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Here is the Error:
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)
Ok, thank you for your answer. That did solve the problem. I was copy pasting the command directly from the website, which has only one dash before each flag. Once, i added t dashes it worked.
The command ran but i still have a problem which was later one. Here is the error i got.
I searched online, but the only solution is to replace the NaNs with zeros!Oh sorry even though it appears that i am using a single dash, i am actually using 2 (- – )!
It is only when i paste it here does it look like that!
I think you had the same problems when you pasted. Check your reply.
Any other thing that might be wrong for this to work?Hi, thanks.
But i am getting the same error!BDP Version: 18a (build #0073), released 2018-02-14
================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…***************************************
* *
* Error running BDP *
* *
* A MANDATORY INPUT IS NOT DEFINED *
* *
***************************************Error message:
Diffusion data is a mandatory input. –nii flag must be used to define input
diffusion data.Error help/resolution:
BDP could not find any flag defining a mandatory input. Please refer to error
message above. You can visit the BrainSuite website at following url for
documentation of BDP Usage:
http://brainsuite.org/processing/diffusion/flags/Thank you very much.
Here is the output.
surface registration and labeling (svreg)
This is the main program for surface registration. First, the surface is
smoothed to create a multiresolution representation of the surface. An
initial registration is performed by aligning the 3D coordinates of this
smoothed surface. This is followed by p-harmonic mapping to a square and
curvature-based registration.
For more information, please see http://brainsuite.org
Authored by Anand A. Joshi, Signal and Image Processing Institute
Department of Electrical Engineering, Viterbi School of Engineering, USCusage: svreg_label_surf_hemi.sh [subject fileprefix] [atlas fileprefix]
[hemi] [flags]required input:
subject fileprefix path and filename prefix of the subject’s output
from BrainSuite’s Cortical Surface Extraction
Sequence
atlas fileprefix path and filename prefix of atlas files and labels
to which the subject will be registered
hemi the hemisphere to refine; either left or rightoptional flags:
-v# Controls the verbosity of output messages (# is 0, 1, or 2)
-t display timestamps along with output messagesHere is one of the errors i am getting from the run..
Using Executable /Applications/BrainSuite18a/svreg/bin/warp_points_mac
A matrix with a negative or zero determinant was encountered. (AIR_NON_POSITIVE_DETERMINANT_ERROR)
SVREG Warning: .warp file was not in correct format. Continuing after trying to fix.
Error using readdfs (line 61)
Unable to read:~/study/BS_SPGR/A11/A11.svreg.tmp/A11.target.left.mid.cortex_smooth10_smooth10.dfs
Error in surf_align_autocorrect_with_AIR (line 159)
Error in align_surf_curves (line 62)
Error in surf_flatten_newbs (line 32)
Error in svreg_label_surf_hemi (line 163)another is the pial line. While brainsuite is running, i can see that it was too much inside the brain, sometimes including the inner temporal!!!
