[Freesurfer] nii format input for recon-all

Dear all, I have done the recon-all for DICOM format input of all subjects. Part of subjects extracted brain volume not very perfectly. I want to use brain volumes nifti format which have strip the skull and neck well. My question is how to use the brain volume in nii format to segment and next

[Freesurfer] glmfit error

Dear FS experts I'm running glmfit with FS v5.1 and get the following error:ERROR: matrix is ill-conditioned or badly scaled, condno = 1.75146e+07Possible problem with experimental designcommand line:mri_glmfit --surf

[Freesurfer] Cortical thickness/surface area in volume-defined ROIs

Dear Freesurfer experts, I want to use volume-defined ROIs (obtained in a VBM study) to extract mean thickness and surface area, in a total group of 138 participants. I followed the tutorial 'Cortical Thickness of a volume-defined ROI'. I have a few questions regarding this analysis: 1. The

Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs

Dear Anita, Would you please tell me where I can find Cortical Thickness of a volume-defined ROI? Thanks, All the best. 2013-11-29 Rujing Zha 发件人：Anita van Loenhoud acvanloenh...@gmail.com 发送时间：2013-11-29 21:51 主题：[Freesurfer] Cortical thickness/surface area in volume-defined ROIs

Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs

Hi Rujing Zha, Click this link: http://freesurfer.net/fswiki/VolumeRoiCorticalThickness Anita ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is

Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs

Hi Anita the problem is that the cortex is not well aligned in the avg152 space, and so a volume-defined ROI will not follow the contours of the cortex well. Not sure that there's much you can do about this except possibly map the ROI back to the individual subjects, and recreate it in

Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs

Dear, I get it. Thanks. All the best. 2013-11-29 Rujing Zha 发件人：Anita van Loenhoud acvanloenh...@gmail.com 发送时间：2013-11-29 22:18 主题：Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Hi Rujing Zha, Click this link:

[Freesurfer] major lobes

Hi all, Since I haven't heard back about my question so far, I'm posting it again! Sorry about this but I really need your help! As mentioned in my previous posts, I'm interested in having the GM volumetric lobar masks (frontal, parietal, temporal, occipital, and insular) with the final goal

Re: [Freesurfer] major lobes

The commands look right and it sounds like you might have the right result. What do you mean you are getting a detailed WM + GM segmentation? If you just load freeSurfer_lobes.nii.gz into tkmedit, the label names will be all messed up because you don't have the proper color table, but you

[Freesurfer] how to recon-all multiple participants simultaneously? thanks

Dear Freesurfers, I'd like to ask how could we recon-all multiple participants at the same time? My laptop has a 32G ram and a 8-core-intel-Core-i7 CPU, i expect it could speed up the surface construction by running several participants simultaneously. When i use the following command: