Does T2-weighted MR imaging improve preoperative detection of malignant hepatic tumors? Observer performance study in 49 surgically proven cases

The purpose of our study was to determine whether or not the addition of T2-weighted fast spin-echo (SE) imaging to gadolinium-enhanced spoiled gradient-recalled-echo (GRE) imaging improves the observer performance in the preoperative detection of malignant hepatic tumors. Gadolinium-enhanced GRE and fat-suppressed T2-weighted fast SE images obtained in 49 patients with 82 surgically confirmed malignant hepatic tumors (40 hepatocellular carcinomas and 42 metastases) were retrospectively reviewed by three independent off-site observers. In the random review of images, gadolinium-enhanced GRE images were reviewed first; thereafter, T2-weighted fast SE images were added for combined review. Observer performance was evaluated with the McNemar's test and receiver operating characteristic curve analysis. For gadolinium-enhanced GRE images alone vs. combined images, sensitivities for detection were 78% vs. 79% for hepatocellular carcinomas (P>.05), 67% vs. 71% for metastases (P<.05) and 72% vs. 75% for tumors overall (P<.05), respectively. The Az values were 0.892 vs. 0.889 in hepatocellular carcinomas (P>.05), 0.797 vs. 0.828 in metastases (P<.05) and 0.839 vs. 0.846 in tumors overall (P>.05), respectively. Our results showed that the addition of T2-weighted fast SE imaging to gadolinium-enhanced GRE imaging improved the observer performance in the detection of metastases.     

A prospective assessment of breath-hold fast spin echo and inversion recovery fast spin echo techniques for detection and characterization of focal hepatic lesions

The purpose of this study was to prospectively assess two breath-hold T(2)-weighted fast spin-echo sequences and two breath-hold inversion recovery fast spin-echo sequences to determine their relative ability to detect and characterize focal hepatic lesions. Fourteen patients with a total of nineteen proven focal hepatic lesions were imaged with two breath-hold T(2)-weighted (T2W) fast spin echo sequences (HASTE TE = 66 and HASTE TE = 120), two breath-hold inversion recovery fast spin echo sequences (IRFSE TE = 64 and IRFSE TE = 95), and a nonbreath-hold T(2)-weighted fast-spin echo sequence (FSE TE = 96-120). Contrast-to-noise ratios (CNRs) were measured for all proven lesions on all sequences. Both IRFSE sequences and the HASTE sequence with TE = 66 showed an improvement in lesion-liver and liver-spleen CNRs compared to the nonbreath-hold T2W sequence. The mean difference in CNR between benign and malignant lesions was largest for the HASTE TE = 120 sequence. These preliminary results suggest that a breath-hold IRFSE sequence (TE = 64 or 95) has an equal ability to detect focal hepatic lesions as a nonbreath-hold T2W FSE sequence (TE = 96-120). The HASTE TE = 120 showed the greatest ability to discriminate between benign and malignant lesions.     

Manifestation of magic angle phenomenon: comparative study on effects of varying echo time and tendon orientation among various MR sequences

The purpose of this study was to systematically investigate the effect of varying the echo time (TE) values and angle of the tendon to the main magnetic field (B(o)) upon the signal intensity observed with the magic angle phenomenon in tendons among most commonly used MR pulse sequences, including conventional spin echo (CSE), fast spin echo (FSE) and gradient echo (GRE) sequences. The intact bovine Achilles tendon was imaged using a clinical 1.5-T MR scanner. Magic angle phenomenon occurs in CSE, FSE and GRE sequences with different grade, appearing most severe in CSE, middle in FSE, and weakest in GRE sequence. In addition, the tendon signal changes produced by the magic angle phenomenon could be greatly reduced by increasing the TE to above a certain critical value in all three sequences. These critical TE values were different among CSE (40 msec), FSE (70 msec), and GRE (30 msec) sequences.     

