[Freesurfer] CorticalParcellation for mask

External Email - Use Caution Dear freesurfer experts, I am trying to make mask for '1027 ctx-lh-rostralmiddlefrontal, 2027 ctx-rh-rostralmiddlefrontal ' on MNI standard image (MNI152_T1_2mm_brain.nii) (FreeSurferColorLUT

[Freesurfer] freesurfer error in matlab

External Email - Use Caution Dear Freesurfer devs, I am trying to run FreeSurfer in Matlab and I received the following error message dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1

[Freesurfer] Affine registration 2 input images

External Email - Use Caution Hello all, I need to perform an affine registration between two input images. Please, which Freesurfer tool does enable to perform affine registration (12 DOF) ? Does the command mri_robust_register enable to do that? Thanks a lot Regards Adam __

Re: [Freesurfer] Affine registration 2 input images

Hi Adam yes, mri_robust_register should do the trick. You will need to specify --affine as rigid is the default cheers Bruce On Fri, 7 Feb 2020, Adam Rytina wrote: External Email - Use Caution Hello all, I need to perform an affine registration between two input images. P

[Freesurfer] New release plans?

External Email - Use Caution Hi folks! I checked the wiki and github, but couldn't find anything about milestones or plans for the next major release of Freesurfer. Are there any loose dates or targets? (We're near the start of a 5-year imaging study, and trying to plan for trai

[Freesurfer] qdec / tksurfer GUI

External Email - Use Caution I've noticed an issue when trying to manually input values into fields with Qdec. This problem has been reported before. I thought perhaps it was because Qdec is deprecated, so I loaded the results into tksurfer, and I can't change fields in this pro

[Freesurfer] Cluster-wise correction for multiple comparisons

Hi there, First, I ran "mri_glmfit" using mask including 4 ROIs(file name: 4_ROI.label) as follows: mri_glmfit --glmdir g2v3.wls --y ces.nii.gz --wis cesvar.nii.gz --fsgd 2group.fsgd --C group.diff.mtx --lable 4_ROI.label --surface fsaverage lh - --fwhm 5 -eres-save. Second, I'm going to proc

[Freesurfer] some basic questions regarding longitudinal analyses in Freesurfer

External Email - Use Caution Hello, I'm analyzing a large dataset using an LME model to examine longitudinal changes in brain structure that vary as a function of group (patients vs controls). Because some participants were scanned several years apart in early childhood, the i

Re: [Freesurfer] DWI EPI correction

External Email - Use Caution Hi, Adam, while reading this thread, I would like to clarify: bbregister does rigid body registration, so you could use this tool for registering EPI to structurals, indeed. But this tool only registers, it does not unwarp the distortions in the EPI

Re: [Freesurfer] DWI EPI correction

Bbregister is affine, not rigid. Affine registration can account for the geometric distortion of EPIs along the phase encode direction (stretching or compression, depending on the polarity), if the target of the registration is an image that does not have that distortion, such as an MPRAGE.

Re: [Freesurfer] DWI EPI correction

External Email - Use Caution Hi, according to help, bbregister is rigid: bbregister --help                Help NAME     bbregister SYNOPSIS     bbregister --s --mov --reg \         -- DESCRIPTION     This program performs within-subject, cross-modal registration using

[Freesurfer] mri_glmfit-sim error

Hi there, I ran “mri_glmfit-sim -glmdir g2v3.wls -2spaces -perm 1000 1.3 abs”. But, there was error message as follow: “design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with -perm-force” Please let me know how to process mri_glmfit-

Re: [Freesurfer] Extract specific LGI and Volume values

External Email - Use Caution Thank you for your email. I run exactly the command mri_label2label as you suggested, and the command finished without any problem. But I did not know why I could not open the label. Please help me. Thank you once again. On Tue, Feb 4, 2020 at 2:55 AM

Re: [Freesurfer] DWI EPI correction

External Email - Use Caution Hello both, thanks a lot for your answer. Adam Od: freesurfer-boun...@nmr.mgh.harvard.edu za uživatele Yendiki, Anastasia Odesláno: pátek 7. února 2020 23:44 Komu: freesurfer@nmr.mgh.harvard.edu ; Antonin Skoch