External Email - Use Caution Thank you Paul for your help!
This seems to have solved the issue, as I can now run the command fs_install_mcr R2019b. It has ended successfully with this end message stated below: mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to '/usr/local/freesurfer/7.3.2/MCRv97': Permission denied I think this problem persists with my next issue, which is using the command segmentHA_T1.sh. When I try to run this command again it gives me the following error: ERROR: cannot find Matlab 2019b runtime in location: /usr/local/freesurfer/7.3.2/MCRv97 It is looking for either: bin/glnxa64/libmwlaunchermain.so (Linux 64b) or bin/maci64/libmwlaunchermain.dylib (Mac 64b) The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime. You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b. To do so, please run the following command (you might need root permissions): fs_install_mcr R2019b I have seen that the pathway for fs_install_mcr is located in the usr/local/freesurfer/7.3.2 instead of in the location stated in the error above. When I try to search this location there is no such existing directory. This can be the same for bin/glnxa64/libmwlaunchermain.so. Do I need to create a new file for where the runtime should be stored? Or create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should the fs_installl_mcr R2019b be stored under bin for this command to work? Hope you can continue to help me with my follow-up issue, I appreciate it a lot. Thank you so much. Sincerely, Justina On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul <pwigh...@mgh.harvard.edu> wrote: > Hi Justina, > > It looks like the matlab installer is trying to use unzip but it can't > find it. > > Can you try running: > `sudo apt-get install unzip` > > To install unzip then try the matlab installer again? > > -Paul > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of You Na Lee < > justinale...@gmail.com> > *Sent:* Tuesday, September 13, 2022 9:01 AM > *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> > *Subject:* [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not > found > > > External Email - Use Caution > > To whom it may concern, > > > > Apologies for my first post, I was a little bit confounded as to how I can > reach for help. > > I would like to use the segmentation of hippocampal subfields and the > nuclei of the amygdala. > Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2. > > > I am trying to install MATLAB Runtime 2019b to run the command > segmentHA_T1.sh for the segmentation as described above. The following > command shows the corresponding error: > > > > ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr > R2019b > > % Total % Received % Xferd Average Speed Time Time Time > Current > > Dload Upload Total Spent Left > Speed > > 100 2657M 100 2657M 0 0 10.0M 0 0:04:25 0:04:25 --:--:-- > 10.1M > > /usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command > not found > > > > I am currently struggling to find the solution to this issue. Is the > installation not in the correct path? Is MATLAB Runtime installed at all? > Should an already existing matlab file be deleted? > Any help would be much appreciated. > > > > Sincerely, > > Justina > > > > > > > > Sent from Mail > <https://secure-web.cisco.com/1JF-rDYMVgKJTrVPsWHUacVbsZGxWoxGE8qofNJGanBLzB5H4xG_TSIyr-kKCyfB-OL5ahOLtropBWGT0WNStX9nlY96XmLI4PEcLyxRbpYACqwCkjWGnJ97rPRssexnOq1RJRlrOg_69B_HLSu5yX5bgMIHOh0IfF9pQcTT3TVu3DK8hZxWZSK0gfICgCNrQacXt91cfezI3FeQnjTGxoKqOqzHBsXJaNuI8JxuVMfCrweNj79o9pN5_cVgjrPSCSa5uR_IxkKANQ87K9laDUXpbpf1YpKyxu3k05hdqJLTPSgkt-wfEOgojaS7t3BsJWoxyJ2fHAPhk2SP958H0aA/https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986> > for Windows > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/13hztnzjV4NG8MRS_WPAvkQDaoH3MtDTzQGVDegG1V9tB3vNAeQxThejPX_wGtCRjJ3QWFM_JqnS5VBaOktcLzveKxjIX3MA5p2FjSdBZCoFXLtQ8Z1KyKvtTr-aGSjUmS03KRcPg02rCBvEhWmoJbDCQsf8zWfExuxR-u4fl-PYnkCrPWM9hUnmXrZd2WEFL8AmEvxNDuEdQuaMSEDPGPtvx0RN5AfCTFUb79CJ6vuveAr1iWf0-gU3NHQNZ1vKIkflLgYP8q2yBFTSLhEcUy23TWxVYYoANhKGSeUYuR2Lsdk56Uy1D8vvtTbV9Gc1XKCXLh1Ig_3pL6k_OJiakhw/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. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1uh4d7COjqc1bVLQiDQ6jL1-x2Cu8sxhgIgLz_dog41oDIhM8fTuq3I9l7A0U-S9vXLh2c1HYERWjWRDQ-P2tWah3tgAODl_BVpGrfPQJxSZ8b8tp7bvDrlIRPyYHe8ECeQXKKqR7HYYpsuj0W_eRlliRf3RLFliUMla_Vy1nvCsCWKN59zIJU6vuMQBLr4CA59yuzbdUHZILOlvkicohmO7PykYU9hr5BSqesguhC_1lxDY8I9qdnTi5s4tCkXPSfFtbxb55fm4pVQZ0nnJA_KXGIZRe3MPUbu14WNhHM4FWqJ1XnV2IAma2oaH_RGZ6gdRtBIUdPiGIAx6gluvoiQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1uh4d7COjqc1bVLQiDQ6jL1-x2Cu8sxhgIgLz_dog41oDIhM8fTuq3I9l7A0U-S9vXLh2c1HYERWjWRDQ-P2tWah3tgAODl_BVpGrfPQJxSZ8b8tp7bvDrlIRPyYHe8ECeQXKKqR7HYYpsuj0W_eRlliRf3RLFliUMla_Vy1nvCsCWKN59zIJU6vuMQBLr4CA59yuzbdUHZILOlvkicohmO7PykYU9hr5BSqesguhC_1lxDY8I9qdnTi5s4tCkXPSfFtbxb55fm4pVQZ0nnJA_KXGIZRe3MPUbu14WNhHM4FWqJ1XnV2IAma2oaH_RGZ6gdRtBIUdPiGIAx6gluvoiQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
