A large sample size, uniform data collection methodology and robust statistical analysis are strengths. Instructions freesurfer subcortical segmentation quality check. Reduced cortical thickness as an outcome of differential sensitivity to environmental risks in schizophrenia. For this report, only baseline total right plus left hippocampal volumes mm3 were used. Using mri images of 262 males and 402 females aged 38 to 84, we directly compare estimates of hippocampal volume from multiple versions of freesurfer, its hippocampal subfield routines, and our manual tracing protocol. Chapter 4 freesurfer neuroimaging protocols bookdown. Loss of nucleus accumbens lowfrequency fluctuations is a. Freesurfer parcellation of brains containing large infarcts niharika gajawelli1. How is the freesurfer subcortical training set derived. It is therefore necessary to determine whether there is an interaction between the sequence parameters and the effect of interest, and to minimise. Brains were preprocessed for shape analysis using free surfer software version 5.
Subcortical brain volume abnormalities in individuals with. Using a set of 30 anatomical t1weighted 3t mri scans, we investigated the effects of data processing variables such as freesurfer version v4. Fslsienax relies on registration to the montreal neurological institute 152 template for skull strip. We found that there was bias between measurements made with first, multiatlas, as well as freesurfer. The open source license agreement that allows you to use freesurfer.
Measurement of cortical thickness and volume of subcortical. Multicenter magnetic resonance imaging mri studies present an opportunity to advance research by pooling data. Preprocessing by free surfer resulted in final 3d brain images with a voxel. Abnormal subcortical volumes and cortical thickness in. We evaluated the algorithm both qualitatively and quantitatively using manually labeled datasets, relevant comparator. In the segmentation procedure, each subcortical region was assigned 1 of 39 labels including wm regions, excluding ventricles and global regions. Group differences in regional volumes within each protocol were examined and listed in supplementary table 5. The effect of duration of illness and daily dose and type of antipsychotics were assessed using the linear mixed effect model where the volumes of subcortical structures computed by freesurfer.
However, little if any is known about measurement reliability across various data processing conditions. Whole brain volume loss and widespread sub cortical regional atrophy was noted in both tle with and. Automated whole brain segmentation using freesurfer. Abnormal asymmetries in subcortical brain volume in. Means and standard deviations of regional volumes for each protocol for each diagnostic group can be found in supplementary table 4. Subcortical volume loss in the thalamus, putamen, and. Different software packages such as freesurfer and fsl 14 use. Segmentation generated with freesurfer was used to derive volumes of the total intracranial volume and the volumes of five subcortical structures. Freesurfer outputs from all studies were evaluated quantitatively by comparing ratios of the cortical and subcortical volumes to their ground. Mriderived measurements of human subcortical, ventricular and intracranial brain volumes. Freesurfer parcellation of brains containing large infarcts. Automated whole brain segmentation using freesurfer s. A mipav plugin for the visual and quantitative comparison.
Heres an email i wrote to the freesurfer mail archive. Mriderived measurements of human subcortical, ventricular. For bilateral subcortical volumes, age, age 2, sex, hemisphere, assessment centre and icv were set as covariates in a repeatedeffect linear model to test for an association between both probable. Freesurfer software is now a frequently used tool for the estimation of subcortical structure volume. Unhealthy aging is a risk factor that can contribute to the formation of brain diseases, and as the central processor of human life activity, the cerebral structure changes in many ways with increasing age. Dickerson110 used freesurfer software to generate a surface map of cortical. Alterations of subcortical regional volumes in schizophrenia. Cortical thickness, gray matter volume, and white matter anisotropy and. In a previous article, a method to import cortical meshes from freesurfer into blender and other cg applications was presented. We covered the steps taken to accomplish each and introduced quality control steps that can be implemented for both subcortical volumes and for cortical surfaces before parcellation. For caudate segmentation, first and freesurfer performed more similarly.
Here it is complemented with a method to import the subcortical structures. Label subcortical structures and wmgm determine volumes of subcortical structures used to fill in subcortical structures for later steps aseg volume steps 6. An open source software suite for processing and analyzing human brain mri images. Neuroimaging analysis software package fully characterizes anatomy cortex folding patterns, thickness, rois subcortical structure boundaries longitudinal surfacebased intersubject registration multimodal integration fmri task, rest, retinotopy tractography. These structures are segmented as part of freesurfer subcortical stream, and are stored in a volumebased representation. Importing freesurfer subcortical structures into blender. This allows the practitioner to see the portions of the hippocampus that are most affected at. Publications home of jama and the specialty journals of. Freesurfersubcorticalsegmentationqualitycheckinstructions. I am not aware of any other functionality that other software has and is missing in brainsuite for structural analysis.
