| Deletions are marked like this. | Additions are marked like this. |
| Line 5: | Line 5: |
| In the following, we assume each subject has two repeated scans, for example, 1001 and 1001a are two scans for the first subject. | In the following, we assume that each subject has two repeated scans, for example, 1001 and 1001a are two scans for the first subject. |
| Line 7: | Line 7: |
| the following steps. | the following 4 steps. |
| Line 9: | Line 9: |
| Step 1. Compute the linear alignment between the two repeated scans of each subject. Taking 1001 and 1001a as example, we use FLIRT for the linear registration, and the command line is: | Step 1. Compute the linear alignment between the two repeated scans of each subject. Taking 1001 and 1001a as an example, we use FLIRT for the linear registration, and the command line is: |
| Line 13: | Line 13: |
| "1001_to_1001a.lta" is the output registration file that will be used later. | "1001_to_1001a.lta" is the output registration file that will be used later. The output $SUBJECTS_DIR/1001a/mri/orig_o_to_a.mgz can be used to check the registration accuracy. |
| Line 19: | Line 19: |
| The above need be run for the right hemisphere (rh) as well. | The above command need be run for the right hemisphere (rh) as well. |
| Line 23: | Line 23: |
| "-xform" specifies the registration file to be applied to align the first surface to the second. | "-xform" specifies the registration file to be applied to align the first surface to the second. If not specified, an identity transformation is assumed. |
| Line 27: | Line 27: |
| "-out" specifies the output thickness difference map filename. | "-out" specifies the filename for the output thickness difference map. |
| Line 29: | Line 29: |
| "-nsmooth" specifies the number of smoothing steps applied to the original thickness maps before their point-wise differences are computed. | "-nsmooth" specifies the number of smoothing steps applied to the original thickness maps before their point-wise differences are computed. If not specified, default will be zero. |
| Line 31: | Line 31: |
| "-abs" tells the program to compute the overall standard deviation of the absolute thickness differences; without it, the std of the signed differences is computed. | "-abs" tells the program to compute the overall standard deviation of the absolute thickness differences; if not used, the std of the signed differences is computed. |
| Line 34: | Line 34: |
| Line 35: | Line 36: |
| Note that the computed thickness difference map is sampled on the first surface: $SUBJECTS_DIR/1001/surf/lh.white in this case. This means the number of entries matches the number of vertices of that surface. | Note that the computed thickness difference map is sampled on the first surface, $SUBJECTS_DIR/1001/surf/lh.white in this case. This means the number of entries in the output curvature file matches the number of vertices of the first surface. |
| Line 37: | Line 38: |
|
The above two steps complete the thickness difference measurement for an individual subject, and the output difference map indicates the relative error in thickness measurement along the cortical surface of the subject. |
The above two steps complete the thickness difference computation for an individual subject, and the output difference map indicates the relative error in the thickness measurement along the cortical surface of the individual subject. |
| Line 40: | Line 41: |
|
To compute the group-wise statistics of such thickness error, the thickness difference or error maps need be resampled to a common template, and then the statistics can be computed along the template surface. This resampling requires a nonlinear alignment across different subjects, which is provided by the spherical registration results. Difference choices of the template is possible. One straightforward option is to simply select one subject as the template. In the following, we assume the subject 1001 is chosen as the template. |
To compute the group-wise statistics of such thickness error, the thickness difference (or error) maps need be resampled to a common template, and then the error statistics can be computed point-wise along the template surface. This resampling requires a nonlinear alignment across different subjects, which is provided by the spherical registration in FreeSurfer. Different choices of the template is possible. One straightforward option is to simply select one subject from the group as the template. In the following, we assume the subject 1001 is chosen as the template. The group analysis requires the next two steps. |
| Line 62: | Line 62: |
| "-mask" specifies a surface mask, where vertices within the mask will be excluded in all the computation (smoothing and statistics); | "-mask" specifies a surface mask, where vertices within the mask will be excluded in all the computation (smoothing and statistics). If not specified, all vertices are used. |
| Line 64: | Line 64: |
| "-nsmooth" specifies the number of smoothing iterations before statistics are computed; N=60 roughly corresponds to a surface based Gaussian kernel of size 6mm; | "-nsmooth" specifies the number of smoothing iterations before statistics are computed; N=60 roughly corresponds to a surface based Gaussian kernel of size 6mm. If not specified, no smoothing is performed. |
| Line 66: | Line 66: |
| "-surf_name" is the template surface (can be any surface of the template subject); | "-surf_name" is the template surface (can be any surface of the template subject). This option is required. |
| Line 70: | Line 70: |
| "-out_name" stores the standard deviation map of the input thickness difference maps; | "-out_name" stores the standard deviation map of the input thickness difference maps. This option is required. |
| Line 72: | Line 72: |
| "-absmean" stores the absolute average map of the input thickness difference maps; | "-absmean" stores the absolute average map of the input thickness difference maps. |
This wiki page describes how to compute the difference map of cortical thickness from two repeated scans of the same subject, and how to compute the overall statistics from a group of such repeated scans. This computation is needed in validation studies of cortical thickness measurement using FreeSurfer.
In the following, we assume that each subject has two repeated scans, for example, 1001 and 1001a are two scans for the first subject. We also assume that recon-all has been completed for all the data. The thickness reliability study will consist of the following 4 steps.
