External Email - Use Caution
Hello FreeSurfer Developers,
I downloaded Freesurfer v7.3.2 https://secure-web.cisco.com/1VuI2ndzXo5YBm-YeBraBeuWIVo2R7T-txZ30nSNYbmoPIkZ_3efq7PwRz6v6fLQ1pJlC62uAiZWEhoVn6TIP5AOC-fROlzfAXjpzBrhxOHTJD623bsr4Uy1g1CNJIrppL4ErFgccvgKfYMUKMpd1Mtd9LphNF1EzivYUbHHkO5us06GaXqFoIK58GT34oOb05UlLsCY5E80ZYb2YF4T_bzqK8EvCRd7mqezBcB5HNN58i32ZQ7Sv2U1pw14I7geTK0HBpESKhWXaMDpJFIFscIMo-OCdvDuTRDYPbzNlqEox4UsLm-KEODc30uQFKUqGrzBIaypcrdAH_0Mt2YFzSg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2F%2FFS7_mac 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
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 https://secure-web.cisco.com/1VuI2ndzXo5YBm-YeBraBeuWIVo2R7T-txZ30nSNYbmoPIkZ_3efq7PwRz6v6fLQ1pJlC62uAiZWEhoVn6TIP5AOC-fROlzfAXjpzBrhxOHTJD623bsr4Uy1g1CNJIrppL4ErFgccvgKfYMUKMpd1Mtd9LphNF1EzivYUbHHkO5us06GaXqFoIK58GT34oOb05UlLsCY5E80ZYb2YF4T_bzqK8EvCRd7mqezBcB5HNN58i32ZQ7Sv2U1pw14I7geTK0HBpESKhWXaMDpJFIFscIMo-OCdvDuTRDYPbzNlqEox4UsLm-KEODc30uQFKUqGrzBIaypcrdAH_0Mt2YFzSg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2F%2FFS7_mac 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?
Best,
Gillian Grennan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 CautionHello 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 $FREESURFER_HOME/SetUpFreeSurfer.sh
However, when I run preproc-sess in my analysis folder I get the following error:
command: preproc-sess -sf subjectlist -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
error message:
++ Initializing alignment base
Choleski factorization failure in startup_lsqfit
mri_startup_lsqfit: bad call to startup_lsqfit!
++ Starting final pass on 44 sub-bricks: 0
Fatal Signal 11 (SIGSEGV) received
mri_3dalign_one
3dvolreg main
Bottom of Debug Stack
** AFNI version = AFNI_2011_12_21_1014 Compile date = May 22 2013
** [[Precompiled binary macosx_10.7_Intel_64: May 22 2013]]
** Program Abort **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
ERROR: 3dvolreg.afni
Invalid null command.
I'm confused on what more I need to install? Is there a way I can get an updated link to the tar file with the relevant software packages needed to run FSFAST?
Best,
Gillian Grennan
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [mail.nmr.mgh.harvard.edu] https://secure-web.cisco.com/1MmcjuSnuyWjg-dYqgkMfVF6Ry_iivvRGHfcACdangA1md4Kv0EiQdK-ZuTtApT-mlb6M_FKOUTEQKpakXX2_rq1EQ5nQsRM2J5Bd8EQtKroVKPSHSUa7kTIw6AmrlAmrnaqd-QQJpluRziAqzYqyx-6JSz9VOjbN4X5MpjpNTrQ_mFafmHegzThBZ_qJbOv5So3L6l-7T4lLKz3F0ai_Q3vPPTL_vl_RzMysXKtWN1TUY9Uxtt1cYxxu8FKsQcsJMoksxFq08m1CsRbjcrR_8gh9duPgwWCdpUxm3NNErV5teVhaJSIYRV-A7W8VRNhZ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!K-Hz7m0Vt54!nIO2Gt4p5_-GhOMJr2b5x3BkM9lGBHt3ri7BqYm_wNV3BkjUoH3mvyEXKBHgo8R63ohGTDOQvlq8fWq2p6qF$
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1MmcjuSnuyWjg-dYqgkMfVF6Ry_iivvRGHfcACdangA1md4...
