Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

Hi Doug, thank you for the detailed response. Highly appreciated! Kindly. I want to register FA map to structural T1 image using the command mri_spmregister as follow: mri_spmregister move FA.nii --s subj1 --reg reg dat --o FA_2_T1.nii.gz Is this correct? Original Message

Re: [Freesurfer] Disastrous Soft Error

Glad to hear it worked out Bruce > On Feb 24, 2017, at 5:01 PM, Rockers, Elijah D. > wrote: > > OK, sorry for spamming the list. I fixed the the faulty skullstrip by using > > recon-all -skullstrip -clean-bm -no-wsgcaatlas -subjid > > Currently redoing the

Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

Dear Doug, I was wondering, why do you prefer mni152reg to mri_coreg for gregistration to MNI? According to help, mri_coreg is also able to do 12 DOF registration. Antonin mri_coreg is the FS implementation of spm_coreg (spmregister) both of which use normalized mutual info. bbregister

Re: [Freesurfer] bbregister vs spmregister vs mri_coreg

mri_coreg is the FS implementation of spm_coreg (spmregister) both of which use normalized mutual info. bbregister uses the BBR cost function and is preferred for all MRI. For registration to MNI space, we usually use mni152reg (a wrapper around fsl's flirt) On 2/25/17 8:49 AM, John Anderson

Re: [Freesurfer] Intensity information of Hippocampal Subfields

Thank you so much Dr. Doug! I just have one more question: Now I want to compute the same information for our second modality (i.e., mean and std intensity of different HP_subfields for our additional scan, e,g., T2 or FLAIR).My question is that how could I use .FSspace.mgz (in mri folder) and

Re: [Freesurfer] lh.white.H , Failed to create

Dear Vasudev, on what filesystem does your working directory reside? According to the path to your data it seems that you use some external drive, probably with non-unix-like filesystem. The error most probably means, that your filesystem does not support symbolic links. Regards, Antonin

[Freesurfer] bbregister vs spmregister vs mri_coreg

Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the

[Freesurfer] lh.white.H , Failed to create

Dear all , I have been incurring lot of problems while running recon-all on ubuntu 16.04 , recon-all throws following error : " #@# Curv .H and .K lh Sa 25. Feb 04:09:16 CET 2017 /media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/surf mris_curvature -w lh.white.preaparc total