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Hi Nabin Have you modified accordingly the bvals and bvecs? I.e. add zero entries for bvals and zero vector entries for bvecs at the corresponding locations? Cheers Stam > On 17 Jun 2016, at 11:12, Nabin Koirala <[log in to unmask]> wrote: > > Sorry but the problem was I did not changed the bvals and bvecs, now its working fine. Many thanks again for your support. > > Regards, > Nabin > > On Fri, Jun 17, 2016 at 11:52 AM, Nabin Koirala <[log in to unmask] <mailto:[log in to unmask]>> wrote: > Dear Stam , > > Thank you for the response but now I am stuck with another error. I created the data file as you suggested with b0 image before every volume and also the qshell text. But the error now is as follows: > > Log directory is: logdir+++ > Multiple b-values have been detected. Three shells are assumed, acquired one after the other! > Mean b-values for detected shells are 900, 1800 and 2700 > > > An exception has been thrown > Logic error:- detected by Newmat: incompatible submatrix dimension > > Trace: SubMatrix(evaluate). > > I checked the input data as well as I saw in forum some of them had this error because of the concatenation issue or so but when I do fslinfo to check the dimensions, I have following outputs and looks fine to me. > > data_type INT16 > dim1 128 > dim2 128 > dim3 62 > dim4 93 > datatype 4 > pixdim1 2.000000 > pixdim2 2.000000 > pixdim3 2.500000 > pixdim4 9.700000 > cal_max 0.0000 > cal_min 0.0000 > file_type NIFTI-1+ > > Could you please suggest. > > Thank you. > > Regards, > Nabin > > On Thu, Jun 16, 2016 at 1:31 PM, Stamatios Sotiropoulos <[log in to unmask] <mailto:[log in to unmask]>> wrote: > > Yes, the simplest solution would be to insert a b=0 (you can simply replicate the first volume you have) at the beginning of each shell. E.g. in the data file you will have a b=0, just before the b=1800 volumes start and another just before the b=2700 start. Then you provide a qshells.txt with three entries, one per non-b0 shell. In each of these you count both the DWI images and the first b=0 you have included, i.e. your entries should be > > 31 31 31 > > Best wishes > Stam > > >> On 16 Jun 2016, at 12:21, Nabin Koirala <[log in to unmask] <mailto:[log in to unmask]>> wrote: >> >> Dear Stam , >> >> Could it be because I have only one b0 image ? Do you think adding more b0s at the beginning is worth a try ? >> >> Thank you. >> >> Regards, >> Nabin >> >> >> On Mon, Jun 13, 2016 at 11:15 AM, Nabin Koirala <[log in to unmask] <mailto:[log in to unmask]>> wrote: >> Hi Stam , >> >> Yes it does. Here is how my bvals looks like >> >> 0 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 900 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 1800 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 2700 >> >> Thank you. >> >> Best, >> Nabin >> >> On Mon, Jun 13, 2016 at 11:00 AM, Stamatios Sotiropoulos <[log in to unmask] <mailto:[log in to unmask]>> wrote: >> Hi Nabin >> >> Do your bvals contain b=0 entries? Could you send the content of your bvals file? >> >> Cheers >> Stam >> >> >>> On 12 Jun 2016, at 13:23, Nabin Koirala <[log in to unmask] <mailto:[log in to unmask]>> wrote: >>> >>> Dear FSL team , >>> >>> I am trying to use qboot function to reconstruct q-ball ODFs using the following command but unfortunately it does not recognize my bo image. I am getting the error message as follows : >>> >>> Log directory is: logdir++ >>> Multiple b-values have been detected. Three shells are assumed, acquired one after the other! >>> Mean b-values for detected shells are 900, 1800 and 2700 >>> At least one b=0 image is required! Exiting now! >>> >>> The command I used is as follows: >>> >>> qboot -k /qball/data.nii.gz -m /qball/nodif_brain_mask.nii.gz -r /qball/bvecs -b /qball/bvals --q=/qball/qshells.txt >>> >>> My qshell contains 1 30 30 30 (each for b=0, b=900, b=1800 and b=2700 respectively). >>> >>> Since the b values are in arithmetic progression and as I also provided the qshells.txt, could not quiet figure out what I am missing. >>> >>> Thank you in advance for your support. >>> >>> Best, >>> Nabin >>> >> >> >> > > >