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banikr2@banikr:~$ bash banikr2@banikr:~$ export FREESURFER_HOME=/usr/local/freesurfer banikr2@banikr:~$ source SFREESURFER_HOME/SetUpFreeSurfer.sh
bash: SFREESURFER_HOME/SetUpFreeSurfer.sh: No such file or directory
Instead, I changed the command as: banikr2@banikr:~$ source /usr/local/freesurfer/SetUpFreeSurfer.sh
gives the following: banikr2@banikr:~$ source /usr/local/freesurfer/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl
How do I check the installation is done properly? FYI, I have used mri_convert from python script.
Rana Banik
________________________________ From: fsbuild fsbuild@contbay.com Sent: Thursday, September 23, 2021 4:11 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Banik, Rana rana.banik@vanderbilt.edu Subject: Re: [Freesurfer] freesurfer running error at start
OK, then try setting FREESURFER_HOME and setting the environment in a terminal window with the commands,
$ bash $ export FREESURFER_HOME=/usr/local/freesurfer $ source $FREESURFER_HOME/SetUpFreeSurfer.sh
Then you should see what the output reports for the freesurfer version.
- R.
On Sep 23, 2021, at 15:30, Banik, Rana rana.banik@vanderbilt.edu wrote:
External Email - Use Caution External Email - Use Caution Hello,
There is no directory called /7.2.0 rather the directory i am finding the files is: <pre><font color="#8AE234"><b>banikr2@banikr</b></font>:<font color="#729FCF"><b>/usr/local/freesurfer</b></font>$ pwd /usr/local/freesurfer </pre>
Trying the same in the /freesurfer folder
Rana Banik
________________________________ From: fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: Wednesday, September 22, 2021 7:11 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Banik, Rana <rana.banik@vanderbilt.edumailto:rana.banik@vanderbilt.edu> Subject: Re: [Freesurfer] freesurfer running error at start
Hello Rana,
Running that script (or any other freesurfer commands/binaries) assumes you’ve setup the freesurfer environment by,
1) setting FREESURFER_HOME in your shell to point to the top of the freesurfer tree 2) source’ing a shell init file to set PATH and other environment variables in order to run freesurfer commands
There is info on the wiki about this for linux, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linuxhttps://secure-web.cisco.com/1QpMzTE-zbTJySwlKQDL7mcidRtrzPrB1dj-S_gaiJUCK1Qts1yFn3wS1JHfp-BMtzwmheGnhdNAfQ-tOLvXoY38yUeuZ1E-RhSgbLmLlGZ7emCxg__V-GmDhB8kzAKCClDgsT5Rhx-hjx_T7hmNhE4sGHCj_WX2NzPeQIwx3V6N6c3JWv2z889Z6wZQYK7GLpGQKUbOBGQjOdYUSzOk5RlDjevBWXOF-AfJILXbZHSpbQQGSQPM8NlCNKDCw54L3BC3S_IyuACcJV13owB9yvA/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1KblWUQeIgtfi1xhoULwyKCDGOenXqp5DpmlkzMyJfl3V0JCE2Sv57wq-9_iz9XTRQoWLrYwUI2krh4bwn6qNXLotogbez_tP0_xGU3wCmu8oSs5rYn8EvwrOHEX9i4CCskwGUsHP2GZgLIYER83dq3dIQ_7n1eYbOwdA3dcG3sfqBkWo2qeQoaMacUhC-x2ZzqLAEMXvYVxMfZGTKA0C5b1JvZwcauWoz8nC1IfDbWAdklE1rcdmus9strhD5tX3IxNeAcM6rek7yYjGp97IdA%252Fhttps%25253A%25252F%25252Fnam04.safelinks.protection..outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsurfer.nmr.mgh.harvard.edu%2525252Ffswiki%2525252FSetupConfiguration_Linux%252526data%25253D04%2525257C01%2525257Crana.banik%25252540vanderbilt.edu%2525257C0cfd7b6cc7a04ed9835a08d97e26a795%2525257Cba5a7f39e3be4ab3b45067fa80faecad%2525257C0%2525257C0%2525257C637679526782697368%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253DBcgBWXfSIWw6CibO415nuDyPG%2525252BTDUgGZfTNDVnl%2525252BhWY%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Crana.banik%2540vanderbilt.edu%257C50046ea887e84cb636e708d97ed6be64%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C637680283056168653%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3Dr8hkYjWjHqu%252FZbGoS1nQbsOSqdCD0fyqSG64xPTzmOI%253D%26reserved%3D0 - and the Mac, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Machttps://secure-web.cisco.com/15FASmMoxhLV_e7BQhp6qh-mhqDvPeoaykCLqu3M6pCdtIm1id5UfWpeZOgzt8kMpKV5jSDVH7a1gOgiKSGuuKapAsk1D_c8yfYapI9s2ao5AyvPxNjo4Zxqphj6NoG_YA1OU7q-2qyhafR27_XG7501800kdasNy3omnS1X-EO_76QZECBeIc4m9jwRHU0juDqD5ATAulDyFvPV0gzXg7MwK2_NUGnxTYtrEYbxUQ2GlhDakIFwaNtFoecKuFgXyijNfpiK4OjFframLr2Msug/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F11428f2JP4hBcdrc21932t8Wfe7tg3j1G0E_O43MOrZ6Ie-tkQbiBJu3nwXsq77l8xjAdclAxmLiI89y9UvWFUEX1zzrs2zRToneWE0nD7WOMckmF2MuqXNs4mRQHAF_pqFdqMF87yDDz2JdwPf6hMBfzRF89W0if3GBd8vEz3IC_HxDDIaGYOiMIpFynxpRyDhaghdkP_thbyTpEAuSKOOMoGBxtrdsIR3mKO_0m04Yuni8SH0IezEvEKtwW7c4--28_gwq_iWx51MvL0pGMjQ%252Fhttps%25253A%25252F%25252Fnam04.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsurfer.nmr.mgh.harvard.edu%2525252Ffswiki%2525252FSetupConfiguration_Mac%252526data%25253D04%2525257C01%2525257Crana.banik%25252540vanderbilt.edu%2525257C0cfd7b6cc7a04ed9835a08d97e26a795%2525257Cba5a7f39e3be4ab3b45067fa80faecad%2525257C0%2525257C0%2525257C637679526782707362%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253DzQRsG%2525252Bk%2525252BjuVtPww5ZJNpNrMwytbdI7fbaFmwKgbmT8s%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Crana.banik%2540vanderbilt.edu%257C50046ea887e84cb636e708d97ed6be64%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C637680283056178648%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DNSupG0lXaOaF1jWXdWmxLbCJkSbmZMGMaOY5qGLICxE%253D%26reserved%3D0
Just find the absolute path to the top of the freesurfer tree. For the latest 7.2.0 release installed by the package installers the version number is already in the absolute pathname to the top of the freesurfer tree. On linux that path would be /usr/local/freesurfer/7.2.0 and on the Mac that path would be /Applications/freesurfer/7.2.0
For that linux path using bash you would do, $ bash $ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh
When you run the source command to read the SetUpFreeSurfer script for the shell you are using, the version of freesurfer will get printed out automatically for you.
Using the 7.2.0 linux release you would see the string between the dashes no matter what the absolute path is to FREESURFER_HOME on your system.
tmp$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0 tmp$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.2.0 FSFAST_HOME /usr/local/freesurfer/7.2.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.2.0/subjects MNI_DIR /usr/local/freesurfer/7.2.0/mni FSL_DIR /usr/pubsw/packages/fsl/current
… now run any freesurfer commands …
- R
On Sep 22, 2021, at 18:04, Banik, Rana <rana.banik@vanderbilt.edumailto:rana.banik@vanderbilt.edu> wrote:
External Email - Use Caution External Email - Use Caution Running freesurfer from terminal with the following error:
banikr2@banikr:~/freesurfer/bin$ ./freesurfer
FreeSurfer is a set of tools for the analysis and visualization of structural and functional brain imaging data. FreeSurfer also refers to the structural imaging stream within the FreeSurfer suite.
