon

Hi Bruce, Thanks for the reply. I'm not really familiar with compiling C functions, I have been working all the time with Matlab. Always worth to ask : do you have such set of C functions in Matlab also ? Christopher On 25.07.2012 16:10, Bruce Fischl wrote: Hi Chris, sure, we can compute

[Freesurfer] FW: bringing surfaces from different subjects into the same space in matlab

Dear freesurfer experts, I would like to know how to have paint surfaces (.w) from different subjects into a common surface (fsaverage for example) and/or would like to know if my current approach is correct: I have first used the general recon-all step on some T1-w images. Subsequently I

[Freesurfer] Issues with Tracula

Hi! First of all let me thank you for having put at our disposal such great tools as FreeSurfer and Tracula! I am trying to run Tracula on the sample data that is on the website, but I've been running into some issues. I am attaching the configuration file just in case

Re: [Freesurfer] FW: bringing surfaces from different subjects into the same space in matlab

Hi Jose, why don't you use mri_surf2surf to transfer your T1-w overlays to fsaverage? Alternatively, you can just specify fsaverage as the output subject for mri_vol2surf. Then all of your T1-w overlays will be in alignment. doug On 7/26/12 4:31 AM, Rebelo Ferreira Marques Jose Pedro wrote:

Re: [Freesurfer] WM/Pial surfs Problem with SPGRs from 3T GE

Hi Mehul it's really all empirical. You just don't want the intensity normalization to erode the gray/white boundary. cheers Bruce On Wed, 25 Jul 2012, Mehul Sampat wrote: Hi Thomas,  The following message posted by Michael Harms

Re: [Freesurfer] WM/Pial surfs Problem with SPGRs from 3T GE

Hi Michael that's a good thought. Let me talk to Nick, and see if we should default to it and have a 1.5T flag instead Bruce On Thu, 26 Jul 2012, Michael Waskom wrote: Yes, that flag still works in 5.1. Bruce, think these parameters could be default in 5.2?  It's a long extra flag (that

Re: [Freesurfer] CSF segmentation and cortical ribbon

Hi Christopher see if mris_distance_transform does what you want. cheers Bruce On Thu, 26 Jul 2012, Christopher Coello wrote: Hi Bruce, Thanks for the reply. I'm not really familiar with compiling C functions, I have been working all the time with Matlab. Always worth to ask : do you

Re: [Freesurfer] FW: bringing surfaces from different subjects into the same space in matlab

Hi Jose you should use the sphere.reg, not the sphere, but other than that what you describe is essentially what mri_surf2surf does. You also have to be a bit careful to sample in both directions to avoid holes in the mapping. cheers Bruce On Thu, 26 Jul 2012, Rebelo Ferreira Marques Jose

[Freesurfer] How to converting labels to individual volumetric masks (Repost)

Dear All, I want  to use cingulate bundle as ROIs more exactly mask  for fiber tracking. Can I use different aseg than the one from Freesurfer for examples can I use segmentation from JHU-WhiteMatter-labels-1mm.nii.gz and their labels JHU-WhiteMatter-labels-1mm.txt to get a mask of my

Re: [Freesurfer] Surface number of vertices mismatch

Hi Doug, The sig.nii file is just a single p-value map, so it has only one frame. Thanks! Pablo On Wed, Jul 25, 2012 at 11:15 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: were there multiple frames (time points) in the sig.nii file? The .w format will save only one frame. You can check

Re: [Freesurfer] Issues with Tracula

Hi Sergio - Thank you for your kind words, and also thank you for taking the time to search the archives for answers! The first problems you had with running bedpostx through trac-all have to do with trac-all assuming an older version of FSL than the current one, and this'll be fixed in the

Re: [Freesurfer] stats

Hi Viola, I have a different work flow for you. When you run FDR, it will change the Min value under Threshold. Go to a terminal and cd to the contrast directory of your qdec output folder, then run the commands below. It is assumed below that the threshold you want to use is 3.37. You should

Re: [Freesurfer] tcsh: tailarach_avi: Command not found

Thanks for your prompt reply, Doug.I've been checking and following the wiki instructions with regards to setting up proper paths, and I could not find an obvious (to me) problem there.I attach a file with things I have tried and issues I have found.Further advice will be greatly appreciate

Re: [Freesurfer] tcsh: tailarach_avi: Command not found

Are the missing files in $FREESURFER_HOME/bin and is that path in your system PATH variable? On 07/26/2012 01:29 PM, Fidel Vila wrote: Thanks for your prompt reply, Doug. I've been checking and following the wiki instructions with regards to setting up proper paths, and I could not find an

[Freesurfer] Trouble downloading tutorial data

Dear surfers, I'm having trouble downloading the longitudinal data form the website. This is the command I used: curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.tar.gz Error message: curl: (56) FTP response reading failed Am I typing the filename in wrong? Also, I tested the

Re: [Freesurfer] tracula -bedp - path

Hi Keith - This seems to be a different problem here, since all the bedpostx outputs are there and are loaded in without a problem. The error occurs after that. What's the size of your images? Does the mask file look normal? Thanks, a.y On Thu, 26 Jul 2012, Keith Yoder wrote: Hi, Was

[Freesurfer] CSF and brain volume quantification.

Dearest gurus of all things Freesurfer, I am looking for a simple way to quantify the amount of CSF, the total volume of brain matter (excluding ventricular space if possible) and, as a check on these two, the total intracranial area. Essentially I need a way to compare how much room there