Re: [Freesurfer] bbregister: PET and MRI

why are you using the --t1 option? Looks like gray matter is brighter than white matter, so --t2 (same as --bold) is more appropriate. Rafa x wrote: Dear FS Team, I have a problem with the bbregister command. I used it for coregister a MRI with a PET. My first step is set the same origin and o

[Freesurfer] Qdec question

Hi, I am using qdec for analysis and noticed that in addition to thickness measures I can select others such as area and volume. I have been trying to figure out what exactly the area measure refers to (surface area, etc.). I did not find it on the website. Can someone clarify that for me? If t

Re: [Freesurfer] selxavg3-sess error (??? Error using ==> fclose)

All, Nevermind. It looks like the error was being caused by a space issue. Sorry for eating up your time, Avram On 2/16/2009 1:34 PM, Avram Holmes wrote: All, I'm encountering an error when I run selxavg3-sess and I am not sure how to get around the problem, or what it means. I am running

RE: [Freesurfer] still exiting with errors

the current versions should have aseg.auto_noCCseg.mgz. When you rerun recon-all doesn't it create them? On Sun, 15 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote: The aseg files in mri are aseg.auto.mgz and aseg.auto_CCseg.mgz. The scans that are working seem to have aseg.auto_noCCseg.mgz i

Re: [Freesurfer] manual segmentation of subcortical structures

Hi Jose, not sure I understand. Do you mean to edit the aseg.mgz to improve hippocampus and thalamus? We don't have any protocols for this, although you could certainly do it in tkmedit or freeview. Changing these shouldn't have much affect on cortical thickness. cheers, Bruce On Mon, 16

Re: [Freesurfer] Wrong Red Line and Yellow Line

Haobo, Adding a control point might help. See this tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints which describes the problem you are seeing and how to fix it. Don't put the control point at the very end of the gyrus, as this voxel might be partial-volumed and mark

Re: [Freesurfer] Version re-run

Martin, There is no need to rerun the -autorecon1 step as long as you are happy with the brainmask.mgz (ie, miminal or no skull, and cerebellum retained), and the talairach.xfm is good (which would be the case if your prior runs completed successfully). We'll probably release another version in m

Re: [Freesurfer] In common stereotactic space?

Jurgen, To create thickness difference maps, follow the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility In your case, you would skip step 1, since the recon-all -long will create the .lta transform (from tp1 to tp2) already (look for it in the tp2subj/m

[Freesurfer] manual segmentation of subcortical structures

Hi there, we have a bunch of MRI scans already segmented by using the typical FS recons protocol. Now we would like to improve the hippocampus and thalamus delimitation by manual segmentation, but several basic questions arose: 1. Are there radiological protocols (commonly used) to segment thes

[Freesurfer] selxavg3-sess error (??? Error using ==> fclose)

All, I'm encountering an error when I run selxavg3-sess and I am not sure how to get around the problem, or what it means. I am running the following command, which has worked with the data for the other participants in my study. selxavg3-sess -s c43 -d . -analysis Flanker_nResp -overwrite

[Freesurfer] In common stereotactic space?

Dear FS experts I had run recon-all -long on two time points and would like to subtract the cortical thickness maps of the two time points. Do the two ?h.thickness maps of the different time points are already in the same space so that they can be directly subtracted in MATLAB? Or Do I have to

[Freesurfer] FreeSurfer Tutorial and Workshop in Sao Paulo, Brazil

The FreeSurfer Development Team is hosting a two-day course for beginner and experienced users of FreeSurfer . Day 1 will be an introduction toFreeSurfer

[Freesurfer] bbregister: PET and MRI

Dear FS Team, I have a problem with the bbregister command. I used it for coregister a MRI with a PET. My first step is set the same origin and orientation for both images (approximately) (I use SPM or tkregister2). After, I write in the terminal "bbregister --mov s24PET.img --t1 --s sr24 --init-f

[Freesurfer] Version re-run

Hi all, I have 100-something scans already run on a FreeSurfer version from 2005 that I'd like to re-run with the newest version of FreeSurfer. The subjects contain manual edits to the brainmask.mgz and wm.mgz, as well as control points. As far as I have understood, when running autorecon2 my

Re: [Freesurfer] cortical thickness in temporal pole

Hi Lucia, Just to re-iterate what Bruce already mentioned, you should really inspect the temporal pole areas thoroughly (i.e. make sure the white and pial surfaces are not including neighboring 'artifacts' such as temporal bone, etc.). We usually find the signal intensity is generally decreased in

Re: [Freesurfer] cortical thickness in temporal pole

Hi Lucia, we published maps of mean thickness in our original Cerebral Cortex paper I think, and temporal pole was always among the thickest regions. cheers, Bruce On Mon, 16 Feb 2009, Lucia Garrido wrote: Many thanks for your e-mail, Bruce. Yes, I've inspected all data, and one of the th

Re: [Freesurfer] cortical thickness in temporal pole

Many thanks for your e-mail, Bruce. Yes, I've inspected all data, and one of the things that makes me more worried is that I had to edit many subjects in this area because there was WM/GM that was cut. So, just in case you have previous results of mean cortical thickness for this area, would it be

Re: [Freesurfer] cortical thickness in temporal pole

Hi Lucia, temporal pole is among the thickest cortical regions, but you should visually inspect your data to check that it is accurate. cheers, Bruce On Mon, 16 Feb 2009, Lucia Garrido wrote: Dear all, I'm comparing average cortical thickness values between groups using regions defined in

[Freesurfer] cortical thickness in temporal pole

Dear all, I'm comparing average cortical thickness values between groups using regions defined in the aparc files. I find significant differences in the right temporal pole. I was expecting difference here, but I'm concerned about the mean values of thickness. For controls, that value is 4.01, whe