anatomy
====== Differences ====== This shows you the differences between two versions of the page.
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anatomy [2016/08/17 19:29] bdelab created |
anatomy [2018/09/11 23:12] (current) ekubota |
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| im = niftiRead(T1path); % Read root mean squared image | im = niftiRead(T1path); % Read root mean squared image | ||
| voxres = diag(im.qto_xyz)'; % Get the voxel resolution of the image (mm) | voxres = diag(im.qto_xyz)'; % Get the voxel resolution of the image (mm) | ||
| - | mrAnatAverageAcpcNifti({T1path}, '/mnt/diskArray/projects/anatomy/[subid]/t1_acpc.nii.gz', [], voxres(1:3)')</code> | + | mrAnatAverageAcpcNifti({T1path}, '/mnt/diskArray56/projects/anatomy/[subid]/t1_acpc.nii.gz', [], voxres(1:3)')</code> |
| ====Freesurfer Segmentation==== | ====Freesurfer Segmentation==== | ||
| Freesurfer is a useful tool for segmenting a T1-weighted image and building a cortical mesh. To segment the subject's T1-weighted image using freesurfer from the command line type: | Freesurfer is a useful tool for segmenting a T1-weighted image and building a cortical mesh. To segment the subject's T1-weighted image using freesurfer from the command line type: | ||
| - | <code>recon-all -i /mnt/diskArray/projects/anatomy/[subid]/t1_acpc.nii.gz -subjid [subid] -all</code> | + | <code>recon-all -i /mnt/diskArray56/projects/anatomy/[subid]/t1_acpc.nii.gz -subjid [subid] -all</code> |
| Or even better use this handy matlab function written by Jon Winawer to run freesurfer and then also build some useful files that we like to use for data visualization such as a high resolution gray/white segmentation. | Or even better use this handy matlab function written by Jon Winawer to run freesurfer and then also build some useful files that we like to use for data visualization such as a high resolution gray/white segmentation. | ||
| - | <code>fs_autosegmentToITK([subid], '/mnt/diskArray/projects/anatomy/[subid]/t1_acpc.nii.gz')</code> | + | <code>fs_autosegmentToITK([subid], '/mnt/diskArray56/projects/anatomy/[subid]/t1_acpc.nii.gz')</code> |
| For subjects with multiple scans, the output destination should be [subid]_MR[#]. For example, a subject's (205_AB) second scan for the NLR study would be written: NLR_205_AB_MR2. This is in line with the Freesurfer system of notation. | For subjects with multiple scans, the output destination should be [subid]_MR[#]. For example, a subject's (205_AB) second scan for the NLR study would be written: NLR_205_AB_MR2. This is in line with the Freesurfer system of notation. | ||
anatomy.1471462191.txt.gz ยท Last modified: 2016/08/17 19:29 by bdelab
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