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

2022-04-28 Thread Mateo Jean 
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"  
À: "freesurfer"  
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 
 On Behalf Of Mateo Jean 
Sent: Wednesday, April 27, 2022 8:16 AM 
To: freesurfer  
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" < [ mailto:yhuan...@mgh.harvard.edu | 
yhuan...@mgh.harvard.edu ] > 
À: "freesurfer" < [ mailto:freesurfer@nmr.mgh.harvard.edu | 
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: [ mailto:freesurfer-boun...@nmr.mgh.harvard.edu | 
freesurfer-boun...@nmr.mgh.harvard.edu ] < [ 
mailto: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 < [ mailto:freesurfer@nmr.mgh.harvard.edu | 
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

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

2022-04-27 Thread Mateo Jean 
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"  
À: "freesurfer"  
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 
 On Behalf Of Mateo Jean 
Sent: Tuesday, April 26, 2022 7:51 AM 
To: freesurfer  
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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[Freesurfer] Mri Convert Bruker MGRE files dicom to nii error

2022-04-26 Thread Mateo Jean 
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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[Freesurfer] Mri Convert Brucker MGRE files dicom to nii error

2022-04-06 Thread Mateo Jean 
External Email - Use Caution

Hello FreeSurfer Developers 


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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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.