You could try using MRIConvert to make the bvecs. If you did not rotate the FOV on the scanner, you should be able to just use the gradients in the sequence (though you might have to change the signs of one of the rows, so check that the V1 in lines mode looks like the anatomy should look in the corpus callosum and corona radiata). Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of cathyliu Sent: Wednesday, March 25, 2009 12:41 PM To: [log in to unmask] Subject: Re: [FSL] white FA maps Hi, I use "dcm2niiGUI" to transfer the DICOM images to Nifti, and we could have the bvals and bvecs automatically. I don't know why all the other data have the right bvecs, but the three cases have the same bvecs in the 32 directions repeated over and over. Is there anyway to get the right bvecs? Best Regards, Yan _____ Date: Wed, 25 Mar 2009 12:24:15 -0500 From: [log in to unmask] Subject: Re: [FSL] white FA maps To: [log in to unmask] Your bvecs file contains a b0 and the same b600 direction repeated over and over. Presumably you scanned different 32 directions, so you will need to list them each in the bvecs file, rather than listing direction #1 32 times. Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of cathyliu Sent: Wednesday, March 25, 2009 12:18 PM To: [log in to unmask] Subject: Re: [FSL] white FA maps Hi: Please check the bvecs and bvals in the attachment. As the problem of interpolation, I could discuss it with our physicists. Thanks, Regards, yan _____ Date: Wed, 25 Mar 2009 12:08:43 -0500 From: [log in to unmask] Subject: Re: [FSL] white FA maps To: [log in to unmask] Could you post your bvecs and bvals files also? In future studies, you will want to avoid having scanner interpolation on (the cause of your highly anisotropic voxels 0.85X0.85X2.3mm), as this is not ideal for tractography studies. This is not the cause of your current issue, however. Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of cathyliu Sent: Wednesday, March 25, 2009 12:00 PM To: [log in to unmask] Subject: Re: [FSL] white FA maps 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! <http://im.live.cn/safe/> 现在就下载! -- 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 <http://labnic.unige.ch/> _____ 更多热辣资讯尽在新版MSN首页! <http://cn.msn.com/> 立刻访问! -- 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 <http://labnic.unige.ch/> _____ 更多热辣资讯尽在新版MSN首页! <http://cn.msn.com/> 立刻访问! _____ 立刻下载 MSN 保护盾,保障 MSN 安全稳定! <http://im.live.cn/safe/> 现在就下载! _____ 更多热辣资讯尽在新版MSN首页! <http://cn.msn.com/> 立刻访问!