[Freesurfer] Motor areas from Talairach

Hi I am trying to find different Talairach areas in the motor cortex. I used the mris_convert -t function on the inflated brain (.asc). I selected coordinates using ranges from a paper (for example range x -70 to 4; range y -43 to 7 and range z 19 to 76 for M1). But when I want to see if they

Re: [Freesurfer] Motor areas from Talairach

you could draw a box including those coordinates in a talairach volume then apply the inverse talairach.xfm transform with mri_convert to map it into subect anatomical coords, then sample that onto the surface. Note that the new version of FreeSurfer will include explicit estimates of the

Re: [Freesurfer] White matter hypointensities

Hi Irene, Sorry for the delay. I wrote some tools almost 10 years ago that do lesions/wm/gm/csf segmentations from multi-spectral data; the code is very much outdated (runs on SPM99!) but if you are technically skilled you can certainly still get it running:

Re: [Freesurfer] [fsfast]: temporal overlap of stimuli and concurrent presentation

I have not tried it, but that should work. doug Sebastian Moeller wrote: Dear fellow Surfers, is it possible to model several independent event streams for fs-fast? That is, using the 5 column paradigm file, is it okay to have different condition ID codes that have identical stimulus

Re: [Freesurfer] [fsfast]: temporal overlap of stimuli and concurrent presentation

Hi Doug, thanks alot! But see, I did it again, asking either or questions, and being totally stomed to get a yes as response :). So do you think 1) specifying two ID codes at the same onset time will work? or 2) staggering the onset times of both ID codes around the true onset time with a

Re: [Freesurfer] [fsfast]: temporal overlap of stimuli and concurrent presentation

I think that #1 should work (#2 should work too, but it is less preferable). doug Sebastian Moeller wrote: Hi Doug, thanks alot! But see, I did it again, asking either or questions, and being totally stomed to get a yes as response :). So do you think 1) specifying two ID codes at the

[Freesurfer] more thinner parcelation borders

Hi: I change the color palette of the parcelation borders to white... But, I need thinner parcelation borders... can I change that parameter ?... Or could I specify a transparency factor for the borders ?... Sincerely, Gonzalo Rojas Costa ___

Re: [Freesurfer] more thinner parcelation borders

Hi Gonzalo, I don't think you can make them thinner - they are 1 vertex wide (or 2 if you count each label). I can't remember if there are any transparency settings around, but you can put them under an overlay if you prefer. cheers, Bruce On Fri, 30 Jul 2010, Gonzalo Rojas Costa wrote: Hi:

[Freesurfer] spmregister error

Hello, When running spmregister-sess (standard environment was sourced) I encountered this error: ERROR: matlab exited with errors ERROR: cannot find spm_coreg.m. Make sure that the SPM package is in your matlab path (check ~/matlab/startup) ERROR: spm_coreg ERROR: spmregister failed

Re: [Freesurfer] spmregister error

Hi Sandra, I just had this same problem about a week ago. The solution which worked for me was adding the following line of text into the startup.m file in your matlab folder: path(path,'/usr/pubsw/common/spm/spm5'); I'm not sure it matter exactly where you put it. I put mine in the last

Re: [Freesurfer] spmregister error

Yes, that should work. doug Adam Nitenson wrote: Hi Sandra, I just had this same problem about a week ago. The solution which worked for me was adding the following line of text into the startup.m file in your matlab folder: path(path,'/usr/pubsw/common/spm/spm5'); I'm not sure it

Re: [Freesurfer] spmregister error

That seems to now work with those changes. Thanks so much to Adam and Doug! Sandra Yes, that should work. doug Adam Nitenson wrote: Hi Sandra, I just had this same problem about a week ago. The solution which worked for me was adding the following line of text into the startup.m

[Freesurfer] Freesurfer and AFNI - 3dmaskave problems

Hello, I am trying to create white matter, grey matter, and CSF masks (along with some other finer segmentations) using Freesurfer, and then use these to find the average BOLD response for all voxels within each mask using AFNI's 3dmaskave. So far, I have performed the following steps.