Re: [Freesurfer] Base Misalignment during Longitudinal Image Processing

Hi xuan, You can try freesurfer 5.3 for the base creation and see if that fixes it. If not, send me the two norm.mgz of the cross time points and I take a look. Thanks, martin Sent via my smartphone, please excuse brevity. Original message From: XUAN AMELIA TRAN Date:07/04/

Re: [Freesurfer] Get mean thickness after qdec monte-carlo simulation.

Dear Douglas, Thank you for your advice. It works like magic. I have one more question. In qdec gui, I found some small areas in two-group comparision with two discrete variables (diagnosis and gender) and two nuisance variables (ICV, age). Then processed monte-carlo simulation with 1.3 abs. ->

Re: [Freesurfer] problems with Surface-based Interhemispheric Registration

Just to provide some additional insight, I noticed that the xhemireg file was missing from the ftp on January 28th, 2014 and emailed the listserv: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33639.html

Re: [Freesurfer] Overlay onto surf file

Hi Bruce, This will help me move in the right direction. I still need to figure out a way to find the closest voxel given (theta, phi) for every voxel on the surface, but this seems tractable. Thank you for your help. Paul On Thu, Jul 3, 2014 at 6:07 AM, Bruce Fischl wrote: > Hi Paul > > the

Re: [Freesurfer] Voxels included in wm.mgz but not in white matter surface

Hi James, If you draw in 255 voxels on the wm.mgz to connect that stray blob of red voxels to the others, then the wm surf should include it on a rerun. Look through a couple slices in that area for any disconnected wm voxels since it may be occuring on multiple slices. -Louis On Thu, 3 Jul

Re: [Freesurfer] problems with Surface-based Interhemispheric Registration

Hi all, I am trying again to perform Surface-based Interhemispheric Registration in another computer (same version of FS 5.0) and by building my own atlas. However, there is an error while running xhemireg command (please find the log attached). I also noted that the command xhemireg took a lot of

Re: [Freesurfer] localGI problems

Hi Elisa, Thanks for the update, does that mean that just adding -f to all rm in load_mgh.m worked for you? Sounds great, thanks for keeping us posted! Indeed, it's not that nobody computed the lGI, lots of people used it in published studies and from what I see in the mailing list, and I def

Re: [Freesurfer] -normalization all black

Hi Teo, You might just need to adjust the contrast/brightness settings when viewing the volume in freeview. If you move your mouse around do any non-zero values appear in the bottom right voxel info panel? The T1.mgz for bert should be 4.6mb, so you can see if what you have matches that. O

Re: [Freesurfer] recon-all CUDA error

Hi, I'm not sure which ones you want or are interested in. In the ~/freesurfer/bin/ you can find the mri_em_register_cuda as well as other *cuda binaries. In ~/Freesurfer/lib/cuda you can find some other files that may be of importance to you. I haven't had time to dig through them so far. Hav

[Freesurfer] mkcontrast manual weighting?

Hi, I’m making contrasts, and my 6 conditions are as follows: #1 female approach #2 male approach #3 female withdraw #4 male withdraw #5 car approach #6 car withdraw If I want to create the contrast all-approaching-things minus fixation, I’m dealing with #1 female approach, #2 male approach, and

[Freesurfer] freeview error

Hi All, I was hoping that someone might be able to help me. When I load a surface into freeview (e.g. /Applications/freesurfer/subjects/fsaverage/surf/lh.inflated), I get an error in my terminal: Did not find any volume geometry information in the surface When I go on to load in my multiple co

[Freesurfer] Problem of Volumes differ in dimension in Longitudinal pipeline

Dear experts Today, I conduct the longitudinal analysis according to tutorials of freesurfer (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing). But, when I do recon-all -base -tp -tp ... -all, it report the error: ---

[Freesurfer] Voxels included in wm.mgz but not in white matter surface

Hi, I'm working on some subjects with gray matter lesions, where usually these lesions happen at the boundary of GM and WM (mostly patients with MS). The problem is that Freesurfer can not follow the cortex past this areas. I have tried to use control points, white matter edits and even editing t

Re: [Freesurfer] Overlay onto surf file

Hi Paul the 130K vector is a scalar for each vertex, so there is no projection in freeview - it was already done by mri_vol2surf. Using mri_vol2surf you get to pick your projection method (check out the help). To convert from sphere to volume, you simply find the vertex on the ?h.sphere.reg fil

[Freesurfer] Freesurfer Help

Dear Sir/Madam, I am a masters student at Newcastle University using Freesurfer to extract data from MRI scans. When trying to use the command lines in terminal, I seem to be getting an error message which I was wondering if you could help me with. The command line I am using is : recon-all

[Freesurfer] MINC_BIN_DIR

HI, I am trying to use recon-all for brain analysis work. I have managed to get 4 of them done, but after being away for a couple of days I not get this error: firstly: MINC_BIN_DIR not defined nu_correct also shows to be missing therefore the analysis does not work. I have searched throug

[Freesurfer] Overlay onto surf file

Hello, Could anyone give me some insight into how freeview projects an overlay onto a surface? For example, I have an overlay generated though mri_vol2surf for subject pq, call it stats.nii. Opening the nifti in MATLAB, I see that the image it stores is a single, flat vector (had about 130,000 ent

Re: [Freesurfer] recon-all CUDA error

Hi again, Sorry I think that we have a missunderstanding. I was talking about the freesurfer mri_em_register_cuda and other mri_* binaries of freesurfer. Having the freesurfer files compiled in newer versions of cuda could include some optimizations at compiler level to run freesurfer processing i