Tissue Classification & Segmentation
Brain tissue is classified into gray matter, white matter and CSF and a segmented brain volume is generated based on the tissue classification.
Summmary of Tissue Classification
Outline of Process
- 120 points need to be tagged in the raw resliced scan. When selecting the tag points, all three views need to be examined to make sure the tag is fully volumed. Although all views are used to view the tag point, it is only selected in the coronal view. Try to take samples from posterior to anterior, and equally in both hemispheres.
- Open the raw resliced. register case#_reslice_raw.mnc
- Select the 120 tag points. Do not take any of the tag points in the cerebellum.
- Total samples taken is 40
- Must label white matter samples “1”
- Do not take samples in the corpus callosum, in the anterior or posterior limbs of the internal capsule, or near the lateral ventricles.
- Samples should tend to be taken more laterally in the hemispheres to avoid abnormal white matter that is frequently associated with the ventricles in the center of the brain.
- Samples should be evenly distributed across approximately 10 coronal sections, evenly spaced across the sagittal extent of the brain. Roughly 4 samples should be taken in each of the middle 7 or 8 sections
- Start taking samples in the posterior 1/10th of the brain, taking the first in the most posterior section where cortical gray can be clearly distinguished from white matter. In the most posterior sections, only one sample should usually be taken in each hemisphere, unless there is adequate distinction to get two, because there is less white matter in those regions (Fig. 6)Required Samples:
- 1 left and 1 right hemisphere temporal lobe sample in a coronal section about where you see the anterior extent of the superior colliculi (near the pulvinar nucleus of the thalamus. (Fig. 7)
- 1 left and 1 right hemisphere sample in the posterior 1/10th of the brain in the occipital poles (Fig. 6)
- 1 left and 1 right hemisphere sample in the anterior 1/10th of the brain in the frontal poles (Fig. 8)General Guidelines:
- Many samples in the middle 8/10ths of the brain will be taken in regions of the centrum semiovale extending from the parietal to the frontal lobes (points lateral to the cingulate cortex (Fig. 4)
- Many other samples should be taken superior to the lateral fissure–and parietal operculum–across the extent of the parietal and into the frontal lobe (Fig. 4)
- Others more anterior to the lateral ventricles can be taken in the center of the frontal white matter (Fig. 8) and more laterally in each hemisphere closer to the cortical ribbon (Fig. 4)
- After the 40th sample, type the number 1 in the far right window for later editing purposes
- Total samples taken is 40. Samples must be labeled “2”.
- Take the required 12 subcortical samples first, then distribute the remaining 28 samples across the posterior to anterior extent.
- Cortical samples should tend to be evenly distributed across approximately 10 coronal sections evenly spaced across the sagittal extent of the brain. Roughly 3 samples should be taken in each of the middle 7 or 8 sections (Fig. 1, Fig. 2, and Fig. 5 for various examples).
- Start taking cortical samples in the posterior 1/10th of the brain, taking the first in the most posterior section where the cortical gray ribbon can be clearly distinguished from white matter. In the most posterior sections, only one sample, unless you can find two good ones, should usually be taken in each hemisphere because there is less gray matter in those regions.
- Be especially careful to examine the sagittal and axial views to ensure fully volumed samples (excluding samples with partially volumed white and partially volumed CSF. See Fig. 11 for an example of an inadequate sample). Also avoid samples in the very center of a gyrus where there is inevitably a sulcus containing CSF.Required Samples:
- Try to take these samples from posterior to anterior.
- The required tag points are listed by tissue type, but the number reflects the order in which they are picked as you move posterior to anterior.