Hepatic alveolar echinococcosis: MRI findings

The purpose of this study was to describe the magnetic resonance imaging (MRI) appearance of hepatic alveolar echinococcosis (HAE) on T(1)-weighted, T(2)-weighted and postgadolinium images. A total of 13 lesions were demonstrated in 13 patients. All patients underwent MR examination at 1 T imager. MR examinations included precontrast T(1)-weighted breathing averaged spin echo (SE), breath-hold spoiled gradient echo, T(2)-weighted TSE sequences with and without fat suppression, and T(1)-weighted breath-hold spoiled gradient echo (SGE) sequence following i.v. after gadolinium administration. All lesions were confirmed with histopathology. HAE hepatic lesions revealed geographic patterns of variable signal intensities on noncontrast T(1)- and T(2)-weighted images. Slightly hyperintense, iso- and hypointense signal on T(1)-weighted images corresponded to calcified regions, which appeared hypo-isointense signal on T(2)-weighted images. Necrotic areas were hypointense signal on T(1)-weighted and hyperintense signal on T(2)-weighted images. On postgadolinium images, lesions did not reveal enhancement. Dilatation of intrahepatic bile ducts distal to HAE abscesses were observed in five patients and portal vein invasion or compression was observed in four patients, lobar atrophy of the liver was coexistent finding in cases with portal vein compression. The MRI appearance of HAE abscesses included large irregularly marginated masses with heterogenous signal on T(1)- and T(2)-weighted images and lack of enhancement with gadolinium.     

Preoperative fast MRI of brain tumors using three-dimensional segmented echo planar imaging compared to three-dimensional gradient echo technique

The purpose of this study was to compare the diagnostic efficacy of a newly developed T(1)-weighted three-dimensional segmented echo planar imaging (3D EPI) sequence versus a conventional T(1)-weighted three dimensional spoiled gradient echo (3D GRE) sequence in the evaluation of brain tumors. Forty-four patients with cerebral tumors and infections were examined on a 1.0 T MR unit with 23 mT/m gradient strength. The total scan time for the T(1) 3D EPI sequence was 2 min 12 s, and for a conventional 3D GRE sequence it was 4 min 59 s. Both sequences were performed after administration of a contrast agent. The images were analyzed by three radiologists. Image assessment criteria included lesion conspicuity, contrast between different types of normal tissue, and image artifacts. In addition, signal-to-noise and contrast-to-noise-ratio (C/N) were calculated. The gray-white differentiation and C/N ratio of 3D EPI were found to be inferior to conventional 3D GRE images, but the difference was not statistically significant. In the qualitative comparison, lesion detection and conspicuity of 3D EPI images and conventional 3D GRE images were similar, but a tow-fold reduction of the scanning time was obtained. With the 3D EPI technique, a 50% scan time reduction could be achieved with acceptable image quality compared to conventional 3D GRE. Thus, the 3D EPI technique could replace conventional 3D GRE in the preoperative imaging of brain.     

Comparative study of fast MR imaging: quantitative analysis on image quality and efficiency among various time frames and contrast behaviors

The purpose of this study is to quantitatively compare the image quality and efficiency provided by widely available fast MR imaging pulse sequences. A composite phantom with various T1 and T2 values and subjected to periodic motion was imaged at 1.5 T. The fast MRI sequences evaluated included fast spin-echo (FSE), single shot fast spin-echo (SSFSE), echo-planar imaging (EPI), multi-slice gradient recalled (MPGR), fast MPGR (FMPGR), and fast multi-slice spoiled gradient echo (FMPSPGR). T1-weighted (T1WI), T2-weighted (T2WI), proton-density-weighted (PDWI), and T2*-weighted (T2*WI) images were evaluated in breath-hold and non-breath-hold time frames. Analysis included measurement of image signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), nonuniformity, ghosting ratio, SNR per unit time and CNR per unit time. Among fast T2WI sequences, FSE with breath-hold time frame resulted in the highest image quality and in superior SNR and CNR efficiency by a factor of 5 or 6 as compared with conventional spin echo sequence. Among fast T1WI sequences, FMPGR and FMPSPGR both with non-breath-hold time frame produced the highest image quality and SNR and CNR efficiency by a factor of greater than 5 as compared with conventional spin echo. Among fast PDWI and T2*WI sequences, FSE produced the highest SNR and CNR, and was maximally efficient with a factors of greater than 6 as compared with conventional spin echo.     

Hepatocellular lesions with increased iron uptake on superparamagnetic iron oxide-enhanced magnetic resonance imaging in cirrhosis or chronic hepatitis: comparison of four magnetic resonance sequences for lesion conspicuity

Purpose

The aim of this study was to determine the adequate MR sequence for the lesion conspicuity of hepatocellular lesions with increased iron uptake on superparamagnetic iron oxide (SPIO)-enhanced MRI.

