Freesurfer

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Mri Convert Bruker MGRE files dicom to nii error
by Mateo Jean 28 Apr '22

28 Apr '22

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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Re: [Freesurfer] FreeSurfer 7Zip archive passcode
by fsbuild 28 Apr '22

28 Apr '22

External Email - Use Caution I will send you an alternate way to download the file. - R. On Apr 28, 2022, at 04:15, Katharina Hense <Katharina.Hense(a)klinik.uni-regensburg.de> wrote:        External Email - Use Caution        Dear FreeSurfer team, Thank you for providing the passwords and some instructions for the installation.However, I encountered a problem while unzipping the file. Both 7zip and WinRAR show me that something is wrong with the file or the password is wrong. I tried to enter the provided password by copy+paste and as manual input. I also deleted the file and downloaded it again from the FreeSurfer homepage and tried this on a different computer. Unfortunately, none of this worked.Attached you will find the error message from WinRAR.C:\Users\user\Downloads\FS_7_2_0_ubuntu_18_04_06.ova.7z: Checksum error in the encrypted file C:\Users\user\Downloads\FS_7_2_0_ubuntu_18_04_06.ova.7z. Corrupt file or wrong password. Best regards,Katharina>>> Katharina Hense 25.04.2022, 10:59 >>>Hello, I'm trying to expand the 7Zip archive for FreeSurfer on the VirtualBox. Can I get the passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z? Sincerely,Katharina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer 7Zip archive passcode
by Katharina Hense 28 Apr '22

28 Apr '22

External Email - Use Caution Hello, I'm trying to expand the 7Zip archive for FreeSurfer on the VirtualBox. Can I get the passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z? Sincerely, Katharina

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Cortical depth at each cortical voxel
by Fotiadis, Panagiotis 28 Apr '22

28 Apr '22

External Email - Use Caution Hi FS experts, I was wondering whether there was a way to assign each cortical voxel within the T1w (volumetric) scan an index corresponding to its “cortical depth.” I have essentially taken the cortical ribbon .mgz file, assigned each cortical voxel a voxel ID, and wanted to associate each ID with its corresponding cortical depth. I would normally use the *h.sulc files but I didn’t think this would properly translate here since it’s a volumetric analysis. Thank you in advance for your time and help! Best Panos -- Panagiotis Fotiadis Ph.D. Candidate | Neuroscience Graduate Group Perelman School of Medicine, University of Pennsylvania

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Re: [Freesurfer] VirtualBox pass code
by fsbuild 28 Apr '22

28 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 27, 2022, at 21:54, JESS WOOLF <jwoolf(a)deakin.edu.au> wrote:       External Email - Use Caution        Hello,Will you please send me the pass code for the Virtual Box  ova.7z file?Thank you,Jess_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] help - unzip Ubuntu ova password
by fsbuild 28 Apr '22

28 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 27, 2022, at 15:31, Dan Lerner <dan(a)findsurgicalsciences.com> wrote:        External Email - Use Caution        Hi,Setting up the Ubuntu vm provided by FreeSurfer. I'm emailing for the password as per the instructions.Thanks,Dan_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Request for 7Zip Archive passcode
by fsbuild 28 Apr '22

28 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 26, 2022, at 14:01, Logan Tate <lwtate21(a)gmail.com> wrote:        External Email - Use Caution        Hi, I made a prior request but believe the passcode was sent to someone who posted under my request, and not myself. I just need a passcode to archive the zip folder for file FS_7_2_0_Ubuntu_18_04_06.ova.7zSorry for the spam! Thank you._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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VirtualBox pass code
by JESS WOOLF 27 Apr '22

27 Apr '22

External Email - Use Caution Hello, Will you please send me the pass code for the Virtual Box ova.7z file? Thank you, Jess

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Re: [Freesurfer] recon-all error
by Huang, Yujing 27 Apr '22

27 Apr '22

Hi Rebecca, I’m trying to get more information to determine how it core dumped. 1. Can you confirm that you are running Freesurfer 6.0? 2. From which directory, did you run recon-all and dcmunpack? 3. Can you try dcmunpack by passing it full path to dicom directory? Thanks. Yujing -------- Forwarded Message -------- Subject: [Freesurfer] recon-all error Date: Sun, 10 Apr 2022 07:01:30 +1000 From: cooperr1(a)student.unimelb.edu.au<mailto:cooperr1@student.unimelb.edu.au> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> External Email - Use Caution Dear FreeSurfer developers, I’m attempting to run recon-all on a set of T1-weighted images acquired in the 1980s-1990s and am having trouble with the recon-all pipeline. I have used the original dicom files in the recon-all using the command below. Command: recon-all -s 1003156_dicom -i 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all Error message: /Applications/freesurfer_v6/bin/mri_convert: line 3: 8196 Segmentation fault: 11 mri_convert.bin "$@" The recon-all.log is also attached. I’ve also explored using dcmunpack and obtain the following result: Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 Message: cat: /tmp/dcmdir-all.89439: No such file or directory Found 0 unique series: Patient: Undefined variable. Do you have any idea what might be the problem? Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: Mac OS X 10.13.3 Recon-all.log: attached. With warm regards, Rebecca Cooper

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Does PETSurfer calculate ROI-wise values by averaging?
by Zhener Zhang 27 Apr '22

27 Apr '22

External Email - Use Caution Hello, I have a question regarding the way ROI-wise values are calculated using PETSurfer. We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively small ROI like Putamen has one of the highest values of regional distribution of a PET tracer. Is it the case that the PETSurfer ROI-wise value outputs were averaged, or normalized by each ROI’s volume? And what measure was divided, GM volume, number of voxels, or something else? Thank you in advance! Best regards, Zhener

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