External Email - Use Caution 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 Freesurfer v7.3.2 [secure-web.cisco.com] > <https://secure-web.cisco.com/1RxY3QLXqeD31630faIKfjDR5-JIonSY8mQxDWzEe01qo24BL7BPzpZPmDA36tKFOVjIm1HjA8Ob-v8lfe5qpCgnSp9Cto6QAuPBJtFLiK0gtNkjLcYupf-cXT1IYY2CUbysB5ktptk61bq1rloueIou0lTb8JYz-N2mdZwNvXM1YxpqLn6VWpgKPI0MqxPaAZmhe41bSjiHGntbjvuVCsp8z4Q4rL7VCcTOiiQtpS5dA1H6T5G0r5_W-iwTDVVU84d1l6BuQM8y9bmWey8twbB8PS9X9SDChlYXE7MxVogszKISXl4xsK7i0HJodBQ_u/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1VuI2ndzXo5YBm-YeBraBeuWIVo2R7T-txZ30nSNYbmoPIkZ_3efq7PwRz6v6fLQ1pJlC62uAiZWEhoVn6TIP5AOC-fROlzfAXjpzBrhxOHTJD623bsr4Uy1g1CNJIrppL4ErFgccvgKfYMUKMpd1Mtd9LphNF1EzivYUbHHkO5us06GaXqFoIK58GT34oOb05UlLsCY5E80ZYb2YF4T_bzqK8EvCRd7mqezBcB5HNN58i32ZQ7Sv2U1pw14I7geTK0HBpESKhWXaMDpJFIFscIMo-OCdvDuTRDYPbzNlqEox4UsLm-KEODc30uQFKUqGrzBIaypcrdAH_0Mt2YFzSg%2Fhttps*3A*2F*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2F*2FFS7_mac__;JSUlJSUl!!K-Hz7m0Vt54!nIO2Gt4p5_-GhOMJr2b5x3BkM9lGBHt3ri7BqYm_wNV3BkjUoH3mvyEXKBHgo8R63ohGTDOQvlq8fbb4LBG7$> > onto my local drive and am attempting to run preprocessing through FSFAST. > I wasn't able to get access to the .tar.gz Darwin file but downloaded > Xquartz, Freesurfer, FSL, and Matlab individually and was able to source > Freesurfer using the following commands: > > export FREESURFER_HOME=/Applications/freesurfer/7.3.2 > > export > PROJECT_DIR=/Users/angelafang/Library/CloudStorage/OneDrive-UW/VicExt > > export SUBJECTS_DIR=$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.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > [mail.nmr.mgh.harvard.edu] > <https://secure-web.cisco.com/1MmcjuSnuyWjg-dYqgkMfVF6Ry_iivvRGHfcACdangA1md4Kv0EiQdK-ZuTtApT-mlb6M_FKOUTEQKpakXX2_rq1EQ5nQsRM2J5Bd8EQtKroVKPSHSUa7kTIw6AmrlAmrnaqd-QQJpluRziAqzYqyx-6JSz9VOjbN4X5MpjpNTrQ_mFafmHegzThBZ_qJbOv5So3L6l-7T4lLKz3F0ai_Q3vPPTL_vl_RzMysXKtWN1TUY9Uxtt1cYxxu8FKsQcsJMoksxFq08m1CsRbjcrR_8gh9duPgwWCdpUxm3NNErV5teVhaJSIYRV-A7W8VRNhZ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!K-Hz7m0Vt54!nIO2Gt4p5_-GhOMJr2b5x3BkM9lGBHt3ri7BqYm_wNV3BkjUoH3mvyEXKBHgo8R63ohGTDOQvlq8fWq2p6qF$> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > https://secure-web.cisco.com/1MmcjuSnuyWjg-dYqgkMfVF6Ry_iivvRGHfcACdangA1md4Kv0EiQdK-ZuTtApT-mlb6M_FKOUTEQKpakXX2_rq1EQ5nQsRM2J5Bd8EQtKroVKPSHSUa7kTIw6AmrlAmrnaqd-QQJpluRziAqzYqyx-6JSz9VOjbN4X5MpjpNTrQ_mFafmHegzThBZ_qJbOv5So3L6l-7T4lLKz3F0ai_Q3vPPTL_vl_RzMysXKtWN1TUY9Uxtt1cYxxu8FKsQcsJMoksxFq08m1CsRbjcrR_8gh9duPgwWCdpUxm3NNErV5teVhaJSIYRV-A7W8VRNhZ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!K-Hz7m0Vt54!nIO2Gt4p5_-GhOMJr2b5x3BkM9lGBHt3ri7BqYm_wNV3BkjUoH3mvyEXKBHgo8R63ohGTDOQvlq8fWq2p6qF$ > > The information in this e-mail is intended only for the person to whom it > is addressed. 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