Multiple sclerosis is a disease generally has been considered as white matter disorder. Recently, the increasing number of gray matter involvement has been proved by pathophysiological reviews in MS patients [15, 16].
An obvious histopathological variation, particularly in patients with primary progressive or secondary progressive MS is cortical demyelination, so it is required to demonstrate cortical and subcortical lesions by different pulse sequences [5, 17].
Although conventional MRI sequences are not successful in cortical lesions demonstration, and despite the advances in new MR techniques such as magnetic resonance spectroscopy (MRS) and diffusion tensor imaging (DTI), still conventional MRI protocols playing an important role in early diagnosis of MS or CIS (suggestive of MS) [4,5,6].
Previous study stated MS plaques better displayed in axial plane in the area of subcortical and juxtacortical, while the sagittal plane is appropriate to demonstrate MS lesions in collo-septal and corpus callosum regions [13, 18]. T2-weighted TSE sequences are more sensitive to detect infratentorial lesions compared to FLAIR imaging sequences and FLAIR sequences have adverse results in the evaluation of the infratentorial parenchyma which it may be due to the differences in relaxation times compared to the supratentorial parenchyma [19,20,21]. Whereas, FLAIR has the highest sensitivity in the supratentorial area, near the CSF such as juxtacortical and the periventricular white matter. The signal from CSF will be suppressed in FLAIR and DIR pulse sequences while on the contrary, DIR also attenuates the signal from white matter (WM) and the sensitivity of DIR pulse sequence increases to detect brain lesions in WM and gray matter (GM) compared to sequences such as proton density (PD) or T2WI and T1-weighted (T1W) MR sequences at 1.5 and 3.0 T [18, 22].
DIR has potential advantages over conventional MRI protocols to demonstrate both infratentorial and supratentorial MS lesions and also provides improved appearance of early lesions [20, 23]. Various pulse sequences are used recently to enhance the sensitivity of MRI to identify more MS plaques. The difference T1 relaxation times between GM/CSF and GM/WM results in optimized contrast between gray and white matter and it demonstrates a great boundary of GM. DIR was developed by Redpath and Smith. It produces a dual contrast of FLAIR and short tau inversion recovery (STIR) [24, 25].
Two-dimensional (2D) and 3D FLAIR imaging have shown the increased displaying of cortical and subcortical lesions. FLAIR sequence is extremely sensitive to detect supratentorial MS lesions due to the CSF attenuation, especially for juxtacortical and periventricular white matter. But, unlike the DIR sequence, these sequences do not have this potential to determine the exact boundary between the cortex and subcortical WM clearly, cortical and juxtacortical lesions detection have improved beyond DIR sequence [24, 26]. Nowadays, numerous MR techniques such as MRS, DTI, and pseudo-continuous arterial spin labeling have been used to detect MS lesion and determine its relation to patient's disability [25, 27].
Recent studies have shown that the extent of gray matter damage is strongly correlated with the spread of the disease and the degree of physical disability and cognitive disorders [28, 29].
In a previous study, Chard  introduced the DIR sequence as a diagnostic criteria in MS patients, especially for the acute symptoms and gray matter injuries produced by new MS plaques in the cerebral cortex [30, 31]. Two different inversion pulses are set in DIR sequence, which remove the CSF and white matter as well, so it attains a greater delineation between gray and white matter [18, 31].
In our study, brain MRI was performed using conventional sequences as well as DIR, FLAIR, and T2W_TSE techniques. The number of MS plaques in each anatomical region and the total number of MS lesions were calculated separately in each sequence in all patients.
The result of our study was quite promising, DIR showed significantly higher total MS lesions load (N = 3647) in all anatomical regions compared to FLAIR imaging (N = 2896) and T2W_TSE (N = 2697), our overall findings were in agreement with the findings reported in different studies of Abidi et al. , Umino et al. , Prosperini et al. , and Hickman et al. .
With respect to infratentorial region, DIR identified increased number of lesions in cerebellum and brain stem with better delineation, even compared with the T2W_TSE which still considered as a gold sequence at this region. These findings were also in agreement with the findings reported by Abidi et al. , Umino et al. , Prosperini et al. , and Hickman et al. .
A noticeably higher number of lesions seen in juxtacortical white matter, these findings were in agreement with those reported from Abidi et al.  and Hickman et al.  but, Umino et al.  reported a slightly lower number of detected lesions in this region, they noted slightly more lesions in the juxtacortical with FLAIR imaging. And also, Prosperini et al.  noted statistically significant increase in juxtacortical and mixed WM/GM lesions detection on DIR imaging compared to FLAIR and T2W_TSE.
Abidi et al. , Umino et al. , Prosperini et al. , and Hickman et al. , differed in their findings from our study as they reported a lower number of MS lesions in deep white matter with the DIR and slightly higher number of lesions at this region by FLAIR imaging sequence.
