Freesurfer April 2022

freesurfer@nmr.mgh.harvard.edu

97 participants
155 discussions

Issue with FDR-correction
by Tsiknia, Amaryllis 02 May '22

02 May '22

External Email - Use Caution Dear Freesurfer experts, I want to apply FDR correction to a sig.mgh map I have loaded onto tksurfer, but noticed that the FDR-correction is inconsistent. When I load multiple sig.mgh overlays on tksurfer and then apply FDR correction on all layers I get the following sig.mgh map for the measure I am interested in. [cid:ee22d887-18db-45c4-86b4-134b66ce7b6c] Whereas when I load just the overlay that I am interested in and apply FDR correction to that one layer, I get this FDR-corrected map: [cid:5df909c9-469d-490c-8af6-47cfdb74cd5c] Is there any reason why the two FDR corrected maps are expected to differ? Any insight would be much appreciated. Best, Amaryllis

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Call for papers for the 5th international workshop on machine learning in clinical neuroimaging
by MLCN Workshop 30 Apr '22

30 Apr '22

External Email - Use Caution Dear Colleagues, Please find below the call for papers for the International Workshop of Machine Learning in Clinical Neuroimaging (MLCN) which is held on *the 18th of September 2022 at MICCAI 2022, Singapore*. We welcome contributions to novel machine learning methods and their applications to clinical neuroimaging data. The submission deadline is *25 June 2022*, and all MLCN accepted papers will be eligible for the best paper award of 500 USD. Top accepted papers will be invited to submit an extended version to the MELBA journal. For more information, please visit https://secure-web.cisco.com/1Fj8iLHdu4VLOETa8o2c0ylx17UB3PQp-WKfayO6j5XSuP… Best wishes, The MLCN 2022 steering and organizing committees Christos Davatzikos, Andre Marquand, Jonas Richiardi, Emma Robinson Ahmed Abdulkadir, Nicha C. Dvornek, Mohamad Habes, Seyed Mostafa Kia, Vinod Kumar, Thomas Wolfers *Call for Papers* The International Workshop of Machine Learning in Clinical Neuroimaging (MLCN 2022 <https://secure-web.cisco.com/1B1YWxb-pPXy0e9h8uURMg1bMuCXV3MXCGrqE4pCYthutX…>), a satellite event of MICCAI (MICCAI 2022 <https://secure-web.cisco.com/1Sffs0qU73EnPz7M23Eu9zW55ekCOl5-KN_SWwvJK7BHHq…>), calls for original papers in the field of clinical neuroimaging data analysis with machine learning. The two tracks of the workshop include methodological innovations as well as clinical applications. This highly interdisciplinary topic provides an excellent platform to connect researchers of varying disciplines and to collectively advance the field in multiple directions. In the *machine learning* track, we seek novel contributions that address current methodological gaps in analyzing high-dimensional, longitudinal, and heterogeneous clinical neuroscientific data using stable, scalable, and interpretable machine learning models. Topics of interest include but are not limited to: · Big data · Spatio-temporal brain data analysis · Structural data analysis · Graph theory and complex network analysis · Longitudinal data analysis · Model stability and interpretability · Model scalability in large neuroimaging datasets · Multi-source data integration and multi-view learning · Multi-site data analysis, from preprocessing to modeling · Domain adaptation, data harmonization, and transfer learning in neuroimaging · Unsupervised methods for stratifying brain disorders · Deep learning in clinical neuroimaging · Model uncertainty in clinical predictions · … In the *clinical neuroimaging *track*,* the applications of existing machine learning algorithms are evaluated to move towards precision medicine for complex brain disorders. The discovery of biological markers in medicine is an important challenge across different fields and various experimental procedures and designs are used to detect biological signatures that can be utilized for improvement in diagnostic, treatment, or for other beneficial ends. However, for most complex brain disorders, we do not have reliable biomarkers today. The application of advanced machine learning methods may help to reach this goal. Therefore, we invite the community to submit conference contributions on machine learning approaches with the goal to improve our understanding of complex brain disorders, moving the field closer to precision medicine. Topics of interest include but are not limited to: · Biomarker discovery · Refinement of nosology and diagnostics · Biological validation of clinical syndromes · Treatment outcome prediction · Course prediction · Analysis of wearable sensors · Neurogenetics and brain imaging genetics · Mechanistic modeling · Brain aging · The presentation of clinical neuroimaging databases to stimulate developments in machine learning · … ------------------------------ *Submission Process:* The workshop seeks high-quality, original, and unpublished work that addresses one or more challenges described above. Papers should be submitted electronically in Springer Lecture Notes in Computer Science (LCNS) style (see this link <https://secure-web.cisco.com/1x4sFG0et25l4buDNOLJ4VAhZNyqwuQsbQHKG7FuvJSgzH…> for detailed author guidelines) using the CMT system here <https://secure-web.cisco.com/1PEufL2yn6FIE1GnKz6bmX7m_2F03ZU-8ROdw448s2t3bb…>. The page limit is 8-pages (text, figures, and tables) plus up to 2-pages of references. We review the submissions in a double-blind process. Please make sure that your submission is anonymous. Accepted papers will be published in a joint proceeding with the MICCAI 2022 conference. ------------------------------ *MLCN Special Issue at the MELBA journal:* We will invite the top accepted papers to submit an extended version of their contribution to the MLCN special issue at the Journal of Machine Learning for Biomedical Imaging (MELBA) <https://secure-web.cisco.com/1LI6kPOlmJuM3jc0wntNJ8rEV1ad3v3NyKxy37DtmnrSqg…>. The invited papers will go through an independent review process by the journal. *Error! Filename not specified.* <https://secure-web.cisco.com/1LI6kPOlmJuM3jc0wntNJ8rEV1ad3v3NyKxy37DtmnrSqg…> ------------------------------ *Donders Best Paper Award:* The MLCN’s best paper award is sponsored by Donders Institute <https://secure-web.cisco.com/1ZxIhrR9AWXisP_yTr74CQc-owmRP8MxehA2MSEZAAaJ4f…>. All MLCN accepted papers will be eligible for the best paper award. The recipient of the award will be chosen by the MLCN scientific committee based on the scientific quality, novelty, and clarity of contributions. The winner will be announced at the end of the workshop and will receive a 500 USD honorarium. ------------------------------ *Important Dates:* · Paper submission deadline: June 25, 2022 · Notification of Acceptance: July 23, 2022 · Camera-ready Submission: Aug 6, 2022 · Workshop Date: September 18, 2022

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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 April 2022