mhd/.raw format 3D images in ITK? I have tried to use the following code but it is not getting loaded as the dimension of the loaded image is displayed as 0,0,0.Ĭan someone please point out the mistake I am making? typedef float InputPixelType Inside the Bruker folders, all scans of each set were subdivided according to the different age groups.How to load and write. In case of the diffusion scans in the Leiden-Set, the reference scan is the same as the T2 reference scan and is located in the “\1\pdata\1” folder, the DWI maps (per effective B-value) are located in the “\3\pdata\1” folder and the calculated quantitative ADC maps: signal intensity (SI), standard deviation of SI, diffusion constant (mm 2/seq), standard deviation of diffusion constant, standard deviation of the fitting curve, are located in the “\3\pdata\2” folder. In case of the Cologne-Set-1 and Cologne-Set-2, the echoes and T2 maps are located in the “\1\pdata\1” and the “\1\pdata\2” folders, respectively. In case of the Leiden-Set, the reference scan is located in the “\1\pdata\1” folder, the echoes and the calculated quantitative T2 maps are located in the “\2\pdata\1” and the “\2\pdata\2” folders, respectively. After surgery, the animal was allowed to recover for 2 h in the incubator to maintain body temperature at around 37☌, with easy access to food and water.īruker 2dseq data-files can be loaded using ImageJ 3 with the Paravision 5.1 Bruker plug-in 4 installed. After 30 min of occlusion, the mouse was re-anesthetized in order to remove the suture and withdraw the monofilament to allow reperfusion. During the occlusion period, the mouse was allowed to wake up in a temperature-controlled incubator (V1200 Peco Services Ltd., Brough, UK). During the surgical procedure, a silicone-coated nylon monofilament (7017PK5Re Doccol Company, Redlands, CA, USA) was inserted into the right common carotid artery and advanced via the internal carotid artery and circle of Willis to eventually block the middle cerebral artery (MCA) at its origin (decreasing blood flow substantially in the MCA territory, in the right hemisphere) and the skin was sutured. During surgery, the mouse body temperature was maintained at around 37☌ using a rectal probe and feedback system. Carporal, 50 mg/mL, AST Farma BV, Oudewater, Netherlands) was given before surgery. Mice were anesthetized using isoflurane (3% induction, 1.5% maintenance) in 70% pressurized air and 30% O 2. Infarcts were induced using a modified transient middle cerebral artery occlusion ( tMCAo) model first described by Longa et al. Table Table1 1 shows a complete overview of all scans, together with a summary of the main imaging acquisition parameters. Quantitative T2 and ADC maps were calculated from the raw data using Paravision 5.1 software (Bruker Pharmascan) for the Leiden-Set and IDL software was used to calculate the quantitative T2 maps of the Cologne-Sets. Animals from the Leiden-Set were scanned at 7 T (Pharmascan, Bruker BioSpin, Ettlingen, Germany), whilst animals from the Cologne-Sets were scanned at 11.7 T (Biospec 11.7 T/16, Bruker BioSpin). Scans were performed with small-animal Bruker MRI systems using a Multi-Slice Multi-Echo sequence protocol. All animal experiments conducted at the Max Plank Institute for Metabolism Research in Cologne were performed in accordance with the German Animal Welfare Act and approved by the local authorities (Landesamt für Naturschutz, Umwelt und Verbraucherschutz NRW). All animal experiments performed at the Leiden University Medical Center (LUMC) were approved by the local committee for animal health, ethics, and research of LUMC. Cologne-Set-2: Transgenic mice expressing luciferase under doublecortin control (DCX-Luc, Couillard-Després et al., 2008) ( n = 10 2- and 12-month-old) were scanned at 48 h after infarct induction.Īnimals were housed with littermates, in a temperature-controlled environment, with food and water ad libitum.
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