[Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

Hi, I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` to `T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs). The following produces a well-aligned output: mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii As does the following:

Re: [Freesurfer] cortical/subcortical volume based analysis

Hello Bruce, Thank you for the response. I was able to look into CVS command and I wrote a command on how to register each subjects to cvs_avg35_inMNI152 template using the following: mri_cvs_register --mov subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz --step1 --step2

[Freesurfer] How to obtain a label for Custom ROI mask

Dear all, I have custom ROI mask ( MNI Space ) that i have prepared from Jülich atlas , I would be like to obtain corresponding surface label file, Could you please guide me necessary the steps that i have to follow inorder to obtain corresponding label for my mask. Thanks Vasudev

Re: [Freesurfer] cortical/subcortical volume based analysis

Hello Bruce,  Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface?  ‎If yes, please what are the steps to achieve this? can I still analyze it with mri_glm? Best,  Paul Sent from my BlackBerry 10 smartphone.   Original Message  

Re: [Freesurfer] cortical/subcortical volume based analysis

Hi Paul I guess you could use CVS for this. cheers Bruce On Sat, 14 Oct 2017, miracle ozzoude wrote: Hello Bruce,  Thank you very much. Can I still general cortical and subcortical maps with the Spherical warp of r/lh.white surface?  If yes, please what are the steps to achieve this? can

Re: [Freesurfer] freesurfer output

thanks a lot for your help best, hessam On Sun, Sep 24, 2017 at 6:51 PM, Bruce Fischl wrote: > Hi Hessam > > yes, check the stats subdir for each subject (e.g. stats/aseg.stats) > > cheers > Bruuce > On Sun, > 24 Sep 2017, Z Hessam wrote: > > > > > Hello FreeSurfer

Re: [Freesurfer] cortical/subcortical volume based analysis

Hi Paul if you use a property (like gm) to drive intersubject registration it then becomes difficult to also analyze it. If your warp was truly perfect you could just analyze the properties of the warp, but even then it is hard to localize effects (e.g. if you changed the smoothness of the