Re: [Freesurfer] TRACULA preprocessing errors: cannot create dwi_orig_las.nii.gz

Hi Rita - Can you share this volume with me? I haven't been able to replicate your error message so far.

/home/rita/Desktop/test/diffusion_dcm/MRI_20160226_2_PHD003/MRI_20160226_2_PHD003_dwi.nii.gz

Thanks, Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Rita Vieira ritagonvieira@gmail.com Sent: Thursday, March 4, 2021 4:34 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA preprocessing errors: cannot create dwi_orig_las.nii.gz

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Hi Anastasia,

Thank you for helping me.

When I run mri_info /home/rita/Desktop/test/diffusion_dcm/MRI_20160226_2_PHD003/MRI_20160226_2_PHD003_dwi.nii.gz

I get this: Volume information for Desktop/test/diffusion_dcm/MRI_20160226_2_PHD003/MRI_20160226_2_PHD003_dwi.nii.gz type: nii dimensions: 128 x 128 x 62 x 62 voxel sizes: 2.000000, 2.000000, 2.000000 type: SHORT (4) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -62.0, zend: 62.0 TR: 9100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 62 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9980, y_r = -0.0471, z_r = -0.0416, c_r = -2.7172 : x_a = -0.0505, y_a = 0.9950, z_a = 0.0856, c_a = 24.3838 : x_s = -0.0374, y_s = -0.0875, z_s = 0.9955, c_s = 35.3273 Orientation : LAS Primary Slice Direction: axial

voxel to ras transform: -1.9960 -0.0941 -0.0833 133.6350 -0.1010 1.9901 0.1712 -101.8270 -0.0748 -0.1751 1.9909 -10.3990 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -8

ras to voxel transform: -0.4990 -0.0252 -0.0187 63.9202 -0.0235 0.4975 -0.0438 53.3510 -0.0208 0.0428 0.4977 12.3162 -0.0000 -0.0000 -0.0000 1.0000

Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> escreveu no dia quinta, 4/03/2021 à(s) 03:03: Hi Rita - From the log file, the first error occurs when it tries to convert your DWI nifti volume to LAS orientation:

mri_convert -oni 128 -onj 128 -onk 62 -oid 0 0 0 -ojd 0 0 0 -okd 0 0 0 -oc -2 24 35 -rt nearest /home/rita/Desktop/test/diffusion_output/MRI_20160226_2_PHD003/dmri/dwi_orig.nii.gz /home/rita/Desktop/test/diffusion_output/MRI_20160226_2_PHD003/dmri/dwi_orig_las.nii.gz

mri_convert: directions must have non-zero magnitude; out_i_direction = (0, 0, 0)

Is there something up with the header of your nifti? What do you see when you run this command?

mri_info /home/rita/Desktop/test/diffusion_dcm/MRI_20160226_2_PHD003/MRI_20160226_2_PHD003_dwi.nii.gz

Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rita Vieira <ritagonvieira@gmail.commailto:ritagonvieira@gmail.com> Sent: Wednesday, March 3, 2021 1:12 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] TRACULA preprocessing errors: cannot create dwi_orig_las.nii.gz

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Dear FreeSurfer experts,

I am a new user of FreeSurfer and I am trying to apply TRACULA to my data. However, I am stuck in the pre-processing part.

I have the following error at the end: ERROR: Transform file should be eddy_correct/eddy log file or .mat file

But, the problem starts early because it cannot create the dwi_orig_las.nii.gz file.

Also, the bvecs.norot is filled with zeros.

I checked the bvals and bvecs file and they follow the format required by TRACULA.

In attachment, you can find the configuration and trac-all.log files.

Thanks in advance! Rita

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