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]> 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]> 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]> 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]> 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]> 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