8 Nov
2022
8 Nov
'22
9:05 a.m.
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 dgreve@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] <https://secure-web.cisco.com/1tiBTDSIKHZAXAscmH9db6FcWDLKketTuenGCyVr66eBXV16Mate9HFQHUFTQl-RGwoc3mWv18rSDW-_h9WiyLNm0VI6gdw6hTp9A6HenEdskg2yZTa4Drf9UwpdZRpKG3vQeNej7woabPTzDnIJGq3rr8H6HQC7r4xGP4RHCSYbtBgdMK81X2ezz2ii3PbQxD2xq4xZipLCQgEb8bogP2zBcllb2L7mSD-PTSvPlfR4405F_kbUODeCRiAN3dRQDz5HQTWnBrl04qcEGR1q4pLHpul0hbmN4tUvOZx2vnBXqQLf4tkK2P2SghJ6g1tTRTw9FOXH5nBifIBMNCuSNMw/https%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> 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_1014Compile 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? 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