Users should consult the online documentation available at:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/12UDOTlI6dR37bcxQD5lqYyEvMSy7IWMpCC-vJxFNOPLinHZ...https://secure-web.cisco.com/18r-5uzSeUXixzMzXBm46xXTTG8Wne1lcPqbqsOtW9pi_0MZjFzbe0lbS8oRrwmAkC3Zgf4CLuxC5pbpUNYqan85aOK-fsIj12c-T8AfmK_Bode9MRF1IK2nFrw39Xd640zhddv5TbEXFJ7Ba0yK-D8-UsqDT5q-t21xdmUwsYvK9uEoNXpZQ9HkpCO_CW8kP6mNt11LtZwHGCgDJEPO23YdpzwTF30rTGJNtO7DPblQYU95oM1-1c9rY67jnnYegWE0qCusY7diqekLc-ldChw/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsecure-web.cisco.com%252F1UJbCgWACYDBthAI6jH7S1Bh028oqkxPj_kAjfcArRMEL9XdTQrJWRVGYaD-YP90phlRhkdvEWruuJjRqTvFr7_YGJEplmduGyXbv8-dHlSIEZ5uEcqXmrgde7NJA1-YRfI9QcwLPmcrgiIbm-G3SCHVpweaFL6U2OSDbfGfOUxhmDHKuxCKmc-a9EGHs1orfp40TCNCjkJkwZiPPXlaReyk9r4DZHoaZvJHM12No_e9os_Nks5Zte24dupCRL75EQRYPmvfEz2Z9FXSOfrcINw%252Fhttp%25253A%25252F%25252Fsurfer.nmr..mgh.harvard.edu%25252F%26data%3D04%257C01%257Crana.banik%2540vanderbilt.edu%257C50046ea887e84cb636e708d97ed6be64%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C637680283056188642%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DasHDAHERzbwUvVNPz2XaxqGO2wHo4909THwD%252BpeFyVQ%253D%26reserved%3D0
Alternatively, the 'recon-all' command help-text provides adequate information to begin processing subject data, such as the sample subject 'bert' found in the 'freesurfer/subjects' directory. Type 'recon-all --help' to view this help-text.
Direct comments and questions to:
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
You are running this version of FreeSurfer:
cat: /build-stamp.txt: No such file or directory
Any idea what went wrong or how to fix it?
Rana Banik Graduate Student Dept. of Biomedical Engineeringhttps://secure-web.cisco.com/1KvOwEKpd5-nNjouebIoP0BRCrUz3Om6nXI8b2258yOnQ5o6Jx7GzkbV5nEfZJEwOwJdRdNV2Nf4d6seJygNetzrd2AsRYl2Db8IRewpJte4ctPoWV0SgMO8p9cGav4U-AOxh-SQwUa3Ro-RnAgdviOYs8jcXxZG2gZmJTYUwqrcEco3-tcJG7Lep2Yc7BTdxUNoZDymeVeHftrbh1alUF0nNfgsQl6QiY2aLT8kCpXM/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1pBZ3pA3v8d9GhcP6HtqSTZjrFx9bAoh1Fx1dxAh8cWrAxrzj4NGPPHPIxQDGh7k7ru4ZxMR1ph_Uo-o9sF6jVwpHvcZ-epwqDv3OQ2ta6QfHFsIzcpVTMDi_gFjRXniJAYjvVKOeA8JLZsh70gOoRPuvZ_mPZM_GzS7hsC6zjWjbuuC-NrFiHglAwDQ67wqvU0rjO6i_Ha2d4DPNn_mBT0DppFvOueCEAZkwpooMZzTp1UQtEgmbfNMZiAfKzEFTm9za1C-jM1cAiWitTebpcA%252Fhttps%25253A%25252F%25252Fnam04.