Re: [Freesurfer] Creating and analyzing combined ROIs, combining different FreeSurfer versions

the FS permutation tutorial with the output from above (after including the --eres-save flag in the mri_glmfit command)? Kind regards, Carl On 12/12/2022 6:14 PM, Trolle, Carl wrote: > Thank you for the reply, > > 1. Once each participant's aparc has been broken and we'v

[Freesurfer] Creating and analyzing combined ROIs, combining different FreeSurfer versions

Dear FreeSurfer team, 1. We're trying to focus our cortical analysis following suggestions here https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23939.html. The FS ROI tutorial page mentions that labels should be drawn or registered on the fsaverage template; could we then

[Freesurfer] Specifying contrasts for an unbalanced design

Dear FreeSurfer team, We are investigating if there is a difference in cortical thicknesses between persons with a condition and controls, regressing out the effect of site, sex, age, but have some concerns on how to specify our contrasts. We don’t think that the age-slopes will be different

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

Hi, I believe so, I ran the following commands: mris_register -L subject/label/?h.central_sulcus.label $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central subject/surf/?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

Hi! Thank you, yes, using the Freesurfer dev-version available through the Martinos cluster produced the desired result with the Destrieux-atlas. I’ve been using the 711-version throughout, I hope that I specified the version in my first email. Is it possible to use these commands

[Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

Ok. I'm trying to attach a copy of the output I get in the terminal-window. The commands I've been running for the mris_register and mris_ca_label are "mris_register -L subject/label/?h.central_sulcus.label FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central

Re: [Freesurfer] Using averaged T1-images to calculate cortical thickness

Hi, yes that’s correct, one of the sites gets us both axial and sagittal T1s at 1mm isotropic. Ok, after some discussion I think we’ll move along without using averaged images. Thank you for taking your time! Kind regards, Carl ___ Freesurfer

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

, Carl From: Trolle, Carl Sent: 09 August 2022 12:37 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution Sorry, been trying to get this right for some time before getting back to you

Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

Sorry, been trying to get this right for some time before getting back to you, but not sure that I have. I'm attaching screenshots of the ?h.sphere.reg for the original, processed and the fsaverage-subjects with the destrieux-annotation. To me, it looks slightly worse after the mris_register

[Freesurfer] Using averaged T1-images to calculate cortical thickness

Hello dear FreeSurfer team, We are undertaking a multicenter study analyzing cortical thickness of controls and persons with a neurological condition. Unfortunately, there are issues with motion artifacts and image quality. To counter this, we’ve created averaged T1-images by combining one