Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30060 discussions

Online Machine Learning School 25th-29th of September!
by Dominic Dwyer 01 Sep '23

01 Sep '23

External Email - Use Caution Join our global Online Machine Learning School from 25th-29th of September! Our hub is in Munich where Prof. Nikolaos Koutsouleris and his team are organizing the school together with the ECNP Neuroimaging Network<https://secure-web.cisco.com/1Q0FlhdtDGhI4WHxL_BSCDIgIHZwPXEgZ-7jlpgcSuSd57…>. This will enable participants to join hands-on tutorials within the Central European Summer Time zone. Register here.<https://secure-web.cisco.com/1BYsTzN1nhmVNzh6r5AoBaSAkpWKFBxVxaXIgDhzpYA7K9…> For the first time, this school is also being conducted in Melbourne by Dr. Dom Dwyer and the Orygen<https://secure-web.cisco.com/1aZHFQk-5Dsi42Di-c8ps6w3mqfwrnj_8R4DnFXmP3azoi…> Youth AI team, supported by The University of Melbourne<https://secure-web.cisco.com/1sxj8NxhZY9uUVdg4iyEjGtPTQ0EcGuVHbxcmn5NF4faXf…> and the PRE-EMPT<https://secure-web.cisco.com/1k4FvOxOJLCojOsS86LCRKoWF7G7zHllWukVfBKmKxKMQY…> project. This school is for participants in Asia-Pacific time zones and we offer tutorials in English, Vietnamese, and Mandarin Chinese. Register here<https://secure-web.cisco.com/1lBX__FRY65kQLCeJ-wlEVb7l0tyf52gSeE2rUEj7vgWMv…>. People with all levels of experience are encouraged to apply because you do not need coding experience to implement the cutting-edge machine learning techniques we teach. The school is tailored to online learning by providing different learning formats, including: * Seminars covering essential concepts * Hands-on tutorials using NeuroMiner<http://secure-web.cisco.com/1e0kasQJFGVzBzsH2XCpQGi7634oTmal96N_CgD6Hd2C37I…> that do not require coding experience * Application of learnt material in a machine learning competition with continuous assistance from tutors * Daily lectures from international experts in the field There are only 100 full course places available in total - so be quick! The school is supported by the Section for Precision Psychiatry (LMU Klinikum)<https://secure-web.cisco.com/1tsLPyg2gGodLtS69Jl8b-LklQ8KsPuhm7a9E6noa_4v19…>, the Max Planck Fellow Group for Precision Psychiatry<https://secure-web.cisco.com/1V2yN_65ALR2c7A7oKS6fBZnSzF3iWUIB_gf3fvav8iP-n…>, the Artificial Intelligence in Mental Health Lab (KCL)<https://secure-web.cisco.com/1GnD6RqYQ0zIwDigj2i14eK0sTQiINppUXPi3V8Gx8KtKl…>, the ECNP<https://secure-web.cisco.com/1Iu8Q5wDp3OgungBbANpPK5lHxoL0sECWxf_ob-uKu5lgv…> and the ECNP Neuroimaging Network<https://secure-web.cisco.com/1cJgS2dFS--j-LLASxoIo4d9dwaW0OAHFrqEpvft0DQSpC…>. It is also supported by Orygen, the University of Melbourne, and the Orygen Data Science and Analytical Methods team. For more information and to register for the school, please see the attached flyer or visit our website at https://secure-web.cisco.com/1BYsTzN1nhmVNzh6r5AoBaSAkpWKFBxVxaXIgDhzpYA7K9…<https://secure-web.cisco.com/1BYsTzN1nhmVNzh6r5AoBaSAkpWKFBxVxaXIgDhzpYA7K9…>. Looking forward to hearing from you! Best wishes, Your Online Machine Learning School Team

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passcode
by Alex Gomez 31 Aug '23

31 Aug '23

External Email - Use Caution Hi, I would like to request the passcode for unzipping the Virtual Box Image file (i.e. FS_7_2_0_ubuntu_18_04_06.ova.7z). Best regards Alex