Materials and Methods

SPIO-enhanced MRI was performed using a 1.5-T system. Among 25 patients with hypovascular hepatocellular nodules on contrast-enhanced dynamic CT (no early enhancement at arterial phase and hypoattenuation at equilibrium phase), 39 lesions with increased iron uptake on SPIO-enhanced MRI were evaluated. SPIO-enhanced MRI included (1) T1-weighted in-phase gradient recalled echo (GRE) images, (2) T2-weighted fast spin echo (FSE) images, (3) T2*-weighted GRE with moderate TE (7 ms) and (4) long TE (12 ms). The lesion-to-liver contrast-to-noise ratios of the hepatocellular nodule and the signal-to-noise ratio (SNR) of the hepatic parenchyma were calculated by one radiologist for a quantitative assessment. MR images were reviewed retrospectively by two independent radiologists to compare the subjective lesion conspicuity in each image set based on a four-point rating scale.

Result

The mean lesion-to-liver contrast-to-noise ratios with T2*-weighted GRE with moderate TE (7 ms) was highest (5.79±3.71) and was significantly higher than those with T1-weighted, in-phase images (3.79±3.23, P<.01), T2-weighted images (2.72±1.52, P<.001) and T2*-weighted GRE with long TE (12 ms) (3.93±2.69, P<.05). The subjective rating of lesion conspicuity was best on the T2*-weighted GRE with moderate TE (7 ms), followed by that on the T2*-weighted GRE with moderate TE (7 ms; P<.05).

Conclusion

T2*-weighted GRE sequence with moderate TE (7 ms) showed high lesion-to-liver contrast-to-noise ratios in hepatocellular lesions with increased iron uptake on SPIO-enhanced MRI, indicating better lesion conspicuity of hypointense hepatocellular nodules in cirrhosis or chronic hepatitis.     

Ovarian Brenner tumors: MR imaging characteristics

This study describes the appearance of Brenner tumors on MR imaging and compares quantitative signal intensity measurements of Brenner tumors with that of other ovarian tumors. A search of pathologic and MR records disclosed patients who had MRIs showing Brenner tumors prior to surgical excision. Patients (21) with other surgically proven ovarian masses were randomly selected for comparison. MR imaging was performed at 1.5 T with phased array multicoils and fast spin echo T2-weighted images. Region-of-interest measurements of signal intensity (SI) were made to calculate signal intensity ratios (SIR = mass SI/muscle SI). Brenner tumors showed significantly lower SIR than other tumors on T2-weighted images (p = 0 .004) and similar SIR on T1-weighted images. Brenner tumors show lower signal intensity on T2-weighted images than other non-fibrous ovarian tumors. This lower signal intensity may result from the extensive fibrous content of these tumors.     

A fast spin echo two-point Dixon technique and its combination with sensitivity encoding for efficient T2-weighted imaging

A fast spin echo two-point Dixon (fast 2PD) technique was developed for efficient T2-weighted imaging with uniform water and fat separation. The technique acquires two interleaved fast spin echo images with water and fat in-phase and 180° out-of-phase, respectively, and generates automatically separate water and fat images for each slice. The image reconstruction algorithm uses an improved and robust region-growing scheme for phase correction and achieves consistency in water and fat identification between different slices by exploiting the intrinsic correlation between the complex images from two neighboring slices. To further lower the acquisition time to that of a regular fast spin echo acquisition with a single signal average, we combined the fast 2PD technique with sensitivity encoding (SENSE). Phantom experiments show that the fast 2PD and SENSE are complementary in scan efficiency and signal-to-noise ratio (SNR). In vivo data from scanning of clinical patients demonstrate that T2-weighted imaging with uniform and consistent fat separation, including breath-hold abdominal examinations, can be readily performed with the fast 2PD technique or its combination with SENSE.     

Liver imaging at 1.5 tesla: pulse sequence optimization based on improved measurement of tissue relaxation times

In order to predict the most sensitive MR imaging sequence for detecting liver metastases at 1.5 T, in vivo measurements of T1 and T2 relaxation times and proton density were obtained using multipoint techniques. Based on these measurements, two-dimensional contrast contour plots were constructed demonstrating signal intensity contrast between hepatic lesions and surrounding liver parenchyma for different pulse sequences and pulse timing parameters. The data predict that inversion recovery spin echo (IRSE) imaging should yield the greatest contrast between liver metastases and liver parenchyma at 1.5 T, followed by short tau inversion recovery (STIR) and spin-echo (SE) pulse sequences. T2-weighted SE images provided greater liver/lesion contrast than T1-weighted SE pulse sequences. Calculated T1, T2, and proton density values of the spleen were similar to those of hepatic metastatic lesions, indicating that the signal intensity of the spleen may be used as an internal standard to predict the signal intensity of hepatic metastases on T1- and T2-weighted images at 1.5 T.     