DIR revealed significantly higher mean number of lesions in the periventricular WM compared with both FLAIR and T2W_TSE, but there was no significant difference between the mean number of lesions between FLAIR and T2W_TSE at this region.
Abidi et al. , Hamed et al. , and Wattjes et al.  reported a slightly increasing number of lesions regarding to FLAIR but statistically difference for T2W imaging at periventricular region.
By using the DIR sequence, 64 cases of 97 cases in our study were found to have cortical lesions as well as white matter lesions, while FLAIR displayed the lesions in 48, and T2W indicated them in 26 cases in the cortex. By DIR imaging radiologist could differentiate the exact location of the lesion whether the lesion was pure cortical or mixed WM/GM or juxtacortical.
Our main interest at this study was to identify gray matter lesions in patients who are affected by MS disease and better detected by DIR sequence. MR imaging with 3D DIR enabled markedly increasing number of intracortical lesions (N = 231) compared to FLAIR (N = 130) and T2WI (N = 72) Fig. 4. Our results were consistent with the findings of the study done by Abidi et al. , Prosperini et al. , and Hickman et al. .
In connection with the number of lesions and EDSS score in different anatomic regions, our study with increased number of lesions in infratentorial and higher EDSS score is worth discussing.
It is important to diagnose infratentorial lesions because these findings indicate long-term disability in patients with MS which are along with early detection of the disease . Performing DIR sequence is a beneficial method which may affect the diagnosis and deciding the treatment at the onset of the disease or especially in patients with CIS. The number of lesions in infratentorial area is an important factor to predict the disease with long-term disability throughout the patient's life. So, appropriate treatment decisions increases by higher diagnostic accuracy of these lesions and it has a significant effect to decrease the long-term disability in patients with MS [20, 27].
The specific structure of the infratentorial region regarding to high density of neural fibers in this region [32, 33] can explain importance of our results and the correlation between clinical outcomes and MRI findings in the infratentorial region more strongly than other areas of the brain.
Two employed inversion pulses improve the detection of cortical lesions on DIR sequence by nulling the signal from CSF and white matter as well. Subsequently, this double suppression design produces a lower SNR image. The lower SNR as well as the greater tendency to pulsation artifacts than FLAIR and T2_TSE should be considered. Also, previous studies pointed out non-uniform signal of the magnetic field in the cortex of the limbic region, as well as the cortex of the central salcus. They indicated lower SNR and higher scanning time prevents the high spatial resolution requiring to display the cortex with a thickness of only 2 to 4 mm . However, the CSF nulling was appropriate in our images obtained by DIR sequence even in the worst conditions.
The hyper intense artifacts seen in DIR are ribbon like and characterized by their bilateral prevalence and symmetrical shape, which are characterized by deformations in successive segments and distinguished in successive slices. The observation of their variable appearance in several consecutive slices and other MRI sequences including T1-weight or FLAIR can help to distinguish them as lesions with irregulated shape or as artifacts caused by rounded cerebral cortical vessels. Artifacts usually occur in posterior fossa, choroid plexus, periventricular WM, periaqueductal, and brainstem tissue appear to be as a result of trans ependymal CSF effusion and pulsation, cerebral sinuses or larger vessels. So, the greater the extent of the artifacts at the cortico-sulcal interface, the greater likelihood of counting misinterpreted cortical lesions. Therefore, a significant reduction of such artifacts will increase the quality of the diagnosis [18, 34, 35].
In our study, an acquainted radiologist with these artifacts paid careful attention to exclude artifacts seen in the areas such as the anterior temporal lobes, occipital lobes, insula. and medial frontal lobes. It helped to eliminate cortical vessels not be counted falsely as lesions. There were very few cerebrospinal fluid and vessels artifact by using 3D DIR sequence and higher magnetic field strength comparing with the 2D FLAIR. So, despite the higher acquisition time, we were encouraged to do 3D DIR sequence because of the advantage of the 3D sequence in the lower artifact display.
The various benefits of 3D scans over their identical 2D sequences have encouraged us to do 3D DIR sequence. Having isotropic voxels with equal length in all three directions, are the most important advantages of images obtained from 3D scans and there is no need to scan complementary planes such as separate sagittal and axial. Since there are no gaps between the slices, so 3D scans can easily keep the image quality in term of contrast-to-noise ratio (CNR) providing greater spatial resolution. Three-dimensional MRI sequences, due to the use of smaller slice thicknesses, detect smaller size MS plaques especially cortical lesions more precisely and less flow artifacts compared to two-dimensional sequences [34, 36].
There are no artifacts of blood flow and CSF in 3-D sequences because of non-selective inversion pulses. Three-dimensional MRI is crucial for the diagnosis of cerebral atrophy and evaluation of the cortical lesions load that cause more cognitive impairment and physical disability than white matter [34, 35].