FLIRT/FAQ - FslWiki
brain area, a recent automatic method available in FSL was used. The execution .. A - CT-MRI co-registration, using FLIRT, (left) in patient 1 and (right) in patient. 3; B - T1 image, In contrast, the opposite occurs using a pial In order to detect the exact position of the electrodes a trigonometric. perinatal complications and are inversely related to gestational age at birth,29 Smaller of 90 – mL non- ionic contrast media into an antecubital vein at 3 –5 mL/s, auto-trig- The FSL registration tool FLIRT (http://. sequence (T1 and T2-weighted MRI) is multiplied with the inverse of the bias cylinder r, the projection can be gained using simple trigonometry p(s, θ)=2ρ. √ using FSL's FLIRT and FNIRT  and both HARDI and mcDESPOT were.
There are many reasons why a registration may not work well. Here is a general checklist of things to test and try in order to improve the registration results please do not post a query to the FSL email list about registration results until you have gone through this list: For 2D images single slices you must use one of the valid 2D degrees of freedom options or -2D and appropriate schedules from the command line - see below If there is large bias field slow intensity variation - especially near the end slices then try using fast to create a restored image one with no bias field and then register using the restored image.
If there are relatively small errors in some crucial region of interest e. To do this a weighting image must be made which has the value of 1. Using this weighting volume in either the GUI or command line registration calls should improve the fit in this region.
This works in either registration mode where it is finding the transformation that aligns the input and reference images and also in applyxfm mode where it is applying a saved transformation to the input image. Note that only in registration mode does it use the intensity information from the reference image. To apply saved transformations, the GUI ApplyXFM can also be used which provides the option of specifying the number of voxels and voxel size directly. There are two main types of cost function: If you are registering two images of different modality then you must use an inter-modal cost function, whereas for images of the same modality either can be used, although the intra-modal options may be more accurate.
- Login using
Within each category there is not much to choose from - it is a practical, experience-based decision. The recommended options to try first are: If the scanner voxel size may have changed due to calibration shifts then it is appropriate to use 7 DOF instead of 6 or 4 instead of 3 to compensate for global scale changes. Note that for difficult registrations there is a translation only schedule file which is effectively 3 DOF, but only includes x,y,z translations.
This is useful for obtaining initial position estimates when matching small FOV to large FOV, and can then be further refined.
Transforming masks with FSL requires a little extra care. To steps are needed: Masks can be transformed from one space to another by using either one of the command line tools flirt or applywarp, or the ApplyXFM GUI. The threshold used with fslmaths should be set depending on the intended use of the output mask. Note that it does not perform any search in 2D mode, and cannot deal with 2D to 3D registrations. Interpolation Methods This includes Nearest Neighbour, a family of Sinc-based methods three window types - rectangular, Hanning and Blackman with configurable window width, and spline a highly efficient method, with similar output characteristics to sinc.
The interpolation is only used for the final transformation and in applyxfmnot in the registration calculations. In addition, there is the BBR cost function which utilises a segmentation of the reference image to define a boundary, and it is the intensity differences in the input image, across the transformed boundary, that contribute to the cost.
The pre-requisites to use this method are: This script will either use an existing white-matter segmentation of the structural image, or create one itself, to define a white-matter boundary.
We recommend that the structural image is bias-corrected separately beforehand if there is obvious bias field present. The script is also capable of using fieldmaps to perform simultaneous registration and EPI distortion-correction. The inputs echospacing and pedir both refer to the EPI image not the fieldmap and are the same as required for FEATbut be careful to use the correct units.
It can read and write ascii 4x4 matrices. In addition, it can be used to concatenate two transforms using -concat with the second transform or to find the inverse transformation using -inverse. If the option -mm is used then both input and output coordinates will be in mm coordinates, otherwise with -vox both coordinates will be in voxel coordinates.
For conversion between voxel and mm coordinates it is necessary to use either img2stdcoord or std2imgcoord see below. Note that the source coordinates can either be input via a file or via a pipe and for the latter the "-" symbol is used as the filename. The format in either case is three numbers per line, space separated.
To avoid this use the pipe input format or suppress the final line: The coordinates for the source image can be either in voxel coordinates default, or by explicitly using -vox or in mm coordinates using -mm.
This utility, and std2imgcoord are therefore useful for converting between voxel and mm coordinates within the same image, as well as for mapping coordinates between spaces. Converting from voxel to mm coordinates within the same image can be done with the command: It works the same way but transfers coordinates from "standard space" to the other image IMG space.
It can also convert between mm and voxel coordinates within the same image. See the entry on img2stdcoord above. Sinc interpolation is used internally. Participants were separated by gender, and then into older or younger groups by median split. Within each of those four groups, residuals of eCRF, BMI, pulse, activity score, and global gray matter CBF were calculated by subtracting the group mean from each of the observed scores.
