[Freesurfer] phase data overlay using fsaverage

Dear freesurfer experts, I have used the mri.vol and mri.analyzehdr.vol fields to encode my coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz). I then brought these data into freesurfer using the following: bbregister --s fsaverage --mov

[Freesurfer] Memory allocation problem with mri_robust_template

Hi all, Since upgrading to Freesurfer v5.0, I have been unable to complete the first step of recon-all ('recon-all -autorecon1 -subjid ...') when using 5 anatomical datasets (our typical load for surface reconstruction). The problem seems to come when the third dataset is being registered, at

[Freesurfer] roisummary-sess from binary mask

Hello, I am trying to get a summary of beta value activation for a hand-drawn binary mask. This mask is a sphere, so it does not correspond to a particular anatomical label or functional contrast. Is there any way to apply roisummary-sess to this type fo binary mask (in nii or mgz format)? If

[Freesurfer] Three starting questions

Dear FreeSurfer community, You were very helpful for my last question, thank you. Now I have three basic questions. 1. I would like to check the segmentation by loading T1.mgz and aseg.mgz as an -aux volume, so that I can switch between them. How can I do this? (tkmedit subject T1.mgz -aux

[Freesurfer] tksurfer error

Dear freesurfer community, I am currently trying to view one of the surfaces generated by recon-all command in tksurfer but when I enter the command: tksurfer LuceHR_FS_SURF lh inflated.nofix I receive a series of errors that look like this: Received X error! Error code : 1 Request

Re: [Freesurfer] Abblocked Setup

Dear Doug, Thanks for your response! Our stimuli starts with the null condition, but abblocked assumes it's the ON condition. Is there a way to invert this? When we look at the sig maps, how do we know what the contrast is? Which condition does it think is null/task, negative/positive? From

[Freesurfer] about option -show-edits in version 5.0.0

Hi, I am trying to develop a custom software to run freesurfer, make edits if necessary(user intervention) and rerun the freesurfer from appropriate staring point and also, track/record the user interventions. My prime concern is the tracking of user intervention part, and I came across

Re: [Freesurfer] Slice Order

Hi Rita, I would not automatically assume that regarding slice ordering with interleaved acquisitions, as I don't think that there is necessarily any standard that different manufacturers are committed to following. It is actually a non-trivial issue -- e.g., how do scanner choices regarding

[Freesurfer] surfaces to voxelspace

Dear freesurfer experts, I would like to display freesurfer surfaces in the voxelspace of the original subject image using matlab. Which coordinate transformation do I have to apply to get the vertex-coordinates to the RAS space and finally to the original voxelspace of the subject? (i guess

Re: [Freesurfer] Memory allocation problem with mri_robust_template

Hi Mahen, 4.5 is based on flirt registration which does a pairwise registration to the first image. Since 5.0 we use the mri_robust_template tool (as it can ignore outlier regions and produces more accurate registrations, see Reuter et al Neuroimage 2010 ..robust registration), but it is more

Re: [Freesurfer] Three starting questions

Dear Tanja, Concerning your question 3 do the following: In the System Preferences - Keyboard Mouse you should select the buttons as follows: left one: primary button, right one: secondary button top on: Button 3 You will now have a 3-button mouse that works fine with FreeeSurfer. Ed On 09