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 INT16dim1 128dim2 128dim3 62dim4 93datatype 4pixdim1 2.000000pixdim2 2.000000pixdim3 2.500000pixdim4 9.700000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+Could you please suggest.Thank you.Regards,NabinOn 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 wishesStam
On 16 Jun 2016, at 12:21, Nabin Koirala <[log in to unmask]> wrote:
NabinRegards,Thank you.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 ?
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?
CheersStam
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