Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

Hi Mateo,

Sorry, I’m confused by your question.

Can you try to rerun mri_convert by passing it additional flag ‘--rescale-dicom’, or setting environment variable FS_RESCALE_DICOM to 1?

Hope that will solve your problem. Repost your question in a different thread is a good idea since it is a different problem now.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Thursday, April 28, 2022 10:00 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

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-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 Mateo Jean Sent: Thursday, April 28, 2022 6:06 AM To: freesurfer <freesurfer@nmr.mgh.harvard.edumailto: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" <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> À: "freesurfer" <freesurfer@nmr.mgh.harvard.edumailto: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-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 Mateo Jean Sent: Wednesday, April 27, 2022 8:16 AM To: freesurfer <freesurfer@nmr.mgh.harvard.edumailto: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" <YHUANG43@MGH.HARVARD.EDUmailto:YHUANG43@MGH.HARVARD.EDU> À: "freesurfer" <freesurfer@nmr.mgh.harvard.edumailto: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-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 Mateo Jean Sent: Tuesday, April 26, 2022 7:51 AM To: freesurfer <freesurfer@nmr.mgh.harvard.edumailto: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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