What about the mask ?
MatrixType = Rect # Rows = 65; # Cols = 0Does it contain any non-zero value ?Moises
On 15 October 2015 at 22:38, Kuhn, Taylor <[log in to unmask]> wrote:
Hello,
Thank you for the suggestion. I just reordered the bvec file and reran bedpostx and received the same error message:
An exception has been thrown Logic error:- detected by Newmat: index error: requested indices = 1, 1 MatrixType = Rect # Rows = 65; # Cols = 0DATACHECK OUTPUT FOR ENIGMA PIPELINE DATA AFTER BVEC REORDERING:3
fsl5.0-bedpostx_datacheck Data/
Data//data
data_type INT16
dim1 110
dim2 110
dim3 110
dim4 65
datatype 4
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
Data//nodif_brain_mask
data_type FLOAT32
dim1 110
dim2 110
dim3 110
dim4 1
datatype 16
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
num lines in Data//bvals
1
num words in Data//bvals
65
num lines in Data//bvecs
num words in Data//bvecs
195
Taylor P. Kuhn, Ph.D.Neuropsychology Postdoctoral Fellow
UCLA Semel Institute for Neuroscience and Human Behavior
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Moises Hernandez [[log in to unmask]]
Sent: Thursday, October 15, 2015 2:24 PM
To: [log in to unmask]
Subject: Re: [FSL] Bedpostx Error using ENIGMA pipeline data
Hi Taylor,
BEDPOSTX_DATACHECK FOR DATA PROCESSED USING ENIGMA PIPELINE
num lines in Data//bvecs
65
BEDPOSTX_DATACHECK FOR DATA PROCESSED USING FSL PIPELINE
num lines in Data/bvecs
3
It seems that in the first one you have 65 lines with 3 values,and in the second one 3 lines with 65 values (correct one).
I would try to reorder Data/bvecs
Moises.
On 15 October 2015 at 21:56, Kuhn, Taylor <[log in to unmask]> wrote:
Hello,
I have processed our lab's DTI data using a standard FSL pipeline (eddy_correct, bet, dtifit) and through an extensive ENIGMA pipeline (eddy_correct, bet, bvec rotation, dtifit, epi-correction with processed T1 image, and second DTIFIT). I have been able to successfully run bedpostx on the data processed using the standard FSL pipeline. However, when I attempt to run bedpostx on the data from the ENIGMA pipeline, I get the following error below. I have attached the output file from fslerrorreport to this email. I have run bedpostx_datacheck and I do not get any errors (see below). I have compared the output of bedpostx_datacheck between the standard FSL data that does successfully complete bedpostx and the other data that does not complete bedpostx without error (below). The only noticeable differences are the dimensions and the number of lines in the bvec file. However, both datachecks come back without error. Any suggestions would be greatly appreciated.
ERROR MESSAGE WHEN RUNNING BEDPOSTX: An exception has been thrown Logic error:- detected by Newmat: index error: requested indices = 1, 1 MatrixType = Rect # Rows = 65; # Cols = 0
BEDPOSTX_DATACHECK FOR DATA PROCESSED USING ENIGMA PIPELINE
fsl5.0-bedpostx_datacheck Data/
Data//data
data_type INT16
dim1 110
dim2 110
dim3 110
dim4 65
datatype 4
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
Data//nodif_brain_mask
data_type FLOAT32
dim1 110
dim2 110
dim3 110
dim4 1
datatype 16
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
num lines in Data//bvals
1
num words in Data//bvals
65
num lines in Data//bvecs
65
num words in Data//bvecs
195
BEDPOSTX_DATACHECK FOR DATA PROCESSED USING FSL PIPELINE
fsl5.0-bedpostx_datacheck Data
Data/data
data_type INT16
dim1 96
dim2 96
dim3 60
dim4 65
datatype 4
pixdim1 1.979167
pixdim2 1.979167
pixdim3 2.000000
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
Data/nodif_brain_mask
data_type FLOAT32
dim1 96
dim2 96
dim3 60
dim4 1
datatype 16
pixdim1 1.979167
pixdim2 1.979167
pixdim3 2.000000
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
num lines in Data/bvals
1
num words in Data/bvals
65
num lines in Data/bvecs
3
num words in Data/bvecs
195
Thank you,
Taylor
Taylor P. Kuhn, Ph.D.Neuropsychology Postdoctoral Fellow
UCLA Semel Institute for Neuroscience and Human Behavior
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IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.