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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> À: "freesurfer" <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 <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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1gYetxR1-VwqeD9fRK1VOueswhIHJLqg3UCKtLeFc6lLXvngcAegENSvLmVrTYp19NKCgaA98od-6FCh_3PXMhbsE-K9KLDPAdai3V_fYcJKOI-h3klpzoZgCn6YnfdFNn8kDeOnKViyGj_iKRDovKdtPQDeIG5PvINN9WolDYw1-h6qteoRCivq_d5CTXRwpX_i8uFUMnLM-wXD8cVjHRu3ybo0KcVBM3AYP-xtDnqmsFZ5clOcZeonny3BPrdJSZepf9Io8Ki0IH8Y4TGEmfXhkcmTc8pehBgviPGfViinn7wm-1uQeR0Gnq5-lUOrb/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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