External Email - Use Caution Preproc worked -- it seems it was an issue in setting up my freesurfer set up file!
I am now running into an error with FSFAST functions that require MATLAB. I downloaded MATLAB runtime using the command in freesurfer (fs_install_mcr R2014b) which downloaded the MCRv84 folder in my $FreesurferHome directory. When running mkcontrast, it gives an error that it can't find Matlab. How would I go about adding this MCRv84 to my path? I have seen suggestions to add variables to my startup.m file in the FreesurferHome/matlab folder but there is no startup.m file included there. Thanks for your help! On Tue, Nov 8, 2022 at 6:10 AM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > is it in $FREESURFER/bin ? If so, is that folder in your path? > > On 10/27/2022 12:49 PM, Gillian Grennan wrote: > > External Email - Use Caution > Realized I sent this to the support list not back to you! But it says > "command not found" when I run 3dvolreg and 3dvolreg.afni > > On Wed, Oct 26, 2022 at 7:24 AM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> What happens when your run 3dvolreg.afni by itself (no options) from >> the command line? >> >> On 10/25/2022 4:41 PM, Gillian Grennan wrote: >> >> External Email - Use Caution >> Hello FreeSurfer Developers, >> >> I downloaded *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* Freesurfer v7.3.2 >> [secure-web.cisco.com] [secure-web.cisco.com] >> <https://secure-web.cisco.com/1gcSzm9ul6pzMbqDogW7iZhex-gzF6PII_7-lrbXX9Xgo-cejlx474MxSIgGqBfKepS-wVBsXqoQqkA74k0sPpnc3nkuRCd-dhJ3c-3Ue1xxoAKqZi34YbnlAQP314xp1sbMVKgL2D_gU0ecoT63fB3_GKOSQyXtLcPBDaTWWpWDMBxy45I-zxHLliWJXezDmdjF-H2fCT8fffx5rKxmDlvm-QoCP8hZ6390HBgPVSFA6AXmkmlEh7-yemqPeZsWDA2GSXuW39mnVooiJG0njyNWSkk0uPY6BJFRdGou1oE0vnbY1gHaKsFUn5kRxFFaY/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1tiBTDSIKHZAXAscmH9db6FcWDLKketTuenGCyVr66eBXV16Mate9HFQHUFTQl-RGwoc3mWv18rSDW-_h9WiyLNm0VI6gdw6hTp9A6HenEdskg2yZTa4Drf9UwpdZRpKG3vQeNej7woabPTzDnIJGq3rr8H6HQC7r4xGP4RHCSYbtBgdMK81X2ezz2ii3PbQxD2xq4xZipLCQgEb8bogP2zBcllb2L7mSD-PTSvPlfR4405F_kbUODeCRiAN3dRQDz5HQTWnBrl04qcEGR1q4pLHpul0hbmN4tUvOZx2vnBXqQLf4tkK2P2SghJ6g1tTRTw9FOXH5nBifIBMNCuSNMw%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1VuI2ndzXo5YBm-YeBraBeuWIVo2R7T-txZ30nSNYbmoPIkZ_3efq7PwRz6v6fLQ1pJlC62uAiZWEhoVn6TIP5AOC-fROlzfAXjpzBrhxOHTJD623bsr4Uy1g1CNJIrppL4ErFgccvgKfYMUKMpd1Mtd9LphNF1EzivYUbHHkO5us06GaXqFoIK58GT34oOb05UlLsCY5E80ZYb2YF4T_bzqK8EvCRd7mqezBcB5HNN58i32ZQ7Sv2U1pw14I7geTK0HBpESKhWXaMDpJFIFscIMo-OCdvDuTRDYPbzNlqEox4UsLm-KEODc30uQFKUqGrzBIaypcrdAH_0Mt2YFzSg*2Fhttps*2A3A*2A2F*2A2Fsurfer.nmr.mgh.harvard.edu*2A2Ffswiki*2A2F*2A2FFS7_mac__*3BJSUlJSUl*21*21K-Hz7m0Vt54*21nIO2Gt4p5_-GhOMJr2b5x3BkM9lGBHt3ri7BqYm_wNV3BkjUoH3mvyEXKBHgo8R63ohGTDOQvlq8fbb4LBG7*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!K-Hz7m0Vt54!jdx3deeQPTiH3g4gfQ6xZtDZHK25WDb3yuWJ8CjE-CGsmFJMXtc4M4VAArIYAXD5tc6e1pzIkKep1HUj8O9Z$> >> onto