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Fwd: recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'.
by fsbuild 30 Aug '23

30 Aug '23

External Email - Use Caution If you have not already done so, I would try installing and using the newest version of the Matlab runtime environment that the 7.4.1 release was tested with, i.e. R2019b.  Once you have set $FREESURFER_HOME, then run the fs_install_mcr script included with the freesurfer distribution .... $ export FREESURFER_HOME=<your install path> $ cd $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b … answer y to any installer questions ... Then I think it should work to find the Matlab libraries by at least start off with setting, $ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/bin/glnxa64 Please make sure you have otherwise removed from your environment and references to the previous Matlab R2022b setup. - R. Begin forwarded message:From: Benjamin Cole Sherman <bsherma(a)stanford.edu> Subject: [Freesurfer] recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'. Date: August 30, 2023 at 12:02:09 EDT To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>         External Email - Use Caution        Hi FreeSurfer Team,I'm trying to run recon-all on an MRI nii.gz file and I believe most of the command runs as the error doesn't happen until several hours in, however once matlab is initiated I consistently get the following output:MATLAB is selecting SOFTWARE OPENGL rendering.                            < M A T L A B (R) >                  Copyright 1984-2022 The MathWorks, Inc.                  R2022b (9.13.0.2049777) 64-bit (glnxa64)                              August 24, 2022Warning: Function iscolumn has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function ismatrix has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function isrow has the same name as a MATLAB builtin. We suggest yourename the function to avoid a potential name conflict.Warning: Function narginchk has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function isequaln has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function istable has the same name as a MATLAB builtin. We suggest yourename the function to avoid a potential name conflict.Warning: Function isfile has the same name as a MATLAB builtin. We suggest yourename the function to avoid a potential name conflict.Warning: Function isfolder has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict..Warning: Function isstring has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict. For online documentation, see https://secure-web.cisco.com/1A7cHJG7OTQToCpTNsg3ycqt5UEObzYbnyuy3… product information, visit http://secure-web.cisco.com/1PkNE_zNSBM0yzYMjwH_cGeVC4O7UdJdfnli… Unrecognized function or variable 'make_outer_surface'. >> ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!Command exited with non-zero status 1I haven't been able to find anything in the support archives so I was hoping you could help us out.1)Freesurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb84602)Platform: Ubuntu 20.04.6 LTS3)recon-all.log: see attachedThanks for any help you can provide!_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'.
by Benjamin Cole Sherman 30 Aug '23

30 Aug '23

External Email - Use Caution Hi FreeSurfer Team, I'm trying to run recon-all on an MRI nii.gz file and I believe most of the command runs as the error doesn't happen until several hours in, however once matlab is initiated I consistently get the following output: MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2022 The MathWorks, Inc. R2022b (9.13.0.2049777) 64-bit (glnxa64) August 24, 2022 Warning: Function iscolumn has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function ismatrix has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isrow has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function narginchk has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isequaln has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function istable has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isfile has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isfolder has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isstring has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. For online documentation, see https://secure-web.cisco.com/13dZgITxzA846nUba6W_D2_W9PFkrs3ibHMRaWbFXiq0_q… For product information, visit http://secure-web.cisco.com/1wgw042nbZL0hU6HIRu6Xfp7twuvdIG8MKHiB4v2D5d-qKz… >> Unrecognized function or variable 'make_outer_surface'. >> ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Command exited with non-zero status 1 I haven't been able to find anything in the support archives so I was hoping you could help us out. 1)Freesurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 2)Platform: Ubuntu 20.04.6 LTS 3)recon-all.log: see attached Thanks for any help you can provide!