Step 1. Compute the linear alignment between the two repeated scans of each subject. Taking 1001 and 1001a as an example, we use FLIRT for the linear registration, and the command line is:
- "fsl_rigid_register -i $SUBJECTS_DIR/1001/mri/orig.mgz -r $SUBJECTS_DIR/1001a/mri/orig.mgz -o $SUBJECTS_DIR/1001a/mri/orig_o_to_a.mgz -dof 9 -cost corratio -ltamat $SUBJECTS_DIR/1001/mri/transforms/1001_to_1001a.lta".
"1001_to_1001a.lta" is the output registration file that will be used later. The output $SUBJECTS_DIR/1001a/mri/orig_o_to_a.mgz can be used to check the registration accuracy.
Step 2. Compute the thickness difference map for each subject. Taking again 1001 as an example, the command line is
- "mris_thickness_diff -xform $SUBJECTS_DIR/1001/mri/transforms/1001_to_1001a.lta -src_type curv -trg_type curv -out $SUBJECTS_DIR/1001/surf/lh.thickness_diff.w -nsmooth 0 -abs -S 1001 -L $SUBJECTS_DIR/1001/surf/lh_thickness_diff.log $SUBJECTS_DIR/1001/surf/lh.white $SUBJECTS_DIR/1001/surf/lh.thickness $SUBJECTS_DIR/1001a/surf/lh.white $SUBJECTS_DIR/1001a/surf/lh.thickness".
The above command need be run for the right hemisphere (rh) as well.
Many options are optional.
"-xform" specifies the registration file to be applied to align the first surface to the second. If not specified, an identity transformation is assumed.
"-src_type" and "trg_type" specify the input and output surface data type.
"-out" specifies the filename for the output thickness difference map.
"-nsmooth" specifies the number of smoothing steps applied to the original thickness maps before their point-wise differences are computed. If not specified, default will be zero.
"-abs" tells the program to compute the overall standard deviation of the absolute thickness differences; if not used, the std of the signed differences is computed.
"-L" denotes the logfile, where the following info are recorded "subject-name, surface vertex number, overall mean thickness difference, overall mean absolute thickness difference, std of (signed or unsigned) thickness differences"
The last four arguments are the two surfaces and the two thickness maps. Note that the computed thickness difference map is sampled on the first surface, $SUBJECTS_DIR/1001/surf/lh.white in this case. This means the number of entries in the output curvature file matches the number of vertices of the first surface.
The above two steps complete the thickness difference computation for an individual subject, and the output difference map indicates the relative error in the thickness measurement along the cortical surface of the individual subject.
To compute the group-wise statistics of such thickness error, the thickness difference (or error) maps need be resampled to a common template, and then the error statistics can be computed point-wise along the template surface. This resampling requires a nonlinear alignment across different subjects, which is provided by the spherical registration in FreeSurfer. Different choices of the template is possible. One straightforward option is to simply select one subject from the group as the template.
In the following, we assume the subject 1001 is chosen as the template. The group analysis requires the next two steps.
Step 3. Resample the thickness difference map for each subject to the common template. Taking subject 1002 as an example, and the command line is
- "mri_surf2surf --srcsubject 1002 --sval $SUBJECTS_DIR/1002/surf/lh.thickness_diff.w --src_type curv --trgsubject 1001 --tval $SUBJECTS_DIR/groupstudy/1002_lh_thicknes_diff_resampled_to_1001.w --trg_type paint --hemi lh --surfreg sphere.reg".
The output is the resampled difference map $SUBJECTS_DIR/groupstudy/1002_lh_thicknes_diff_resampled_to_1001.w. The program "mri_surf2surf" doesn't allow the output to be saved in "curv" format, which should be changed in the future. The same computation can be done for the right-hemisphere (rh) as well.
Step 4. Assuming all the thickness difference maps are resampled to the same template (surface), we can now compute the group-wise mean and std of the thickness differences at every vertex of the template surface. The command is:
- "mris_surface_stats -mask some_mask.label -nsmooth $N -surf_name $SUBJECTS_DIR/1001/surf/${hemi}.white -src_type paint
-out_name $SUBJECTS_DIR/groupstudy/${hemi}_std_${N}.w -absmean $SUBJECTS_DIR/groupstudy/${hemi}_absmean_${N}.w -mean $SUBJECTS_DIR/groupstudy/${hemi}_mean_${N}.w -absstd $SUBJECTS_DIR/groupstudy/${hemi}_absstd_${N}.w $SUBJECTS_DIR/groupstudy/1???_${hemi}_thickness_diff_resampled_to_1001.w"
This command computes the mean and std of both the signed and unsigned thickness differences and outputs the results to different files as specified by the different options. The user can define the hemisphere "${hemi}$", and the number of smoothing iterations "$N" applied to the input difference maps. The other options are:
"-mask" specifies a surface mask, where vertices within the mask will be excluded in all the computation (smoothing and statistics). If not specified, all vertices are used.
"-nsmooth" specifies the number of smoothing iterations before statistics are computed; N=60 roughly corresponds to a surface based Gaussian kernel of size 6mm. If not specified, no smoothing is performed.
"-surf_name" is the template surface (can be any surface of the template subject). This option is required.
"-src_type" means the same as in mri_surf2surf or mris_thickness_diff;
"-out_name" stores the standard deviation map of the input thickness difference maps. This option is required.
"-absmean" stores the absolute average map of the input thickness difference maps.
"-mean" stores the average map of the input thickness difference maps;
"-absstd" stores the standard deviation map of the absolute differences.
The statistical maps can be displayed on the template subject's surfaces, which can be used to visualize the spatially varying pattern of the thickness measurement variability.