- The last numbers in parenthesis represent the order of the tag points if they are taken from posterior to anterior.Caudate:
- 1 left and 1 right hemisphere sample in the caudate nucleus in the coronal section where the anterior commissure crosses the midline (decussation: Fig. 1). (5 & 6)
- 1 left and 1 right hemisphere sample in the caudate nucleus in the most anterior coronal section where the putamen is still present (Fig. 2). (11 & 12)Putamen:
- 1 left and 1 right hemisphere sample in the putamen in the same section where the posterior caudate samples were taken at the decussation of the anterior commissure (see Figure 1). Take the sample more inferior and lateral where the most robust gray matter signal can be visualized. (7 & 8 )
- 1 left and 1 right hemisphere sample in the putamen more anteriorally when the subcallosal gyrus can first be distinguished (by a white matter tract between the gyrus and the nucleus acumbens) from the basal forebrain gray matter (Fig. 5). Take the sample in the center of the oval shaped form of the putamen at this level. (9 & 10)Thalamus:
- 1 left and 1 right hemisphere sample in the pulvinar of the thalamus just anterior to the anterior extent of the superior coliculli. NOTE: keep these samples relatively medial where the most robust gray signal can be found in this structure (Fig. 3). (1 & 2)
- 1 left and 1 right hemisphere sample more anteriorally in the dorsomedial nucleus of the thalamus in roughly the center of the thalamus as viewed in the midsaggital plane in the section where the pulvinar sample was taken. NOTE: keep these samples relatively medial where the most robust gray signal can be found in this structure (Fig. 4). (3 & 4)
- After the 40th sample (tag number 80) type the number 2 in the far right window for later editing purposes.
- Fluid Samples
- Total of 20 samples to be taken.
- Samples must be labeled “3”
- The CSF samples should be, to the extent possible, evenly distributed from back to front, top to bottom, and left to right. The samples taken in the lateral ventricles should be, for the most part, taken from posterior to anterior.
- Take the first ten samples in the lateral ventricles, and the last ten in other subcortical CSF locations.
- Make sure not to take samples in the choroid plexus within the lateral ventricles (Fig. 9).
- Generally make sure to take samples in places where the lowest signal value can be seen in the center of the tag circle in all 3 orthogonal views (this will help avoid choroid plexus which has a signal value closer to gray matter) (Fig. 9).
- All of the samples should be taken in the lateral ventricles and the subcortical spaces (e.g., the 4th ventricle, cerebral aqueduct, etc.; See Fig. 9).
- After the 20th sample (tag number 100) type the number 3 in the far right window for later editing purposes.
- Total of 20 samples to be taken.
- Samples must be labeled “4”
- Make sure to lower contrast to 0 or below to ensure visualization of noise in background around the brain. This is the only time the contrast goes under 0.
- Zoom out on the image for visualization of the entire background space (Fig. 10).
- Choose samples in approximately 5 coronal sections equally distributed across the coronal extent of the brain. Take samples from top left, top right, bottom left and bottom right.
- The signal value for each sample cannot be above 4 (for example of signal value above 4, see Fig. 10) (This value might differ depending on scan intensity).
- No more than 4 of the 20 samples should be taken in the 0 background.
- After the 20th sample (tag number 120), type the number 4 in the far right window.
- Save the tag file. case#_reslice_seg.tag
- The tag file now needs to be edited to fill in the 1s, 2s, 3s,and 4s that were not filled in. Highlight all of the numbers until you see a “1” on the far right side. Every row above the row containing the “1” should be highlighted. Go to the search menu and select replace. In the search for box type “”, and in the replace with box type “1”. Select replace in selection, and there should now be ones on the far right of the first 40 lines. Repeat this procedure for 2, 3, and 4. Save the tag file. neditcase#_reslice_seg.tag
- The final step in the segmentation process is done by checking for outliers. If there is any overlap between the 1s and the 2s (or the 2s and the 3s, or the 3s and the 4s), then you must go back into register and select new points that do not overlap. classify -tag case#_reslice_seg.tag -dump_features case#_reslice_raw.mnc> case#_avg.txtIf there is no overlap between the points, transfer the avgerage text file (case#_avg.txt) to a PC using the FTP program. Calculate the average gray matter and CSF intensitities. The mean between those two points will be used as the threshold for brain masking. There is a template on the PC that can calculate those average intensities using Excel’s Macros.
- When there is no overlap between the points, the segmentation tags can be used to create the segmented brain file.classify -verbose -min -tag case#_reslice_seg.tag <br />case#_reslice_raw.mnc<br />case#_reslice_seg.mnc
- Gzip the mnc files. <br />gzip *.mnc &