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/1nX9Atr8opBURNj4AxSIg54jIsVZn6MU1XP6nquHt7oAyhf... < https://secure-web.cisco.com/1nX9Atr8opBURNj4AxSIg54jIsVZn6MU1XP6nquHt7oAyhf...
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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 CautionHello FreeSurfer Developers,
I downloaded Freesurfer v7.3.2 [secure-web.cisco.com] https://secure-web.cisco.com/1Zikia0wMui-E-bXqHSlstSpucl0siIeg4TUfQXeSW74mIGQxO55S9jTAbZB8g0PY30XHMe7FxMrCF7KODq_ecM1FnE0DqxST9XupbbGwtQIg7G99DEtHVk847n6Whqlv6nGq6Q62plx0CgYb0gAcKocWpRNeN9nF9bPLdwsamChq8y12HxVPtSEwtttnNZy4v7K2lQkh7PDOMc8swQa_dWOb-REcJD-azXy6s6CF4gmvirxB3sFIhli8ZTYusUJzhQemp652GcH0Tobhjt5J6QCYrZMr-FlV9WUkzA3h9-RBLk-HOxpv_9fc6DndfhqT6jmsekZKrPtDpKhmcd6p0A/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 $FREESURFER_HOME/SetUpFreeSurfer.sh
However, when I run preproc-sess in my analysis folder I get the following error:
command: preproc-sess -sf subjectlist -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
error message:
++ Initializing alignment base
Choleski factorization failure in startup_lsqfit
mri_startup_lsqfit: bad call to startup_lsqfit!
++ Starting final pass on 44 sub-bricks: 0
Fatal Signal 11 (SIGSEGV) received
mri_3dalign_one
3dvolreg main
Bottom of Debug Stack
** AFNI version = AFNI_2011_12_21_1014 Compile date = May 22 2013
** [[Precompiled binary macosx_10.7_Intel_64: May 22 2013]]
** Program Abort **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
ERROR: 3dvolreg.afni
Invalid null command.
I'm confused on what more I need to install? Is there a way I can get an updated link to the tar file with the relevant software packages needed to run FSFAST?
Best,
Gillian Grennan
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [mail.nmr.mgh.harvard.edu] https://secure-web.cisco.com/1xPU7S-1-h-iU2VhV1pzN1NG1Kjsc4DUVpfONOxBFil9Fb0OlhXFo7X7EE8AD0sByR4pLznS5a6jriiXMLVcsKH53JagSRcvff-D9_9n2TMhbhk0rvX9_is_fItzf_WAaTPKIMtt4D7XIkmro47kHRpQq_KV9a3Kdgq-vRAEzwledLHCwJOZHOQQAnXiMsod2d0p5rYPeT9gKycqN2wVSPwTa6-lp689a0CxUMHfDSr66gYYudANjL1nWFu732Hn5_tixklA1WMT6QHuDoWiEhvwTVZvmBBXRjWYblgQdfyaCo7QTFf1aW5_57TFcFIKy-KYNzS8aVdwSddLVis6Jgw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!K-Hz7m0Vt54!nIO2Gt4p5_-GhOMJr2b5x3BkM9lGBHt3ri7BqYm_wNV3BkjUoH3mvyEXKBHgo8R63ohGTDOQvlq8fWq2p6qF$
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1xPU7S-1-h-iU2VhV1pzN1NG1Kjsc4DUVpfONOxBFil9Fb0...
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/1-mjhpjxL0IrC0QHcclHPrYpN7M015xAI1RUWMF3N0eltH7... < https://secure-web.cisco.com/1-mjhpjxL0IrC0QHcclHPrYpN7M015xAI1RUWMF3N0eltH7...
.
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.