Analysis of Anatomical Volumes In order to investigate whether or not localized CBF was predictive of other local brain measures, we analyzed the correlations between the volumes of the superior frontal and inferior parietal cortex and the regional measures of CBF Table 5. These anatomical parcellations were chosen on the basis of their large size and likelihood to overlap with the frontal and parietal regional masks that were used to assess regional CBF in each individual subject.
Inverse transformation using FLIRT
We observed a dissociation between the relationship of regional measures of CBF and differing regions of anatomy: These results suggest that local CBF may be related to variations in regional cortical volumes. Partial correlations between CBF and normalized superior frontal and inferior parietal anatomical volumes, controlling for gender.
CBF was negatively correlated with systolic blood pressure and pulse pressure, which provides support that CBF is, in fact, measuring perfusion rather than blood flow in the arteries. If CBF was measured in the arteries, we would have expected increases in blood pressure to be positively correlated with increased arterial blood flow.
Furthermore, the fitness effects on CBF in the present analysis fully mediated the age effects on blood flow in the regions of the brain that showed a significant relationship between age and blood flow.
FLIRT/UserGuide - FslWiki
Surprisingly, in frontal regions, no significant effect of aging on CBF was observed over the restricted age-range of our sample of older adults aged 55— This is in contrast to anatomical studies that have reported reliable age-related changes in the frontal areas of the brain, when comparing younger adults college age to older adults for a review of relevant work, see Raz, The limited age range of our study may account, at least in part, for this negative finding.
Our overall observation of a negative correlation between global CBF and age is consistent with previous reports using a variety of imaging techniques, including ASL Parkes et al. The findings reported here corroborate previous research indicating that improving eCRF may provide a route to stave off or even ameliorate the normal age-related declines in CBF, as well as the global cerebral atrophy that usually accompanies it Ainslie et al.
If this is the case, then working to increase eCRF into old age may function as a potent method to preserve brain vascular health and stave off brain pathologies. In our sample, it is clear that self-reported activity level seems to have a strong contribution to the overall impact of eCRF on CBF.
The fact that activity level seems to play such a large role in explaining the impact of eCRF on CBF meshes well with other research that has demonstrated striking changes in the brains of older adults after cardiorespiratory exercise interventions see Bherer et al. However, our analysis shows that the impact of eCRF may be more complex than simply reflecting the level of activity, since BMI shows a negative correlation with CBF only in the frontal brain areas that we examined.
Complicating our interpretation, some of the variables that contribute to eCRF including pulse rate and BMI may have different implications depending on the time of life at which they are measured. For example, typically a higher resting pulse rate is considered to be a risk factor for cardiorespiratory disease Fox et al.
However, in older individuals a low resting pulse may also be indicative of heart disease Ufberg and Clark, Likewise, BMI may be negatively correlated with fitness earlier in life, but as a sample increases in age, many individuals with high BMI will have expired and the correlation between BMI and fitness may reverse, as being underweight may be associated with more health problems Yan et al. It is clear that eCRF is a complex measure, and the intriguing disparities in how the different components relate to flow in specific brain regions warrants future research.
Specifically, given the correlations between many of the variables we analyzed, it is of particular importance to further investigate the relationship between eCRF and CBF in aging adults.
Longitudinal studies and interventions that improve eCRF will help to further elucidate the impact of fitness on the age-related declines in CBF. Although our analysis of the white matter revealed similar patterns to the gray matter analysis, CBF in the white matter may not be functionally equivalent to CBF in the gray matter.
More recently, Lu et al. An age-related increase in white matter CBF alongside of decreases in gray matter CBF may appear to be counterintuitive. A potential explanation was proposed by Aslan et al.
In their study, the authors found an inverse correlation between the anisotropy of water diffusion and the blood flow along white matter fiber tracts. This suggests that the deterioration of white matter integrity is positively related to a local rise in CBF. This inverse relationship is most likely due to the structure of the myelinated axons in the white matter. Demyelination of axons could lead to an increased need for greater ion flux and energy for depolarization, since nodes of Ranvier normally minimize this need.
In addition, it may also reduce the ability of the structure of the white matter to offset the pressure of perfusion. Both of these factors may lead to increased blood flow Aslan et al. Overall, this study points out that the blood flow in the white matter may not be completely determined by neurovascular coupling in the same way that it is in the gray matter. The measures of white matter blood flow we reported likely reflect a combination of blood flow downstream of the gray matter along with the effects of any age-related white matter degradation.
Since these two age-related factors impact blood flow in different directions, it is likely that our measures of CBF in the white matter are much less sensitive to age-related changes, and much more difficult to interpret.