[Freesurfer] recon-all-hippo-subfeilds

Dear FS experts, I've a query regarding the recon-all analysis. I ran recon-all using the following command eg. recon-all -i location/nc.nii -s NC -all I got the analysis done. Now I'm interested to calculate the hippocampal structures. I knw the command line for that also recon-all -i lo

[Freesurfer] talairach transforms

Trying autorecon1 with the example data set Bert,there is error in talairach transforms.What would be the problem? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] make_average_subject without aparc and talairach.xfm

Hi Doug, just a quick follow-up on my previous questions regarding custom average surfaces. I guess I am a bit confused regarding the relationship of custom templates and custom average surfaces. I made a custom template and a custom average surface. However, I don't understand how they are related

[Freesurfer] High intensity GM being omitted

Attached is an image that describes my issue. WM in the temporal region is being omitted after running recon-all. Most of the omitted voxels are in the 120-130 range. It's causing an issue with the underlying WM voxels as well, they've simply disappeared. I can see how this voxel intensity limit w

[Freesurfer] Skull strip

Hi, I am learning to use the program. I have some questions about how to edit skull strip manually. In this procedure is correct to remove only the residual skull or even other non-cerebral elements (eg meninges)? So far I have never found remaining skull but small residual portions of meninges. A

Re: [Freesurfer] (no subject)

Hi again Doug, I'm looking at the stats file associated to aparc and perirhinal is not there. I have looked for perirhinal and I found it in ?h.BA.stats, so I guess what I need to update is the BA annot, right? Thanks a lot! Jesus From: freesurfer-boun...@nmr.

Re: [Freesurfer] mri_glmfit error: negative DOF -10

It usually means that the number of subjects in the input is less (10 less) than the number of regressors. It looks like you have about 14 input subjects and 24=6*4 regressors. You need to add subjects or remove regressors (ie, classes or covariates) doug On 9/18/13 11:41 AM, Robert Schulz wro

Re: [Freesurfer] expanding pial surface

Hi Gabor, it depends on the cause. Typically we fix this by placing control points in the subjacent WM that is < 110 cheers Bruce On Wed, 18 Sep 2013, Gabor Perlaki wrote: Dear all, In the suggested workflow there is clear deescription of how to correct pial surface including non-cortex wi

Re: [Freesurfer] How to convert a thickness file (i.e. lh.thickness) ti a 3D nifti file

Hi Fabrice, what would converting a thickness file (which has one value for each point on the surface) to a volume mean? Would you want just a strand of voxels with the thickness values at the gray/white boundary? At the pial surface? Would you want the ribbon filled with the same value? If you

Re: [Freesurfer] TALx coordinates

Hi Doug, I'm looking at the $FREESURFER_HOME/average/mni152.register.dat and I can see some relation with the formula you provided. It appears that y and z are swapped, and the offsets are all different. Do you know why they are so? By the way, is there a way I can ask mri_surfcluster to read

[Freesurfer] mri_glmfit error: negative DOF -10

Hello, I am using mri_glmfit to perform a correlation analysis between some surface-based DTI measures and a behavioural outcome (grip), aiming to correct for scannertyp (C,I,W), handedness (R,L) as discrete variables and age (AGE) and duration (Mo) as continuous covariates. Please find the fsg

[Freesurfer] expanding pial surface

Dear all, In the suggested workflow there is clear deescription of how to correct pial surface including non-cortex within the boundaries, but there is no description of how to expand the pial surface if it doesn't include the cortex within boundaries. Could anybody help me in this issue? Thanks,

[Freesurfer] How to convert a thickness file (i.e. lh.thickness) ti a 3D nifti file

Dear Freesurfer users, I am searching how to use the mri_surf2vol command in order to convert a "lh.thickness" file into a 3D .nii file (in the original subject space). Many Thanks, Fabrice ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu