[Freesurfer] The sulc file from mris_inflate

Hi, We have used mris_inflate: mris_inflate rh.smoothwm rh.inflated The command generates inflated and sulc files. We would like to do a little bit of smoothing on the sulc file, so that we get rid of few scattered regions where small positive curvature islands are located within negative

Re: [Freesurfer] recon-all on T1s without anterior coil

Hi James it's hard to say. How many coil elements were off? You could try with anterior control points, but you might not be able to include this subject in a group study cheers Bruce On Sun, 11 Jun 2017, Gullickson, James wrote: > Hello all, > We have a subject whose T1s were collected

[Freesurfer] recon-all on T1s without anterior coil

Hello all, We have a subject whose T1s were collected without the anterior head coil engaged, due to a technical error. The posterior coil collected signal. This was on a Siemens Prisma 3T scanner. Would you expect Freesurfer to still be able to process/segment this data accurately, or is it a

Re: [Freesurfer] difference in T1 and T2 resolution

In the log file the error was: ERROR: MultiRegistration::loadMovables: images have different voxel sizes.   Currently not supported, maybe first make conform? Debug info: size(1) = 1, 1, 1   size(0) = 0.7, 0.7, 0.8 MultiRegistration::loadMovables: voxel size is different

[Freesurfer] aseg.stats

Dear FS team, I would like to obtain Total Brain Volume using metrics provided in aseg.stats. I have the idea of obtaining it as a result of white matter + grey matter. WM is provided in CorticalWhiteMatter and GM could be obtained with: TotalGreyMatter -

Re: [Freesurfer] difference in T1 and T2 resolution

What was the error message? Peace, Matt. From: on behalf of John Anderson Reply-To: Freesurfer support list Date: Sunday, June 11, 2017 at 9:06 AM To:

[Freesurfer] difference in T1 and T2 resolution

Dear Freesurfer experts, I have T1 and T2 images were unfortunately acquired with different resolution (i.e the voxel sizes is not the same) T1 is 280X280X208 T2 is 270X270X200 I tried to run "recon-all"  but it failed to process the data. The command that I used is : pbsubmit -c "

Re: [Freesurfer] cortical metrics description

Hi Ani sulcal depth is compute as the integrated signed distance moved by points during inflation (the sum of the movement vector dotted with the surface normal). ?h.curv is the spatially smoothed (10 iterations of nearest neighbor soomthin) mean curvature cheers Bruce On Sat, 10 Jun

[Freesurfer] Merging outputs of mri_label2vol across hemi

Hi Freesurfer Team, I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produced the segmentation for each hemisphere. Is there a way to merge both the left and right volumes together? Thanks for your help. Best Wishes,