Liver metastases from unknown primary site: demonstration on MR images

To demonstrate the MR imaging features of liver metastases in patients with the clinical and histologic diagnosis of tumors of unknown primary tumors, a retrospective 7-year study was performed that included a total of 14 consecutive patients (7 men and 7 women; age range, 39-82 years; mean age, 60.6 years) with liver metastases from unknown primary site who had undergone MR imaging. The following lesion features were evaluated: a) number, b) diameter, c) signal intensity on T1 and T(2)-weighted images, and d) pattern of enhancement on immediate, 45 s and 90 s post gadolinium images. Lesions were classified as hypovascular, hypervascular and nearly isovascular relative to liver parenchyma as shown on immediate post gadolinium images. Patients were separated into four major groups, related to the histologic diagnosis of the lesions: (I) poorly differentiated neoplasms; (II) well-differentiated and moderately differentiated adenocarcinoma; (III) squamous cell carcinoma; (IV) combined poorly differentiated carcinoma and poorly differentiated adenocarcinoma. MRI findings were correlated with histologic information obtained by chart review and confirmed by retrospective histopathology review. All patients had the histologic diagnosis of adenocarcinoma: 8 patients belonged to group II (1 patient with the subtype well-differentiated and 7 patients with the subtype moderately differentiated) and 6 patients to group IV. Eleven patients (79%) presented with multiple lesions distributed throughout both hepatic lobes; 3 patients exhibited solitary lesions. All solitary metastases possessed a diameter equal or larger than 5 cm. Patients with multiple metastases demonstrated a wide range of diameter, ranging from less than 1.5 cm to more than 5 cm. Regarding lesion vascularity, 4 of 13 of the patients had hypovascular metastases and 9 of 13 of the patients had hypervascular lesions. One patient demonstrated both types of lesions. Five of six patients with the histopathologic diagnosis of poorly differentiated adenocarcinoma demonstrated hypervascular metastases. Solitary metastases were most often hypovascular (2 of 3); however no correlation with the histologic subtype was possible. Liver metastases from unknown primary site are often multiple and often hypervascular. Poorly differentiated tumors are the most common histologic type. Metastases are not uncommonly hypovascular, and these are often solitary.     

Flow and oxygenation dependent (FLOOD) contrast MR imaging to monitor the response of rat tumors to carbogen breathing

Gradient recalled echo (GRE) images are sensitive to both paramagnetic deoxyhaemoglobin concentration (via T2*) and flow (via T1*). Large GRE signal intensity increases have been observed in subcutaneous tumors during carbogen (5% carbon dioxide, 95% oxygen) breathing. We term this combined effect flow and oxygenation-dependent (FLOOD) contrast. We have now used both spin echo (SE) and GRE images to evaluate how changes in relaxation times and flow contribute to image intensity contrast changes. T1-weighted images, with and without outer slice suppression, and calculated T2, T2* and "flow" maps, were obtained for subcutaneous GH3 prolactinomas in rats during air and carbogen breathing. T1-weighted images showed bright features that increased in size, intensity and number with carbogen breathing. H&E stained histological sections confirmed them to be large blood vessels. Apparent T1 and T2 images were fairly homogeneous with average relaxation times of 850 ms and 37 ms, respectively, during air breathing, with increases of 2% for T1 and 11% for T2 during carbogen breathing. The apparent T2* over all tumors was very heterogeneous, with values between 9 and 23 ms and localized increases of up to 75% during carbogen breathing. Synthesised "flow" maps also showed heterogeneity, and regions of maximum increase in flow did not always coincide with maximum increases in T2*. Carbogen breathing caused a threefold increase in arterial rat blood PaO2, and typically a 50% increase in tumor blood volume as measured by 51Cr-labelled RBC uptake. The T2* increase is therefore due to a decrease in blood deoxyhaemoglobin concentration with the magnitude of the FLOOD response being determined by the vascular density and responsiveness to blood flow modifiers. FLOOD contrast may therefore be of value in assessing the magnitude and heterogeneity of response of individual tumors to blood flow modifiers for both chemotherapy, antiangiogenesis therapy in particular, and radiotherapy.     