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Converting hyperfine MRI to nifti
by Fatima Karim 29 Aug '23

29 Aug '23

External Email - Use Caution Hello My lab is trying to analyze hyperfine acquired MRI using freesurfer. We are stuck at the step where freesurfer converts the dicom to nifti for analysis. Freesurfer cannot recognize the hyperfine as a manufacturer and exiting with this error. Can you please share the script you used to analyze hyperfine images starting from conversion till the end with me? Best Fatima Get Outlook for Android <https://secure-web.cisco.com/16jfFKrMp4E5uGCHCwQmLcL0M2XuJLc2D1i3F2Ezs1kUcA…>

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Password for extracting VM files
by TISSOT Ugo (NCPS) 29 Aug '23

29 Aug '23

External Email - Use Caution Hello, I am going through the installation of Freesurfer with VM and Ubuntu, could you provide me the password needed to finish it? Best regards, U.T

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[FreeSurfer] ValueError axes don't match array
by Cerri, Stefano,PHD 29 Aug '23

29 Aug '23

External Email - Use Caution Hi Krystal, Can you send your samseg command and the output of mri_info on both the T1 and coregistered FLAIR images? It seems that the two images have different image sizes. Stefano Subject: [Freesurfer] [FreeSurfer] ValueError axes don't match array Date: Tue, 22 Aug 2023 04:22:09 +0000 From: Krystal Xiwing Yau <krystaly(a)hku.hk><mailto:krystaly@hku.hk> 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> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> External Email - Use Caution Dear FreeSurfer experts, I have completed the processes of coregistration of FLAIR to T1 image for the subject. As I ran samseg with lesion contrast, the following error message occurred: writing template transform to /home/admin1/freesurfer/subjects/103_samsegOutput/template.lta writing talairach transform to /home/admin1/freesurfer/subjects/103_samsegOutput/samseg.talairach.lta atlas registration complete: 0:00:17.614971 /home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/_asarray.py:83: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray return array(a, dtype, copy=False, order=order) Traceback (most recent call last): File "/home/admin1/freesurfer/python/scripts/run_samseg", line 190, in <module> _, _, _, optimizationSummary = samseg.segment( File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 255, in segment self.preProcess() File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 318, in preProcess self.imageBuffers, self.transform, self.voxelSpacing, self.cropping = readCroppedImages( File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/SamsegUtility.py", line 139, in readCroppedImages croppedImageBuffers = np.transpose(croppedImageBuffers, axes=[1, 2, 3, 0]) File "<__array_function__ internals>", line 5, in transpose File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 653, in transpose return _wrapfunc(a, 'transpose', axes) File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 55, in _wrapfunc return _wrapit(obj, method, *args, **kwds) File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 44, in _wrapit result = getattr(asarray(obj), method)(*args, **kwds) ValueError: axes don't match array Would somebody be kindly advise? Thank you. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Freesurfer Windows instalation
by Dominika Życka 29 Aug '23

29 Aug '23

External Email - Use Caution Hi, I'm having trouble installing Freesurfer on Windows. I want to use Virtual Machine to open FS_7_2_0_Ubuntu_18_04_06.ova.7z file. Could I get the password for this file please? Freesurfer would be very useful in my research on the analysis of brain symmetry in neurodegenerative and neuropsychiatric diseases. Best regards, Dominika Życka-Malesa Warsaw University of Technology, Faculty of Mathematics and Information Science

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Cerebellum ROI
by Gomar, Jesus 28 Aug '23

28 Aug '23

External Email - Use Caution Hello Freesurfer developers, I want to create a ROI in fsaverage space including only certain regions of the cerebellum cortex. Is it possible to use/extract the labels from the "# Cerebellar parcellation labels from SUIT" or "# Cerebellar lobule parcellations" in the FreeSurferColorLUT color table file? - FreeSurfer version freesurfer-linux-centos6_x86_64-7.2.0.tar.gz - Platform CentOS 6 x86_64 (64b) - Ubuntu 18.04.6 LTS I would appreciate any advice on how to proceed to achieve this. Thank you! Jesus The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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CSF map
by Michael Mc Laughlin 28 Aug '23

28 Aug '23

External Email - Use Caution Hi, recon-all does not seem to produce a map of CSF. My research is especially interested in how CSF is distributed. Is there a way to get this? Michael McLaughlin,

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