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Hi, It is possible that your data file contains an extra entry as the last volume, such as an FA or an MD map, some scanners compute those on the fly. In this case, you have 33 diffusion-weighted volumes and the scheme you think is wrong is the appropriate one. By looking at your data you should be able to find out what is wrong. Cheers, Stam On 15 Dec 2010, at 05:51, 李俏俊 wrote: > hi, > Actally i don't understand too,i just to try to use a bvecs with wrong number(e.g. i have 33 volumes and i write 34 ) and a right number, with the wrong number the dtifit works but i got wrong result. Then i try the right, i get a result which is different with the result with wrong number. i think this result is right (in fact, i don't know which one is really the right one,but i think most people will choose the later one？) > > best~ > > 2010/12/14 Stamatios Sotiropoulos <[log in to unmask]> > Hi, > > I am not sure I understand that, if you rewrote the bvecs file, how is it possible not to match the number of volumes in the data? You are supposed to have one bvals and bvecs entry for each volume in the data. If not, then any results you might get are wrong (actually you are not supposed to get any results). Are your bvals, bvecs ASCII files? > > Cheers, > Stam > > On 14 Dec 2010, at 14:48, 李俏俊 wrote: > >> thanks ignacio, >> my bvecs num match my data but it doesnt work,just now i tried to rewrite my bvecs word by word,it works(even the num of directions in bvecs doesnt match my data,so strange!) >> best regards >> >> >> 2010/12/14 Ignacio Letelier <[log in to unmask]> >> Hi qjili >> >> >> After doing bedpostx_datacheck I realized that there was no match between bvecs and the n° volumes of my data. >> I don't know why but dcm2niigui gave me two series of HDR/IMG series and one bvecs/bvals file. The fact is that one of these HDR/IMG had 33 volumes and the other one had 34 volumes so that's why there was no match with bvec file. After selecting the right combination I had no further problems. Hope this work. >> >> Best regards >> >> >> 2010/12/14 李俏俊 <[log in to unmask]> >> >> hi,ignacio >> I met the same question as yours(in the Fdt,it responed that the number of bvecs and bvals dont have the same entries ),did you solve it and how do you solve it? >> thanks >> qjli >> >> >> On Mon, Dec 6, 2010 at 11:08 PM, Ignacio Letelier <[log in to unmask]> wrote: >> Thanks Stam >> >> >> >> I will upload the data and also dicom files just in case bvals and bvecs have been not well extracted. >> >> Ref num: 924244 >> >> >> Best regards. >> >> 2010/12/6 Stamatios Sotiropoulos <[log in to unmask]> >> OK, you were supposed to have the data file as well in this directory, but that's fine, do you have 34 volumes in your data? If yes, I cannot tell what might be going wrong, please upload your data including the mask, bvals and bvecs on www.fmrib.ox.ac.uk/cgi-bin/upload.cgi an let me know the reference number. >> >> Cheers, >> Stam >> >> >> On 6 Dec 2010, at 14:21, Ignacio Letelier wrote: >> >>> >>> Dear Stam >>> >>> After renaming.... >>> >>> [fsl@localhost ~]$ bedpostx_datacheck /home/fsl/Desktop/subject1/dti/ >>> /home/fsl/Desktop/subject1/dti//data does not exist >>> /home/fsl/Desktop/subject1/dti//nodif_brain_mask >>> data_type INT16 >>> dim1 160 >>> dim2 160 >>> dim3 80 >>> dim4 1 >>> datatype 4 >>> pixdim1 1.4375000000 >>> pixdim2 1.4375000000 >>> pixdim3 2.0000000000 >>> pixdim4 1.0000000000 >>> cal_max 0.0000 >>> cal_min 0.0000 >>> file_type NIFTI-1+ >>> >>> num lines in /home/fsl/Desktop/subject1/dti//bvals >>> 1 >>> num words in /home/fsl/Desktop/subject1/dti//bvals >>> 34 >>> num lines in /home/fsl/Desktop/subject1/dti//bvecs >>> 3 >>> num words in /home/fsl/Desktop/subject1/dti//bvecs >>> 102 >>> >>> Best regards >>> >>> 2010/12/6 Stamatios Sotiropoulos <[log in to unmask]> >>> Hi Ignacio, >>> >>> what names do you use for bvecs, bvals files and the brain mask? Could you please rename them as requested (to bvecs, bvals and nodif_brain_mask) and rerun bedpostx_datacheck? >>> >>> Stam >>> >>> On 6 Dec 2010, at 13:39, Ignacio Letelier wrote: >>> >>>> Ok. >>>> >>>> >>>> bedpostx_datacheck