Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Request for passcode
by Katrine Sand Andersen 30 Apr '22

30 Apr '22

External Email - Use Caution Hi, I am installing Freesurfer. Is it possible to get the passcode for the Ubuntu virtual box? Best, Katrine Sand PhD fellow Authorised psychologist University of Copenhagen Department of Psychology Øster Farimagsgade 2A 1353 København K DIR +45 35 32 51 95 Employee profile<http://secure-web.cisco.com/1CSA4CwBmQSK3B_mFoCLKQt2NW6r8kiykBjF8e2zM1D24_R…> [Logo for Københavns Universitet] How we protect personal data<https://secure-web.cisco.com/1LxNOjreTT-9-2UM-jyoHssPK_o5ToKiRQKobI4-m2p6EX…>

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Re: [Freesurfer] Passcode for 7zip archive
by fsbuild 29 Apr '22

29 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 29, 2022, at 07:33, Lukas Mikula <mikula.lukas(a)mailbox.org> wrote:        External Email - Use Caution        To whom it may concern,I am in the preogress of installing Freesurfer via Virtual box and on the installation instruction page it says i need to send an email to the freesurf help mail to get the passcode to extract the FS_7_2_0_Ubuntu_18_04_06.ova.7z file that contains the VM image . Is this the correct emailing list? thank you sincerely, L.M _______________________________________________Freesurfer mailing listFreesurfer@nmr..mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Request for 7 zip password VM_67
by fsbuild 29 Apr '22

29 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 28, 2022, at 16:10, Bastola, Subrat <sxb2391(a)mavs.uta.edu> wrote:        External Email - Use Caution        Hi, I just need a passcode to archive the zip folder for file FS_7_2_0_Ubuntu_18_04_06.ova.7z so that I can install free surfer virtual disk. Regards,Subrat_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Permission denied error from -localGI
by Billah, Tashrif 29 Apr '22

29 Apr '22

Thank you Douglas. We took our time to install FreeSurfer 7.2 and retry. However, we ran into the same error: >> reading filled volume... /bin/bash: /scratch/tp44447785365264536.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp44447785365264536.load_mgh.m.mgh for reading ERROR: loading /data/pnl/FS_SUBJECTS_DIR/1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz as MGH Struct contents reference from a non-struct array object. Error in make_outer_surface (line 25) volume=vol.vol; >> ERROR: make_outer_surface did not create output file What can we do now? -Tashrif Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700 =================== Can you just try it with 7.2? We had some problems at one point with temporary files in lGI that were fixed with 7.2 =================== On 4/27/2022 9:36 AM, Billah, Tashrif wrote: Sorry about missing your earlier question--our FreeSurfer is 7.1.0 We still need your help with this issue. Thank you, Tashrif Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700 =================== What version of FS are you running? On 3/20/2022 8:47 PM, Billah, Tashrif wrote: It does not exist and cannot be created in a shared cluster. Is there a way to define a different folder for /scratch/tp24093955057547375.load_mgh.m.mgh? =============== Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800 Do you have permission to /scratch? Does it exist? =============== Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800 Hi all, We are trying to run recon-all with -localGI but running into an unknown permission denied error: $ recon-all -s sub-1001 -localGI ``` make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 >> reading filled volume... /bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for reading ERROR: loading /path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz as MGH Struct contents reference from a non-struct array object. Error in make_outer_surface (line 25) volume=vol.vol; >> ERROR: make_outer_surface did not create output file '/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022 ``` Our MATLAB environment is properly setup and we regularly run other FreeSurfer-MATLAB commands. So I do not think that is causing the issue. Best, Tashrif

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Passcode for 7zip archive
by Lukas Mikula 29 Apr '22

29 Apr '22

External Email - Use Caution To whom it may concern, I am in the preogress of installing Freesurfer via Virtual box and on the installation instruction page it says i need to send an email to the freesurf help mail to get the passcode to extract the FS_7_2_0_Ubuntu_18_04_06.ova.7z file that contains the VM image . Is this the correct emailing list? thank you sincerely, L.M

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Request for 7 zip password VM_67
by Bastola, Subrat 28 Apr '22

28 Apr '22

External Email - Use Caution Hi, I just need a passcode to archive the zip folder for file FS_7_2_0_Ubuntu_18_04_06.ova.7z so that I can install free surfer virtual disk. Regards, Subrat

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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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Freesurfer