Pdf the effect of duration of illness and antipsychotics. Findings in this cohort study, brain volumes cortical gray matter, white matter, and subcortical gray matter were measured at the time of discharge from the hospital and at 7 years. Subcortical brain volumes reproducibility reliability structural mri cerebral cortex morphology automated mriderived measurements of invivo human brain volumes provide novel insights into normal and abnormal neuroanatomy, but little is known about. It is immediately obvious that the two methods yield consistent thalamic volumes. Figure 3 presents the relationship between stereological r1 and freesurfer estimates of left and right thalamus volume across the entire sample of 72 subjects investigated in the present study. While reading about the segmentation process on the wiki, i came across this lin. Nevertheless, with first with 2dspinecho, 18% of patients had missegmentation. Cortical thickness, surface area and subcortical volume. Figures 4 and 5 show the reduction in volume from years one to three and years ten to twelve, respectively. The relationship between volumecortical thickness and performance on neuropsychological tests was evaluated in 33 patients. Subcortical brain volume abnormalities in 2028 individuals with schizophrenia and 2540 healthy controls via the enigma consortium. Hello, i am working on comparing handdrawn subcortical volumes to those output automatically by freesurfer.
Freesurfer 2 is a robust validated software package for cortical and sub cortical segmentation of structural mri. We performed a metaanalysis of group differences in regional volumes. Subcortical surface shape in youth at familial high risk. New features and changes in each version of freesurfer current stable release is v6.
Quantification of subcortical graymatter vascularization. The input are the volumes found in files mriorigxxx. In the present study, weevaluated on mri the volume of several cerebral regions in patients with pd, msap, psp and healthy controls by using a relatively new fullyautomated segmentation software freesurfer 8. Subcortical volumes obtained with both freesurfer and first showed good agreement between 2dspinecho and 3dgradientecho images, with 68. Freesurferanalysispipelineoverview free surfer wiki. Freesurfer is the structural mri analysis software of choice for the human connectome project. The algorithm relies on a single channel of t1weighted mr images to achieve automated segmentation of cortical and subcortical brain areas, producing volumes of subcortical structures and surface models of the cerebral cortex. We compared cortical thickness and subcortical volumes in cognitively. To characterize freesurfers validity, we compare several versions of freesurfer software with traditional handtracing. Freesurfer is a popular software package to measure cortical thickness and volume of neuroanatomical structures. The available information about the pattern of the association between brain metrics and substance use is inconsistent, especially in the case of recreational and occasional users. Intraclass correlations revealed a slightly reduced level of consistency between human and freesurfer analysis. Freesurfer is suite of powerful tools that provide extensive and automated analysis of key features in the human brain. Cortical thickness had the lowest intraclass correlation coefficient.
If no runs are found, then it looks for a volume in mriorig or mriorig. Regional specificity of sex effects on subcortical volumes. Department of neurology, national institute of mental health and neurosciences, bengaluru, karnataka, india 2 department of neurology. Sienax, part of the fmrib software library fsl, is computationally less demanding but only provides measurements of the gross tissue volumes wm, gm and csf 12. All cortical and subcortical regions of interest rois are then transformed to the diffusion space using fsls flirt package jenkinson et al. Repeatability and reproducibility of freesurfer, fsl. Low brain volumes observed in preterm infants were exaggerated at 7 years, and low brain volume in infancy was associated with worse longterm functional outcomes. However, brain measurements derived from mrimages are susceptible to differences in mrsequence parameters. Comparison of cortical and subcortical measurements in. This reply was modified 11 months, 1 week ago by anand joshi.
Volume estimation of the thalamus using freesurfer and. The effect of duration of illness and antipsychotics on. Freesurfer is a set of software tools for the study of cortical and. Relative volumes showed a mean correlation coefficient of r 0. This includes volumetric segmentation of most macroscopically visible brain structures fischl et al. Multivariate associations among behavioral, clinical, and. For the subcortex, the total volumes of various structures, as well as gray matter and white matters, are reported in detail by brainsuite. Therefore, using an identical analysis to the one applied to our data in fig. Subcortical brain volume abnormalities in 2028 individuals. The effects of freesurfer version, workstation type, and. Comparison of cortical and subcortical measurements in normal.
Frontiers asymmetry of cerebral gray and white matter. Reliability effects of scan sessions, acquisition sequences, data analyses, scanner upgrade, scanner vendors and field strengths. When there are multiple source volumes, this step will correct for small motions between them and then average them together. Comparison of accuracy between fsls first and freesurfer for. Abnormal subcortical volumes and cortical thickness in parkinsons disease with impulse control disorders shweta prasad 1, venkateswara reddy reddam 2, albert stezin 1, ravi yadav 2, jitender saini 3, pramod kumar pal 2 1 department of clinical neurosciences. Microsoft excel, you can find any bad subjects and mark either its left or right thalamus value with an. From freesurfers cortical parcellation several measures can be obtained from within each region. This class covered the two major components of autorecon2.
Freesurfer segments graywhite matter into different cortical regions based on sulci and gyri pattern, and also segments major subcortical regions in the brain. Is fsl or freesurfer better for subcortical segmentation. What goes into the calculation of subcortical volume. We, however, assessed correlation and system bias between the different popular software packages as well as a multiatlas segmentation approach to measure subcortical volumes.
206 1155 447 1048 269 548 611 616 879 149 647 649 1229 1016 700 1366 1376 566 1410 15 217 1349 338 1380 1529 978 517 832 933 681 745 1228 356 698 76 429 950 1294 810