Hemorrhagic cerebral metastases from thyroid cancer on T2*-weighted gradient echo MRI

We report a case of multiple hemorrhagic cerebral metastases from papillary thyroid cancer, with reference to T(2)*-weighted gradient echo (GRE) magnetic resonance imaging (MRI). Small metastatic nodules were recognized as round nodules with signal loss on T(2)*-weighted GRE MRI, and were more pronounced compared with other sequences. Lesions were later confirmed as hemorrhagic on T(1)- and T(2)-weighted MRI. T(2)*-weighted GRE MRI was a sensitive tool for early detection of metastases displaying hemorrhagic changes.     

Fast magnetic resonance in vascular diseases of the abdomen

Fast magnetic resonance (MR) imaging provides a consistent and predictable appearance of vascular abnormalities as shown by four patients with thrombi, dissection and aneurysm. Fast MR images are obtained during breath-holding, resulting in an absence of respiratory motion artifacts. The time of MR study is much less with fast MR than with spin echo sequences.     

MRI of liver: a comparison of CNR enhancement using high dose and low dose ferumoxide infusion in patients with colorectal liver metastases

The purpose of this study was to compare the effects of high dose (HD) and low dose (LD) ferumoxides infusions on lesion-to-liver contrast-to-noise ratio (CNR) using four different T(2)-weighted MR sequences. Seventy-three patients with known colorectal liver metastases underwent T(2)-weighted fast spin echo (FSE) imaging before and after ferumoxides. After ferumoxides, T(2)-weighted dual echo (DE) and T(2)-weighted GRE FLASH images were also obtained. To evaluate the relationship between TE length and lesion-to-liver CNR, the same FLASH sequence was repeated in 18 LD patients after lengthening the TE. Ferumoxides was administered at a dose of 15 micromol/kg (HD) and 7.5 micromol/kg (LD) in 45 and 28 patients, respectively. The effects of HD and LD ferumoxides infusions were measured as the percentage signal intensity change (PSIC) in the liver and lesions, lesion-to-liver CNR and the change in lesion-to-liver CNR (DeltaCNR). In both LD and HD groups, all CNR values obtained after SPIO were significantly greater than those observed with unenhanced FSE (p < 0.01). There was no significant difference between the mean CNR values obtained with either dose for any sequence. With the FLASH sequence, CNR increased progressively with longer TE. At the longest TE of 26 ms, mean CNR was higher than that recorded with any of the other sequences. Although mean liver PSIC was significantly greater in the HD group than in the LD group (p < 0.01) because the mean lesion PSIC was also greater in the HD group, the mean DeltaCNR after ferumoxides was not significantly different in the two groups. LD SPIO enhanced MR significantly increases lesion-to-liver CNR compared with unenhanced images. At 1. 0 T, HD and LD ferumoxides infusions produce comparable lesion-to-liver CNR. Our results suggest that at 1.0 T ferumoxides may be administered at a dose of 7.5 micromol/kg without loss of image quality.     

Chorioangioma: antenatal diagnosis with fast MR imaging

We report a case of chorioangioma of the placenta, in which fast magnetic resonance imaging (MRI) was useful adjunct to ultrasonography for the antenatal diagnosis. MRI allowed clear demonstration of 6.8 x 6.0 cm solid placental mass along with hydramnios and anatomically normal fetus. On T(1)-weighted breath-hold spoiled gradient-echo (fast low-angle shot [FLASH]) images, chorioangioma was mostly isointense to the placenta, but had an area of high signal intensity near the base and at the periphery, suggestive of hemorrhage. On T(2)-weighted half-Fourier single-shot fast spin echo (HASTE) images, the mass showed heterogeneous high signal intensity, but had an area of low signal intensity near the surface.     

Optimizing T2-weighted magnetic resonance sequences for surface coil microimaging of the eye with regard to lid, eyeball and head moving artifacts

