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That is fine! It tells us that data and brainmask are OK, and bvecs and bvals match these data, and that everything what dtifit needs is recognised correctly. That's all fine. It looks, however, like you running FSL inside a VMwareplayer, right? What is your setup? Your data are quite big 160*116*45 in float32 format. Could it be that while you were running dtifit on these data, there were some other procsses taking ressources? And thus the job was not executed correctly? Have you rerun that subject twice? Why are your data float32 and not Int16? Are they all like this (in other subjects?) Cheers, Markus 2009/3/25 cathyliu <[log in to unmask]> > Hi, > > I have checked by bedpostx_datacheck, but I don't know what it means... > Here is the results: > > [yan@localhost ~]$ /opt/fsl/bin/bedpostx_datacheck > /mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data/ > /mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data//data > data_type FLOAT32 > dim1 116 > dim2 160 > dim3 45 > dim4 33 > datatype 16 > pixdim1 0.8593750000 > pixdim2 0.8593750000 > pixdim3 2.3000710011 > pixdim4 1.0000000000 > cal_max 0.0000 > cal_min 0.0000 > file_type NIFTI-1+ > /mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data//nodif_brain_mask > data_type INT16 > dim1 116 > dim2 160 > dim3 45 > dim4 1 > datatype 4 > pixdim1 0.8593750000 > pixdim2 0.8593750000 > pixdim3 2.3000710011 > pixdim4 1.0000000000 > cal_max 0.0000 > cal_min 0.0000 > file_type NIFTI-1+ > num lines in /mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data//bvals > 1 > num words in /mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data//bvals > 33 > num lines in /mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data//bvecs > 3 > num words in /mnt/hgfs/Data/Yan/NeonatalDTI/AKBULUT/data//bvecs > 99 > > Regards, > > Yan > > > ------------------------------ > Date: Wed, 25 Mar 2009 17:28:20 +0100 > > From: [log in to unmask] > Subject: Re: [FSL] white FA maps > To: [log in to unmask] > > Ok, I see. > > So seems that dtifit did not work... > Have you tried > bedpostx_datacheck <dtifit_directory> > ? > Regards, > Markus > > 2009/3/25 cathyliu <[log in to unmask]> > > Hi, > > > > The white FA maps means that the FA value is 1.06592 everywhere in the > brain mask, so it is quite high anisotropic. > > > > The eddy corrected data look perfect, and the brain mask covers all the > brain. As the FA maps are white, I don't continue to do the bedpostX yet. > > > > Thank you so much! > > > > Regards, > > > > yan > > > > ------------------------------ > Date: Wed, 25 Mar 2009 15:56:33 +0100 > From: [log in to unmask] > Subject: Re: [FSL] white FA maps > To: [log in to unmask] > > > Hi! > What do you mean by white FA maps? > Is fslstat FAmap -R [0 0]? > > How do the eddy_corrected data look like? How the brain mask? > What does "bedpostx_datacheck" on the dtifit directory return? > > Could you give more information, please? > > All the best, > Markus > > > > > > 2009/3/25 cathyliu <[log in to unmask]> > > Hi, > > > > We have some problems to make good FA maps, and L1,L2,L3,MD,V1,V2,V3...maps > don't work either. We do the image preparation following your instructions, > it works in most of our cases, but in 3 of them we have the white FA maps. > We could view the oraginal data 32 directions without any problem, and there > is not error information during the processing. We wonder if it is the > problem of the old scanner version, or the wrong gradient table which FSL > doesn't recognize. These three cases were examined in the machine: > > > > Scanner software version: NT 9.1.1.3 > scanner model: Gyroscan Intera > number of directions: 32 > phase encoding direction: AP > > > > Regards, > > > > Yan > > ------------------------------ > 立刻下载 MSN 保护盾，保障 MSN 安全稳定！ 现在就下载！ <http://im.live.cn/safe/> > > > > > -- > Dr. med. Markus Gschwind, M.D. > Laboratory for Neurology and Imaging of Cognition > Dept of Neurosciences > University Medical Center (CMU) > 1 Michel-Servet - 1211 GENEVA - CH > > Tel 0041 (0) 22 379 5324 > Fax 0041 (0) 22 379 5402 > email: [log in to unmask] > http://labnic.unige.ch > > ------------------------------ > 更多热辣资讯尽在新版MSN首页！ 立刻访问！ <http://cn.msn.com/> > > > > > -- > Dr. med. Markus Gschwind, M.D. > Laboratory for Neurology and Imaging of Cognition > Dept of Neurosciences > University Medical Center (CMU) > 1 Michel-Servet - 1211 GENEVA - CH > > Tel 0041 (0) 22 379 5324 > Fax 0041 (0) 22 379 5402 > email: [log in to unmask] > http://labnic.unige.ch > > ------------------------------ > 更多热辣资讯尽在新版MSN首页！ 立刻访问！ <http://cn.msn.com/> > -- Dr. med. Markus Gschwind, M.D. Laboratory for Neurology and Imaging of Cognition Dept of Neurosciences University Medical Center (CMU) 1 Michel-Servet - 1211 GENEVA - CH Tel 0041 (0) 22 379 5324 Fax 0041 (0) 22 379 5402 email: [log in to unmask] http://labnic.unige.ch