my local drive and am attempting to run preprocessing through FSFAST. >> I wasn't able to get access to the .tar.gz Darwin file but downloaded >> Xquartz, Freesurfer, FSL, and Matlab individually and was able to source >> Freesurfer using the following commands: >> >> export FREESURFER_HOME=/Applications/freesurfer/7.3.2 >> >> export >> PROJECT_DIR=/Users/angelafang/Library/CloudStorage/OneDrive-UW/VicExt >> >> export SUBJECTS_DIR=$PROJECT_DIR/subjects >> >> source $FREESURFER_HOME/SetUpFreeSurfer.sh >> >> >> However, when I run preproc-sess in my analysis folder I get the >> following error: >> >> >> command: preproc-sess -sf subjectlist -fsd bold -stc siemens -surface >> fsaverage lhrh -mni305 -fwhm 5 -per-run >> >> >> error message: >> >> ++ Initializing alignment base >> >> Choleski factorization failure in startup_lsqfit >> >> mri_startup_lsqfit: bad call to startup_lsqfit! >> >> ++ Starting final pass on 44 sub-bricks: 0 >> >> Fatal Signal 11 (SIGSEGV) received >> >> mri_3dalign_one >> >> 3dvolreg main >> >> Bottom of Debug Stack >> >> ** AFNI version = AFNI_2011_12_21_1014 Compile date = May 22 2013 >> >> ** [[Precompiled binary macosx_10.7_Intel_64: May 22 2013]] >> >> ** Program Abort ** >> >> ** If you report this crash to the AFNI message board, >> >> ** please copy the error messages EXACTLY, and give >> >> ** the command line you used to run the program, and >> >> ** any other information needed to repeat the problem. >> >> ** You may later be asked to upload data to help debug. >> >> ERROR: 3dvolreg.afni >> >> Invalid null command. >> >> >> I'm confused on what more I need to install? Is there a way I can get an >> updated link to the tar file with the relevant software packages needed to >> run FSFAST? >> >> >> Best, >> >> Gillian Grennan >> >> _______________________________________________ >> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >> be* >> https://secure-web.cisco.com/1fezVlOH1vEfQRpCaGzis1Z4JVl4MKmN6eznYpU01GXzX-sLDP2bgB4UGslEi1HQ8frNIBMQxYw7GRf3gh2txPC3YMu_5pkYZXFtitZCCfWi9uM4CVDBErdltA1DojGmF1grrOvUGM_pqxAe6onoxltMNqKsr686X9mboEY6i8iQJz1W_KPepyKBuqg9EZyVlJqKLGz93pbcqh6Uu35jOfs1pCpJvfoS2hWpIr6vsKXFeNtzVf_Jo859jAq8zVxcsEH-HJI5fqru5Q2bMyeHH0-NqX39V4dJ2orGsxegyjXLJOhdWU9vLwL3iFfvh4g3C37LkKgBfGgUpcaMBiPkJ1A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> [mail.nmr.mgh.harvard.edu] [secure-web.cisco.com] >> <https://secure-web.cisco.com/1ePZH1FxFYJHegY0TXKrYkxxcv3jfKr1ARF4MtVoBDzqqnMgqYtwI_NAnzwcF1iOgCm3ujorvoRRPmqJVkPBy_xnABhx9eBda6b5-RfmosmlBd