Hi Mateo,
I’m glad mri_convert works for you now.
I’m little confused about the value ranges you saw. We map DT_SIGNED_SHORT
(-32766~32766) to signed short. mri_info should give ‘type: SHORT (4)’.
In Freesurfer 7.2, we don’t support DT_UINT16. We map DT_UINT16 (0~65535) to
signed short. You will see value maxed at 32766 for DT_UINT16. Is this what you
were experiencing?
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Mateo Jean
Sent: Thursday, April 28, 2022 6:06 AM
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error
External Email - Use Caution
Hi,
Thanks!
It works I guess.
I didn't manage to use setenv in the command line before using mri_convert
(command not found)
But I did the following modifications and mri_convert works now (it doesn't put
the error message anymore and I have the nifti file at the end) :
----------------------------------------------------------------------------------------------------------------------------------------
Opening ubuntu
>$cd then >$ nano .bashrc
And I write just before the source /path/freesurfer/7.2.0/SetUpFreeSurfer.sh
the line : export FS_LOAD_DWI=0
Then I change the directory to freesurfer : >$ cd /path//freesurfer/7.2.0 and
open the csh : >$nano SetUpFreeSurfer.csh
I add setenv FS_LOAD_DWI before the line source
$FREESURFER_HOME/FreeSurferEnv.csh
----------------------------------------------------------------------------------------------------------------------------------------
I suppose this locks the DWI to zero and I need to remodify it if one day I
want to use Diffusion data.
So mri_convert for Bruker data now works. The last problem (and I might create
an other post) is that negative values were not kept. When I compared phase
imagec converted in nifti with 3D slicer and phase image converted in nifti
with mri_convert, 3D slicer's nifti have values ranging from - 32 766 to 32 766
while mri_convert's nifti only have values ranging from 0 to 32 767.
How can I set mri_convert to convert values in signed-16 bits ?
Thank you for your previous answer !!!
Best Regards,
Mateo
________________________________
De: "Huang, Yujing" <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
À: "freesurfer"
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Envoyé: Mercredi 27 Avril 2022 15:20:37
Objet: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error
I’m assuming you didn’t source .bashrc after editing it.
You can actually set it on the command line before submitting mri_convert. So,
the setting only affect that window. You can use echo $FS_LOAD_DWI to verify
the setting.
Here is an example for csh:
>echo $FS_LOAD_DWI
FS_LOAD_DWI: Undefined variable.
>setenv FS_LOAD_DWI 0
>echo $FS_LOAD_DWI
0
>mri_convert …
I’m hoping it will solve your problem by setting the environment variable.
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Mateo Jean
Sent: Wednesday, April 27, 2022 8:16 AM
To: freesurfer
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error
External Email - Use Caution
Thank you for your answer.
Even though I don't need the DTI values, I can't avoid this message :
"ERROR: the number of frames * number of slices does not equal the number of
dicom files."
I'm not very familiar with Ubuntu too so I might have made a mistake :
I try to set the environnement variable ‘export FS_LOAD_DWI = 0’ in bash (I
use the command $cd then $nano .bashrc and write after
export FS_LICENSE=/home/jeanmri/license.txt
export FREESURFER_HOME=/home/jeanmri/freesurfer/7.2.0
the line export FS_LOAD_DWI = 0)
Then I open with nano the FreeSurferEnv.csh and add setenv FS_LOAD_DWI 0 at
the end but when I use mri_convert on my bruker dicom files, the same error
reappeared.
Did I miss something ?
Best Regards,
Mateo
________________________________
De: "Huang, Yujing" <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
À: "freesurfer"
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Envoyé: Mardi 26 Avril 2022 21:22:28
Objet: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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<mailto: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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