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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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 dgreve@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 CautionRealized 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 CautionHello 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
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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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/18bjuqOiCDledPaxho4FWso9y4OnPLmoIzWfUoVjsFB8cBe... [secure-web.cisco.com] https://secure-web.cisco.com/1RqyJHD4CBOQCWA6rEcAhrAL9OeRFuYHHMm7UcDMrfVz3l0VG3BSlzuoJhcLZqbjG5C6bMyHEDjzFL_X8dT58CGhdPdljD5xZLP3GkIdMKSGzQPGF-yFATo2RwcMVI3hXKt3QdFbRqOdd6NrTISK9UCg-BTSfy7Zjri7UeUDEbLrurRVGYfn0SUbOoWx6pfeSdSFvewgMsXvt_jEALrbfc3haVxOBngjBGk33SecjnpO-8mrkuvs3UZw4zpYRSh6nGQABzNepzjDcNb2BaTg6TirFVSIktJ0qhmLZ6UdgFqbzOA67Pa1nIR2P5tKExXol/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1bzOu3GuoaH307hKuUziaeyLcVHv5BNdAkrpnKtxOa91WiiYjVHjkPhPLUdmbY7g8xADTVEAvmUZYyVhlNOc7WBr6zZ1Z6w9kWTkQRMzKImgk5cGGIPXJpOii5YMdByAHISJKPqONZfNcMqEXe_3BA8o9NtUeCwlDSVfqrLSo1OreCUKUsOhH4P297rUqtJ9Ow1aaaNgM3jwutinsfLMOq8gA_NSw4hpTJjAqEvAVJsSb43F7IYzR-tJAmQWYzLDNDOjE14at5w0DwwrL_--HKZV4pVc8PcmRp9uZSvuKjf-aIiNpVDlulcVGi1rPH6PqxGRWM_8l_Iy5IgrIIi_UWw%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fwww.massgeneralbrigham.org*2Fcomplianceline__*3B*21*21K-Hz7m0Vt54*21nIO2Gt4p5_-GhOMJr2b5x3BkM9lGBHt3ri7BqYm_wNV3BkjUoH3mvyEXKBHgo8R63ohGTDOQvlq8fRC69JhP*24__;JSUlJSUlJSUlJSUlJSU!!K-Hz7m0Vt54!jdx3deeQPTiH3g4gfQ6xZtDZHK25WDb3yuWJ8CjE-CGsmFJMXtc4M4VAArIYAXD5tc6e1pzIkKep1GsATzbG$ <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/18bjuqOiCDledPaxho4FWso9y4OnPLmoIzWfUoVjsFB8cBe... [secure-web.cisco.com] https://secure-web.cisco.com/1RqyJHD4CBOQCWA6rEcAhrAL9OeRFuYHHMm7UcDMrfVz3l0VG3BSlzuoJhcLZqbjG5C6bMyHEDjzFL_X8dT58CGhdPdljD5xZLP3GkIdMKSGzQPGF-yFATo2RwcMVI3hXKt3QdFbRqOdd6NrTISK9UCg-BTSfy7Zjri7UeUDEbLrurRVGYfn0SUbOoWx6pfeSdSFvewgMsXvt_jEALrbfc3haVxOBngjBGk33SecjnpO-8mrkuvs3UZw4zpYRSh6nGQABzNepzjDcNb2BaTg6TirFVSIktJ0qhmLZ6UdgFqbzOA67Pa1nIR2P5tKExXol/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1bzOu3GuoaH307hKuUziaeyLcVHv5BNdAkrpnKtxOa91WiiYjVHjkPhPLUdmbY7g8xADTVEAvmUZYyVhlNOc7WBr6zZ1Z6w9kWTkQRMzKImgk5cGGIPXJpOii5YMdByAHISJKPqONZfNcMqEXe_3BA8o9NtUeCwlDSVfqrLSo1OreCUKUsOhH4P297rUqtJ9Ow1aaaNgM3jwutinsfLMOq8gA_NSw4hpTJjAqEvAVJsSb43F7IYzR-tJAmQWYzLDNDOjE14at5w0DwwrL_--HKZV4pVc8PcmRp9uZSvuKjf-aIiNpVDlulcVGi1rPH6PqxGRWM_8l_Iy5IgrIIi_UWw%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fwww.massgeneralbrigham.org*2Fcomplianceline__*3B*21*21K-Hz7m0Vt54*21nIO2Gt4p5_-GhOMJr2b5x3BkM9lGBHt3ri7BqYm_wNV3BkjUoH3mvyEXKBHgo8R63ohGTDOQvlq8fRC69JhP*24__;JSUlJSUlJSUlJSUlJSU!!K-Hz7m0Vt54!jdx3deeQPTiH3g4gfQ6xZtDZHK25WDb3yuWJ8CjE-CGsmFJMXtc4M4VAArIYAXD5tc6e1pzIkKep1GsATzbG$
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