[miguel_rivas]

Dear sychoi,

I have successfully run the distortion correction on the BOLD images. The error was that the bvals and bvecs matrices (bvals: 3×246 and bvecs: 1×246) had to have only a zero in the first column and different values to 0 in the rest. However, at this moment I have two important questions:

1- Will it have any effect on the image if there are values other than zero in the rest of the columns? I used the value 1000. I think that this will not be a problem because b=0 will be used as the reference image. That’s right?

2. I would like to do the fMRI analysis in SPM12. In which preprocessing step should I include the EPI distortion correction with brainsuite? Maybe after realignment for motion correction? Pleas any insight about this would be very appreciated. This would be my pipeline

– Slice timing
– Realign: Estimate and Reslice
– Coregister: Estimate
– Segment
– Dartel: create templates
– Dartel: Normalise to MNI structural scans.
– Dartel: Normalise to MNI functional scans.

[miguel_rivas]

Dear sychoi,

Thank your for your reply, I tried to run the bdp.sh script using as input the T1 (skullstripped and bias field corrected) and a 4D image with the 246 bold volumes following (I think) your recommendations. As you said, for the bvals and bvecs files I created:

bvals file: matrix with 3 rows and 246 columns
bvecs file: matrix with 1 row and 246 columns

When I ran the script everything worked fine but stopped with the following error:

rmnlab1:bdp neucoga$ bash bdp.sh /Applications/BrainSuite19a/bdp/sujetos/T1_image.bfc.nii.gz –tensor –nii /Applications/BrainSuite19a/bdp/sujetos/fmri.nii.gz -g /Applications/BrainSuite19a/bdp/sujetos/bvecs -b /Applications/BrainSuite19a/bdp/sujetos/bvals

BDP Version: 19a (build #0074), released 2019-02-14

================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…

Checking input files…

BDP could not find any .mask.nii.gz file. BDP will use input bfc file itself as
brain mask for registration and statistics. All voxels with intensity>0 in bfc
will be treated as voxels in brain. You can specify a custom brain mask by using
flag –t1-mask <maskfile_name>. The custom mask must overlay correctly with
input BFC image in BrainSuite.

Processing data with fileprefix:
/Applications/BrainSuite19a/bdp/sujetos/T1_image

================================================================================
Co-registration and Distortion Correction
================================================================================
Reading the input parameters for co-registration…
Total physical memory found: 64.00GB

Checking orientation information…Done
Extracting 0-diffusion (b=0) image from input DWIs…

DWI mask is not defined in input flags. BDP will try to estimate a (pseudo) mask
from 0-diffusion (b=0) image. Automatic mask estimation may not be accurate in
some sitations and can affect overall quality of co-registration. In case
co-registration is not accurate, you can define a DWI mask by using flag
–dwi-mask <mask_filename>. The mask can be generated and hand edited in
BrainSuite interface. This mask would be used only for registration purposes
(and not for statistics computation).
Saved (pseudo) masks: /Applications/BrainSuite19a/bdp/sujetos/T1_image.dwi.RAS.mask.nii.gz

Starting Registration based distortion Correction…
Loading data…

Starting rigid registration of input images…
Reading input data…
Setting/generating masks…
Matching centroids (approx. align)…Warning: Matrix is singular to working precision.
> In register_files_affine (line 304)
In EPI_correct_files_registration_INVERSION (line 109)
In coregister_diffusion_mprage_pipeline (line 219)
In BrainSuite_Diffusion_pipeline (line 26)
Warning: Matrix is singular to working precision.
> In register_files_affine (line 305)
In EPI_correct_files_registration_INVERSION (line 109)
In coregister_diffusion_mprage_pipeline (line 219)
In BrainSuite_Diffusion_pipeline (line 26)

Matching resolution of the images…Error using eig
Input to EIG must not contain NaN or Inf.

Error in get_original_grid_data (line 44)

Error in register_files_affine (line 313)

Error in EPI_correct_files_registration_INVERSION (line 109)

Error in coregister_diffusion_mprage_pipeline (line 219)

Error in BrainSuite_Diffusion_pipeline (line 26)

MATLAB:eig:matrixWithNaNInf

What could be the error? I have installed the Matlab 2015b runtime…

Thanks for your help.

Best regards,

[miguel_rivas]

Dear BrainSuite members,

We are dealing with b0 distortion correction in diffusion and bold EPI images. Unfortunately we neither have the FIELDMAP acquisition nor the EPI with opposite phase encoding direction (anterior-posterior, posterior-anterior). In this context, we would like to use the toolbox for distortion correction (described in Bhushan et al. 2015) in order to correct the B0 in EPI images. However we would like to know two questions about the toolbox:

1- Is there any incompatibility if I use the EPI corrected images (output of the BDP) in other softwares?

2- Is possible to use the toolbox in bold EPI images? We are conducting a fMRI study and I would like to know if it is possible to correct this artifact in Bold EPI images with this toolbox.

Thanks in advance.

Best regards,

[Author]

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