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttp%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1mnFKS89MuxjwbZ1ZAVLbv3eHsE5vP1Y9jtNdbNSu_AKnZkEGcntBGDzxfI-Fac9oyZ-XbHBwFKS3F7kFv-aDWQU1Nj1_6IELq89g9vnvuVqOLjyFoL1o2vTYV_UafHuFeW0USzSOcWs_4Puc-5COLhSOYTWFnMW76Oekoz959vwrgJ0BO6yA3Q1K7snEVEZHT3fGti4i206VtFOLnr2I13fRkoJmsAOVDstFLh6r1eN5mGzsZ4tEuoVNpIXsRSj4ayPiFl41r2RIpVdWTtIzlQ%2525252Fhttp%252525253A%252525252F%252525252Fengineering.vanderbilt.edu%252525252F%252525252Fbme%252525252F%252526data%25253D04%2525257C01%2525257Crana.banik%25252540vanderbilt.edu%2525257C0cfd7b6cc7a04ed9835a08d97e26a795%2525257Cba5a7f39e3be4ab3b45067fa80faecad%2525257C0%2525257C0%2525257C637679526782707362%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253DUvv697H7%2525252BKU5y7NlQS3%2525252F%2525252FTB0UolRN26j2f%2525252BDM7FGTaQ%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Crana.banik%2540vanderbilt.edu%257C50046ea887e84cb636e708d97ed6be64%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C637680283056188642%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DTYG3BKvnW2aoKvrfcOatyxzCxhewpluXzkGBfVS792c%253D%26reserved%3D0 Vanderbilt University, Nashville, TNhttps://secure-web.cisco.com/1KW0Jzwtwy9a7NtFzP1PMzDNgIGMYZyGRvsxxz7x01uhffMl7B7uQ8WYpOrx-VxpRE-Z6jE-PG3sRvKX6K_yV_g6FKCzEbdGxmLAoGksFNjHPn6Nyn4stdURQRdHCpSahDvrEdQPg8Nc39IpQlj1A_9DJgqyUR9lPFA1JxS1qpm1JVC31BVsM9JJ7ACxEYpZc63VI7S3q0fPprCS0DDsxtXfxoHr0FBm9x5DWmkkFerNZUcPORPQEYZygMLfL7ATbUi5cJsoUKmqVAeUcSs0RGg/https%3A%2F%2Fnam04.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1-48XpIUib_q8n5CN4eR7isvjRrv8pEXXxHrnYbvVm3bszrtKkVJft5gvEx_zUDEFVeCT0t3OfF3wGl_rzGY30L0HWnfztOPsQr5W0zCBky_b858Frz4NHAoKU_NhYEFu-QWsFnriLr25ePf5VrOlhnS3G8N3oGJUoH7uAVoA2X93BMhYZpOE7Rms5zbH76okwQpfvMX8p07t-0P4C3WOLHxFtNLejCt4SRJQoZKq9bT1lLomeIUNhoj-s0x2S-mFaNZcEGbKHwSdFVzZDrHv5A%252Fhttps%25253A%25252F%25252Fnam04.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1U-E0vf5PSBXqDtW08heNI1y7G84w2rcVKfO_YGMrhuSEJZx9qQbVhexregdDkr5xAWQg992RoROFOy0IZexSEHVsNUdSFIbqOeKZM-_qcAHJyk-6ycNI0XtD16WpAirMSw50xRFK8Z93K1QQzKFxdEhnWB_zO1Ahrr1od5Amxgbwq5VqOblr-cT1_Y8fnhTjU7ebaT6LaJZbRBMTbSOFVeot6Dsi52tm9iRi1TuMejcq5tzUYHlYQRnbNf6rba0BIP6RUbGocs6BcKkhAp1H9Q%2525252Fhttps%252525253A%252525252F%252525252Fwww.vanderbilt.edu%252525252F%252526data%25253D04%2525257C01%2525257Crana.banik%25252540vanderbilt.edu%2525257C0cfd7b6cc7a04ed9835a08d97e26a795%2525257Cba5a7f39e3be4ab3b45067fa80faecad%2525257C0%2525257C0%2525257C637679526782717356%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253D%2525252B1pZSmj7TuoyN7CmE7XzSV2RqqIWecGaxEyKUq3whMg%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Crana.banik%2540vanderbilt.edu%257C50046ea887e84cb636e708d97ed6be64%257Cba5a7f39e3be4ab3b45067fa80faecad%257C0%257C0%257C637680283056198633%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DDSMKBmMhwy49pK8mmxSKWhBK9yAGxllyEFHrK5cRcm0%253D%26reserved%3D0
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