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I greatly appreciate your advice. I succeeded to segment gray and white matter regions in younger infant chimpanzees using the method you suggested. I found that myelenated and unmyelenated region could not been segmented in infant chimpanzee brains because these brains were scanned only under T1 weighted. However, I will try to obtain the T2 weighted image of infant chimpanzees next time. Best regards, Tomoko Sakai Primate Research Institute Kyoto University ____________________________________________________________________ Tomoko Sakai Primate Research Institute, Kyoto University Brain Research Section・Department of Behavioral and Brain Sciences Inuyama, Aichi 484-8506, JAPAN TEL. +81-568-63-0567 (Administrative Office) FAX. +81-568-63-0085 E-mail: [log in to unmask] ____________________________________________________________________ > Well, one have to be mindful of basic neurobiology when imaging of primate > infants. Generally, infant's brain is not myelenated in anything other > that > cortico-spinal track. In such a case, T1-w will not give you significant > contrast.However, T2-w contrast is quite high. So I just run a true-fist > sequence which can be used for tissue segmentation. > > ----- Original Message ----- > From: "Matt Glasser" <[log in to unmask]> > To: <[log in to unmask]> > Sent: Friday, December 28, 2007 8:25 AM > Subject: Re: [FSL] Re-forwarding Segmentation of brains of infant > chimpanzees > > > Hi, > > I wonder if there is not enough contrast between unmeylinated white matter > and grey matter? We have gotten FAST to work pretty well in adult > chimpanzees, only making some errors in motor cortex and the sub cortical > grey nuclei. One thing that can help increase the image contrast is to > square the image (fslmaths -sqr), if you do it a couple of times, you may > have to reduce the values in the image by dividing by some large number > (e.g. 1e6) and additionally set an upper threshold to remove any blood > vessels (which will become so high in value that they will be classified > in > a separate tissue category). > > Peace, > > Matt. > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf > Of Tomoko Sakai > Sent: Friday, December 28, 2007 4:08 AM > To: [log in to unmask] > Subject: [FSL] Re-forwarding Segmentation of brains of infant chimpanzees > > Dear FSL list > (I’m sorry to send a garbled e-mail. I send you an e-mail again.) > > I am attempting segmentation of brains of infant chimpanzees using FAST. I > succeeded to segment gray and white matter regions in the older subjects. > However, the white matter regions seemed to be overestimated while the > gray matter regions seemed to be underestimated in younger infants under > one year old. I would like to ask you to give me any suggestion that I > should try. I would also like to learn the method to segment the > unmyelinated white, and myelinated white matter regions using FAST? > > The brains of infant chimpanzees were scanned under T1 weighted, and the > data were processed as follows. > (1) Scans were corrected for fluctuations in average intensity using > SUSAN. > (2) Brains were aligned to anterior commisure‐posterior commisure > orientation in transverse view using MRIcro. > (3) Cerebral portions of brains were extracted using BET (option: -R -m - > s -r 50 -f 0.3 -g 0.2) and FSLview. > (4) Gray and white matter regions were segmented using FAST (option: -t 1 > - > c 3 -a -A -od, -os -ob -i 16 -l 200 -v 1- 5). > > I appreciate for your help in advance. > > Tomoko Sakai > Primate Research Institute > Kyoto University > > ____________________________________________________________________ > > Tomoko Sakai > Primate Research Institute, Kyoto University > Brain Research Section・Department of Behavioral and Brain Sciences > Inuyama, Aichi 484-8506, JAPAN > TEL. +81-568-63-0567 (Administrative Office) > FAX. +81-568-63-0085 > E-mail: [log in to unmask] > ____________________________________________________________________ >