Differences between revisions 14 and 15
Deletions are marked like this. Additions are marked like this.
Line 15: Line 15:
recon-all -autorecon2 -autorecon3 -subjid OAS2_0121_MR1_before
recon-all -autorecon2 -autorecon3 -subjid OAS2_0121_MR2_before
recon-all -autorecon2 -autorecon3 -subjid OAS2_0121_MR1
recon-all -autorecon2 -autorecon3 -subjid OAS2_0121_MR2
Line 21: Line 21:
recon-all -base OAS2_0121 -tp OAS2_0121_MR1_before* -tp OAS2_0121_MR2_before* -all recon-all -base OAS2_0121 -tp OAS2_0121_MR1 -tp OAS2_0121_MR2 -all
Line 26: Line 26:
recon-all -long OAS2_0121_MR1_before* OAS2_0121 -all
recon-all -long OAS2_0121_MR2_before* OAS2_0121 -all
recon-all -long OAS2_0121_MR1 OAS2_0121 -all
recon-all -long OAS2_0121_MR2 OAS2_0121 -all
Line 29: Line 29:

*note: Here we use OAS2_0121_MR1_before and OAS2_0121_MR2_before as the cross ids to keep it consistent with the files you are using for the edits, but note that in your actual data, when rerunning the base or the longitudinals, the ids cannot be renamed to something else (e.g. _before, _edit) unless it's after it's already ran/reran. So if you want a copy of the before version, rename that to tpid_before and edit the tpid version.

top | previous

Using Control Points to Fix Intensity Normalization

  • To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names.

Notice that the intensity for the area in the bottom corner of the right hemisphere around slice 90 is only around 90 something instead of 110, and the surfaces here do not include all of the gm and wm. Because this problem occurs in both cross-sectionals, the base and subsequently the longitudinals are also affected. In cases like this, it depends on which data you are planning to use, you can choose to edit either the cross, base, or long. Control points work in all three stages.

In this example, we're demonstrating what the effect will be when adding control points at the very beginning of the stream - in the cross-sectionals. Find all the slices that have this problem and add control points carefully on the wm voxels.

OAS2_0121_MR1 (slice 87) and OAS2_0121_MR2 (slice 93).

Once you are satisfied with your control points placements, save it, and run the following commands.

recon-all -autorecon2 -autorecon3 -subjid OAS2_0121_MR1
recon-all -autorecon2 -autorecon3 -subjid OAS2_0121_MR2

After that is complete (or when the CA normalization step is complete - you can check in the recon-all-status.log), you can start rerunning the base.

recon-all -base OAS2_0121 -tp OAS2_0121_MR1 -tp OAS2_0121_MR2 -all

The last step is to rerun the longitudinals (it is best to remove the existing longitudinal directories).

recon-all -long OAS2_0121_MR1 OAS2_0121 -all
recon-all -long OAS2_0121_MR2 OAS2_0121 -all


To look at the output, open your subject in tkmedit using the following commands.

tkmedit OAS2_0121_fixed brainmask.mgz -aux T1.mgz -surfs

tkmedit OAS2_0121_MR1.long.OAS2_0121_fixed brainmask.mgz -aux T1.mgz -surfs
tkmedit OAS2_0121_MR2.long.OAS2_0121_fixed brainmask.mgz -aux T1.mgz -surfs

Here are the output images of the base. You can see the difference in the surfaces from the before (left) and after (right) image at slice 108, although no control points were copied over.

As for the longitudinals, control points were copied over from the cross-sectionals, and the surfaces were copied from base, therefore making a great improvement on the surfaces for the longitudinals.

The before (left) and after (right) images from OAS2_0121_MR1.long.OAS2_0121 at slice 107.

The before (left) and after (right) images from OAS2_0121_MR2.long.OAS2_0121 at slice 108.

FsTutorial/LongControlPoints (last edited 2011-05-26 18:48:43 by KhoaNguyen)