1ONv6almEgDTgqVijm-_jv6b59VqmUYCqo0SpdIC-F6kJ_o9bG-CLz8NWBMCqvhk6xMlVrGJ5d5w4j35ptT6du-APqX8oifubbfqmJgHht-C6pW20u7fVDbkrvglr3mFtnlh21cZAscO7AHSDO439woszuHYFGAEt6yUuJbLYGHbgArMIu7brXajT1i_ecQCi8IR-Tc_czNZ9ThfEr3/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1lBs-0duujHytR-P7J8F1m9LSdh6lAryJGNqoqStp94VO1tkK4OiRdP_vnDLJeD4FA0BlJ2-3H16OFX73tAdJgIJeozWp_wen5i8I0yFs9ucaMfsJ9kXqEqcCvDaFWX6iTnVmooCHy2knJatXbSM5GKMUspCVcg6OMvwT5CH0DRvHG1ZzNqPTy1oU699Ww-PQbLQyGYbTCzfjz9Csu2DgaNVZ18gb4NvrE6-wgyoSbYS5qLMZjJPbO-xCy_td_qVpfho_zK-ZOO0nVzd7LuWN9eXySVo2EqoQ1PbycdC9DrAXDl3Nq_8N9ULxjFHgVP68D8WkaaOAgoneIv9eB6rRyw%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21K-Hz7m0Vt54*21nIO2Gt4p5_-GhOMJr2b5x3BkM9lGBHt3ri7BqYm_wNV3BkjUoH3mvyEXKBHgo8R63ohGTDOQvlq8fWq2p6qF*24__;JSUlJSUlJSUlJSUlJSUlJQ!!K-Hz7m0Vt54!jdx3deeQPTiH3g4gfQ6xZtDZHK25WDb3yuWJ8CjE-CGsmFJMXtc4M4VAArIYAXD5tc6e1pzIkKep1JbtykCH$> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1lxMGs-mYr2kpxTYb6zZrsw01q0KwinxK22ey5FPMTypVzRiA5noB8foad1smqw_gJCDcvuvvH_SUc-6OFqS5DOKwN92MNT-XbJFpU1infVA2BWVVTyWt9OfUwUroEoy-Zeh_42K5v8Tt34ACNRHIIWWU2zFW9_WwUjPqlYFeTa-tuBp_ORMNwkF2kTsv9Qtg9Ox2SD_n_AMDajMeO521zEj9zjzC4QGUM_XlahmMf1yksh_wXWQCn3jNFsbSIaRw46BgswuEdouE8hwFuOgJYMP133biqQZdB2SEQGw2VIbRJZlqOhIAhQhoyl9zk4SU/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!K-Hz7m0Vt54!nIO2Gt4p5_-GhOMJr2b5x3BkM9lGBHt3ri7BqYm_wNV3BkjUoH3mvyEXKBHgo8R63ohGTDOQvlq8fWq2p6qF$ >> [secure-web.cisco.com] >> <https://secure-web.cisco.com/1ePZH1FxFYJHegY0TXKrYkxxcv3jfKr1ARF4MtVoBDzqqnMgqYtwI_NAnzwcF1iOgCm3ujorvoRRPmqJVkPBy_xnABhx9eBda6b5-RfmosmlBd1ONv6almEgDTgqVijm-_jv6b59VqmUYCqo0SpdIC-F6kJ_o9bG-CLz8NWBMCqvhk6xMlVrGJ5d5w4j35ptT6du-APqX8oifubbfqmJgHht-C6pW20u7fVDbkrvglr3mFtnlh21cZAscO7AHSDO439woszuHYFGAEt6yUuJbLYGHbgArMIu7brXajT1i_ecQCi8IR-Tc_czNZ9ThfEr3/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1lBs-0duujHytR-P7J8F1m9LSdh6lAryJGNqoqStp94VO1tkK4OiRdP_vnDLJeD4FA0BlJ2-3H16OFX73tAdJgIJeozWp_wen5i8I0yFs9ucaMfsJ9kXqEqcCvDaFWX6iTnVmooCHy2knJatXbSM5GKMUspCVcg6OMvwT5CH0DRvHG1ZzNqPTy1oU699Ww-PQbLQyGYbTCzfjz9Csu2DgaNVZ18gb4NvrE6-wgyoSbYS5qLMZjJPbO-xCy_td_qVpfho_zK-ZOO0nVzd7LuWN9eXySVo2EqoQ1PbycdC9DrAXDl3Nq_8N9ULxjFHgVP68D8WkaaOAgoneIv9eB6rRyw%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21K-Hz7m0Vt54*21nIO2Gt4p5_-GhOMJr2b5x3BkM9lGBHt3ri7BqYm_wNV3BkjUoH3mvyEXKBHgo8R63ohGTDOQvlq8fWq2p6qF*24__;JSUlJSUlJSUlJSUlJSUlJQ!!K-Hz7m0Vt54!jdx3deeQPTiH3g4gfQ6xZtDZHK25WDb3yuWJ8CjE-CGsmFJMXtc4M4VAArIYAXD5tc6e1pzIkKep1JbtykCH$> >> >> The information in this e-mail is intended only for the person to whom it >> is addressed. 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_______________________________________________ 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.