gives the following response: >>>> >>>> /home/fsl/Desktop/subject1/dti/nodif_brain_mask does not exist >>>> num lines in /home/fsl/Desktop/subject1/dti/bvals >>>> cat: /home/fsl/Desktop/subject1/dti/bvals: No such file or directory >>>> 0 >>>> num words in /home/fsl/Desktop/subject1/dti/bvals >>>> cat: /home/fsl/Desktop/subject1/dti/bvals: No such file or directory >>>> 0 >>>> num lines in /home/fsl/Desktop/subject1/dti/bvecs >>>> cat: /home/fsl/Desktop/subject1/dti/bvecs: No such file or directory >>>> 0 >>>> num words in /home/fsl/Desktop/subject1/dti/bvecs >>>> cat: /home/fsl/Desktop/subject1/dti/bvecs: No such file or directory >>>> 0 >>>> >>>> Ignacio >>>> >>>> 2010/12/6 Stamatios Sotiropoulos <[log in to unmask]> >>>> Hi Ignacio, >>>> >>>> what is the output of bedpostx_datacheck on the input directory? >>>> >>>> Stam >>>> >>>> >>>> >>>> >>>> On 6 Dec 2010, at 11:23, Ignacio Letelier wrote: >>>> >>>>> Hi Stamatios >>>>> >>>>> I recieved this message after doing BEDPOSTX: >>>>> >>>>> Errors: child process exited abnormally >>>>> >>>>> But there's also a new file in the directory called bedpostcom_log.tcl wich contains the whole directory name plus -n2 -w1 -b 1000 >>>>> >>>>> Thanks Stamatios >>>>> >>>>> 2010/12/3 Stamatios Sotiropoulos <[log in to unmask]> >>>>> Could you please run bedpostx_datacheck on the directory containing the data and bvecs, bvals files? What is the output? >>>>> >>>>> Cheers, >>>>> Stam >>>>> ----- Original Message ----- >>>>> From: Ignacio Letelier >>>>> To: [log in to unmask] >>>>> Sent: Friday, December 03, 2010 6:38 PM >>>>> Subject: Re: [FSL] DTIFIT Error >>>>> >>>>> >>>>> >>>>> >>>>> Stamatios thanks for your reply >>>>> >>>>> I've just checked the number of entries in bvals and bvecs files and there are 33 entries in each one wich means 33 directions. My acquisition parameters are: TR/TE 9000/65 ms, 80 slices, Nr b-values=2 and 33 directions (inc b=0), so I guess it might be not the problem. >>>>> >>>>> Any idea about what would be the problem? >>>>> >>>>> By the way what software do you use to extract bvals and bvecs files? >>>>> >>>>> Thanks. >>>>> >>>>> 2010/12/3 Stamatios Sotiropoulos <[log in to unmask]> >>>>> Hi Ignacio, >>>>> >>>>> the first thing I would try is to check that the number of entries in bvals and bvecs files is the same as the number of volumes in the data file. >>>>> >>>>> Hope this helps, >>>>> Stam >>>>> >>>>> ----- Original Message ----- >>>>> From: Ignacio Letelier >>>>> To: [log in to unmask] >>>>> Sent: Friday, December 03, 2010 5:12 PM >>>>> Subject: [FSL] DTIFIT Error >>>>> >>>>> Hi everyone. >>>>> >>>>> I'm working with the DTIFIT Reconstruct diffusion tensors tool and I recieved the following message after >>>>> pressing the 'Go' button: >>>>> >>>>> Errors: terminate called after throwing an instance of 'NEWMAT::Incompatible Dimensions Exception' >>>>> >>>>> I've never recieved this message before, so I'm not pretty sure what this could mean. >>>>> >>>>> Any help will be greatly appreciated >>>>> >>>>> Thanks in advance >>>>> -- >>>>> ignacio >>>>> >>>>> >>>>> >>>>> -- >>>>> Ignacio Letelier Aguirre >>>>> Ingeniero Civíl Biomédico >>>>> Clinica Santa María. >>>>> Teléfono: 97139955 >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Ignacio Letelier Aguirre >>>>> Ingeniero Civíl Biomédico >>>>> Clinica Santa María. >>>>> Teléfono: 97139955 >>>>> >>>> >>>> >>>> >>>> >>>> -- >>>> Ignacio Letelier Aguirre >>>> Ingeniero Civíl Biomédico >>>> Clinica Santa María. >>>> Teléfono: 97139955 >>>> >>> >>> >>> >>> >>> -- >>> Ignacio Letelier Aguirre >>> Ingeniero Civíl Biomédico >>> Clinica Santa María. >>> Teléfono: 97139955 >>> >> >> >> >> >> -- >> Ignacio Letelier Aguirre >> Ingeniero Civíl Biomédico >> Clinica Santa María. >> Teléfono: 97139955 >> >> >> >> >> -- >> 李俏俊 >> ------- >> CCM计算医学中心 >> www.ccm.org.cn >> 中国科学院自动化研究所模式识别实验室 >> ------- >> >> >> >> -- >> Ignacio Letelier Aguirre >> Ingeniero Civíl Biomédico >> Clinica Santa María. >> Teléfono: 97139955 >> >> >> >> >> -- >> 李俏俊 >> ------- >> CCM计算医学中心 >> www.ccm.org.cn >> 中国科学院自动化研究所模式识别实验室 >> ------- > > > > > -- > 李俏俊 > ------- > CCM计算医学中心 > www.ccm.org.cn > 中国科学院自动化研究所模式识别实验室 > -------