Hi Mateo,
It looks like mri_convert terminated prematurely when you tried to convert
those 512 dicom files.
Those error messages are printed when mri_convert wasn’t able to retrieve DTI
information from dicom. If you don’t need the DTI values, you can ignore those
error messages.
Also, looking at the codes, I think if you set environment variable FS_LOAD_DWI
to 0 before running mri_convert, it should finish convert all 512 dicom files.
To set the environment variable, you do ‘export FS_LOAD_DWI = 0’ in bash, and
‘setenv FS_LOAD_DWI 0’ in csh.
Can you give it a try?
Thanks.
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Mateo Jean
Sent: Tuesday, April 26, 2022 7:51 AM
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error
External Email - Use Caution
Hello FreeSurfer Developers
I hope i don't spam, if anyone has a clue...
I need to convert 512 dicom files from Bruker into .nii . I firstly add .dcm to
my Bruker multi gradient echo phase files then enter the following command :
mri_convert MRIm001.dcm phaseMGE.nii
Here is the first message :
reading from MRIm001.dcm...
Starting DICOMRead2()
dcmfile =
/mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm
dcmdir =
/mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2
ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH --
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File:
/mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm
break
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/DICOMRead.cpp:4930
Ref Series No = 4
Found 514 files, checking for dicoms
ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH --
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
DICOM File:
/mnt/c/Users/Sahadatou/Documents/Stage_JEAN_2022/data/fantomes/tests/bug_test2/MRIm001.dcm
break
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/DICOMRead.cpp:4930
ERROR: don't know how to get DWI parameters from --Bruker BioSpin MRI GmbH --
ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
Then 508 error messages like the three last lines appear.
It ends with :
First Sorting
Computing Slice Direction
Vs: 0 0 1
Vs: 0 0 1
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 8
nslices = 63
ndcmfiles = 508
ERROR: the number of frames * number of slices does
not equal the number of dicom files.
I did a test with only 448 files (I just copy-paste the first 448 files = 7 TE
* 64 slices) and I obtained the same error messages but the nifti files are
created and seem usable (quick test with Fiji). Here are the last lines :
First Sorting
Computing Slice Direction
Vs: 0 0 1
Vs: 0 0 1
Second Sorting
IsDWI = 1, IsPhilipsDWI = 0
Counting frames
nframes = 7
nslices = 64
ndcmfiles = 448
INFO: rescale not needed
PE Dir = COL (dicom read)
Loading pixel data
TR=50.00, TE=3.10, TI=0.00, flip angle=15.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to phaseMGR.nii...
Saving bvals and bvecs
I'm pretty new with mri convert and I don't understand why it stops converting
to nii with 512 files (8 TE) but not 448 files for Brucker files.
Best Regards,
Mateo
Version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
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