PURPOSE: To acquire high-resolution magnetic resonance (MR) images, we developed a new blinking artifact reduced pulse (BARP) sequence with a surface coil specialized for microscopic imaging (47 mm in diameter). MATERIALS AND METHODS: To reduce eye movement, we ascertained that the subjects' eyes were kept open and fixated to the target in the 1.5-T MR gantry. To reduce motion artifacts from blinking, we inserted rest periods for blinking (1.5 s within every 5 s) during MR scanning (T2-weighted fast spin echo; repetition time, 5 s; echo time, 100 ms; echo train, 11; matrix, 256 x 128; field of view, 5 cm; 1-mm thickness x 30 slices). Three scans (100 s x 3) were performed for each normal subject, and they were added together after automatic adjustment for location to reduce quality loss caused by head motion. RESULTS: T2-weighted MR images were acquired with a high resolution and a high signal-to-noise ratio. Motion artifacts were reduced with BARP, as compared with those with random blinking. Intraocular structures such as the iris and ciliary muscles were clearly visualized. Because the whole eye can be covered with a 1-mm thickness by this method, three-dimensional maps can easily be generated from the obtained images. CONCLUSION: The application of BARP with a surface coil of the human eye might become a useful and widely adopted procedure for MR microimaging.     

MRI of acute cholecystitis: Comparison with the normal gallbladder and other entities

Our purpose was to prospectively compare MRI findings with histopathologic findings in the evaluation of suspected acute cholecystitis. Fourteen patients with clinically suspected acute cholecystitis were entered into the study. MR sequences included T₁-weighted fat-suppression and breath-hold spoiled gradient echo (SGE) before and after intravenous gadolinium chelate administration. Percent contrast enhancement (%CE) of the gallbladder wall and gallbladder wall thickness (WT) were measured and liver enhancement patterns determined prospectively on MR images. Correlation was obtained with pathological findings at cholecytectomy in all patients. In a second phase of the study MR images on 10 additional subjects who underwent MR examination for reasons other than hepatobiliary disease were analyzed to determine normal values for %CE and gallbladder wall thickness. Mean %CE was 124.0% in patients with acute cholecystitis (10 patients), 58.0% in patients with chronic cholecystitis (2 patients), and 73.0% in patients with gallbladder malignancy (2 patients). Mean gallbladder WT was 6.1 mm in acute cholecystitis, 4.5 mm in chronic cholecystitis, and 6.0 mm in malignant disease. There was a significant difference in %CE between acute and chronic cholecystitis (p = 0.03); no other significant differences in %CE or WT were observed among the patients with gallbladder disease. Patients without biliary disease had %CE of 37.3% and WT of 2.9 mm, which were both significantly less (p < 0.001) than in patients with acute cholecystitis. Transient enhancement of pericholecystic hepatic parenchyma on immediate postgadolinium SGE images was seen in 7 of 10 patients with acute cholecystitis, and not observed in other patients. Patients with acute cholecystitis had increased %CE and WT on MR images that were significantly greater than normal and %CE that was significantly greater than in patients with chronic cholecystitis. Transient increased pericholecystic hepatic enhancement was observed in 70% of acute cholecystitis patients and in no other patient groups.     

How size evaluation of lymph node is protocol dependent in MRI when using ultrasmall superparamagnetic iron oxide nanoparticles

In this study, the volume of susceptibility artifact was evaluated in T1 and T2-weighted spin echo (SE) and gradient echo (GRE) images at various parameters using registration and subtraction methods. In order to state an important misinterpretation problem in lymphography, it was demonstrated that a lymph node size may be enlarged approximately 10 times when a T2*-weighted GRE protocol is used. To overcome this problem a technical consideration using multisequence (GRE and SE) paradigm was suggested to ensure both lymph node detection and metastasis identification in lymphatic system. The paradigm was also extended by post-processing manipulation of the SE images using a registration and subtraction approach for detection of lymphatic lesions.     

Optimization of tissue segmentation of brain MR images based on multispectral 3D feature maps

The purpose of this work was to optimize and increase the accuracy of tissue segmentation of the brain magnetic resonance (MR) images based on multispectral 3D feature maps. We used three sets of MR images as input to the in-house developed semi-automated 3D tissue segmentation algorithm: proton density (PD) and T2-weighted fast spin echo and, T1-weighted spin echo. First, to eliminate the random noise, non-linear anisotropic diffusion type filtering was applied to all the images. Second, to reduce the nonuniformity of the images, we devised and applied a correction algorithm based on uniform phantoms. Following these steps, the qualified observer "seeded" (identified training points) the tissue of interest. To reduce the operator dependent errors, cluster optimization was also used; this clustering algorithm identifies the densest clusters pertaining to the tissues. Finally, the images were segmented using k-NN (k-Nearest Neighborhood) algorithm and a stack of color-coded segmented images were created along with the connectivity algorithm to generate the entire surface of the brain. The application of pre-processing optimization steps substantially improved the 3D tissue segmentation methodology.