Re: [Freesurfer] subcortical segment NIFTI files

t list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday, June 17, 2014 at 10:51 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files They look pretty simila

Re: [Freesurfer] subcortical segment NIFTI files

gt;" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files I think I just ran something like bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat --init-fsl Maybe I tweeked it manually On 6/17/14 1:10 PM, Yang, Daniel wrot

Re: [Freesurfer] subcortical segment NIFTI files

d.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to get this file doug Thanks

Re: [Freesurfer] subcortical segment NIFTI files

t 4:30 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created? I performed a r

Re: [Freesurfer] subcortical segment NIFTI files

edu <mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files sorry, don't use the mri.2mm/aseg.mgz use the one from mri/ The --inv take the inverse so it maps in the right direction On 6/16/14 6:16 P

Re: [Freesurfer] subcortical segment NIFTI files

surfer@nmr.mgh.harvard.edu>> Date: Monday, June 16, 2014 at 12:32 PM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files sorry, don't use the mri

Re: [Freesurfer] subcortical segment NIFTI files

arvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files That is not the right registration. Use $FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat specify right_amyg as the --targ and MNI152 as --mov and add --inv and sp

Re: [Freesurfer] subcortical segment NIFTI files

day, June 16, 2014 at 11:43 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files That is not the right registration. Use $FREESURFER_HOME/average/

Re: [Freesurfer] subcortical segment NIFTI files

June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files Sorry, I was trying to find out what it is you are trying to do, not wh

Re: [Freesurfer] subcortical segment NIFTI files

rd.edu>> Date: Monday, June 16, 2014 at 8:16 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] subcortical segment NIFTI files Sorry, I was trying to find out what it is y

Re: [Freesurfer] subcortical segment NIFTI files

Sorry, I was trying to find out what it is you are trying to do, not what your command line is. The command may run, it is not doing anything intelligible, ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm mni152, which does not make sense doug On 6/16/14 1:38 PM, Y

Re: [Freesurfer] subcortical segment NIFTI files

It appears that Email in Plaint Text makes the command line look ugly. Here is a cleaner view. These two should provide the right amygdala as the anatomical ROI in MNI152 2mm space. mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol

Re: [Freesurfer] subcortical segment NIFTI files

Sorry, what are you trying to do with that vol2vol command? The command line is surely wrong ... On 6/16/14 5:57 AM, Yang, Daniel wrote: > Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. > > I am able to obtain, for example, the right amygdala, using the following > commands: > >

Re: [Freesurfer] subcortical segment NIFTI files

Thanks! I see that mri_binarize + mri_vol2vol is what I wanted. I am able to obtain, for example, the right amygdala, using the following commands: mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o right_amygdala.mgz --match 54 mri_vol2vol --mov right_amygdala.mg

Re: [Freesurfer] subcortical segment NIFTI files

mri_vol2vol with the transforms/talairach.xfm as the transform should do the trick. Make sure that the resample type is nearest neighbor Cheers Bruce > On Jun 15, 2014, at 10:28 PM, "Yang, Daniel" wrote: > > Hi Bruce, > > Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very >

Re: [Freesurfer] subcortical segment NIFTI files

Hi Bruce, Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very flexible. I meant to obtain the aseg individual label files in MNI152 space as NIfTI files, for example, the different parts of the CC. Could you please point me to the right direction, as to what tool I should use fo

Re: [Freesurfer] subcortical segment NIFTI files

Hi Daniel Any of our tools can write nifti if you give the output volume the extension .nii or .nii.gz Cheers Bruce > On Jun 15, 2014, at 5:54 PM, "Yang, Daniel" wrote: > > Dear all, > > While it is possible to obtain NIfTI files for cortical parcellation using > mri_annotation2label, I am

[Freesurfer] subcortical segment NIFTI files

Dear all, While it is possible to obtain NIfTI files for cortical parcellation using mri_annotation2label, I am running if it is possible to obtain NIfTI files associated with aseg parts? Thanks! Daniel ___ Freesurfer mailing list Freesurfer@nmr.mgh.