Freesurfer September 2021

freesurfer@nmr.mgh.harvard.edu

76 participants
107 discussions

Re: [Freesurfer] Freesurfer installation error?
by fsbuild 26 Sep '21

26 Sep '21

External Email - Use Caution It looks like you want to install and run the 7.1.1 release on CentOS6. The fsfast and mni subdirectories are in the distribution, so I am not sure why you are getting that output.  I suggest trying to do a clean install from scratch.  There are a couple of ways to do that, i.e., clean install under /usr/local  and-or  clean install under your home ($HOME) directory.  I will list instructions for both. If you already installed under /usr/local, then you should have sudo/admin privileges to write files there.   A simple way to check that is to try and run a harmless command with sudo, e.g., $ sudo date[sudo] password for <your userid>:       <—— enter your password If your password is accepted then the date command will run and print out the date.  If not,  it will ask you to enter a password again.  If your password does not work then it means you do not have sudo privileges and you won't be able to run the installer.  In that case, hit Ctrl-C to get out of the password prompt and go to INSTALL IN HOME DIRECTORY below.  You should not need any special privileges to write or delete files on your home directory. CLEAN INSTALL IN /USR/LOCAL Only try this if sudo/admin privileges worked above for the command “sudo date”. First make sure you have the “yum” command installed,$ which yum/usr/bin/yum If you don’t have the yum package manager command installed, then stop and go to the instructions for  INSTALL IN HOME DIRECTORY. If you do have the yum command, then make sure you can download the CentOS6 installer.  You can download this directly into your home directory from the terminal, $ cd $HOME … get the 7.1.1 installer for CentOS6 … if wget does not work or you don’t have that command you can use that link in your browser to download it ... $ wget  https://secure-web.cisco.com/1B_8WKZfHlV6TNLk-tm-JksrqbEl40VQhIwjbDLmV-ylwU7XH2EAqoO0Q7d0jXgZYHu0VPnch3AqmZKjSQ0Bmdebm4YLKAOoiZw0fR48S37iQnvyrf2KLOnQUwBsuIUSGrYnPw2U_Wj683TRLq66t6yEJulO5HYRowoqIwKAjgfBMEJzXntKwrgg8YAJ6LjGkScOtif3h6bAalhL6heDeKv7_-zsKJMqdQdWWP4ruGGoDgkL9qlD2oRte-HOYVidpbK6L36OK2J0pnVvwuBGFKA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.1.1%2Ffreesurfer-CentOS6-7.1.1-1.x86_64.rpm … wait for the download to finish via its progress bar and then check you have the complete installer file ... $ sum  freesurfer-CentOS6-7.1.1-1.x86_64.rpm53407 3836829 If you did not get those exact numbers from the output of the checksum command, then re-try your download until you get that result.  If you can’t get the download to work then go to instruction for INSTALL IN HOME DIRECTORY. If the download worked, then remove any existing freesurfer installation under /usr/local $ cd /usr/local$ ls If you do not see a freesurfer subdirectory then skip the next 2 commands (chmod and rm) and proceed to running the installer, $ sudo chmod -R 777 freesurfer$ sudo rm -rf freesurfer Now ls and make sure no freesurfer directory is there, $ ls Now try running the installer from your home directory, $ cd $HOME$ sudo  yum  —nogpgcheck  localinstall   freesurfer-CentOS6-7.1.1-1.x86_64.rpm … answer y (for yes)  to any questions and wait for the install to finish … Now do an ls of the new installation, $ ls /usr/local/freesurfer/7.1.1-1 … and you should see both an fsfast and mni subdirectory there. Try setting the environment again but with FREESURFER_HOME set to the new install path,$ export FREESURFER_HOME=/usr/local/freesurfer/7.1.1-1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh CLEAN INSTALL IN HOME DIRECTORY This should work no matter what is or is not installed under /usr/local. Go to your home directory (always set as the value of the environment variable HOME) $ cd $HOME … get the 7.1.1 tar archive for CentOS6 …  if wget does not work or you don’t have that command you can use that link in your browser to download it ... $ wget  https://secure-web.cisco.com/11zPV9NZ3Ex-1wASONnitG0xlqQgwcqw2vL1B1sywAZjAqytIaxxH3dJltyOPZMdcURt-onoPFGK-61rYdFlH39LCy8XGcP_QqK0RQt5n_T6pzBopyhoAr4Lof7I0WVP-JjBVv7HrKUXxGAgT7sFW7w_dK0TUCw6Y8PK7B1C3fC7_v2n38BIM9vsvz_wLV5kt5EBLQIAXxkOfqviOtQPr5szURoGI3FF5LlLJ7gQRT_7n2kOELAjU4wlWpk30C_kYnZbC47IZR8hsoKNNcslc4g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.1.1%2Ffreesurfer-linux-centos6_x86_64-7.1.1.tar.gz … wait for the download to finish via its progress bar and then check you have the complete archive file ... $ sum  freesurfer-linux-centos6_x86_64-7.1.1.tar.gz55852 4560006 If you did not get those exact numbers from the output of the checksum command, then re-try your download until you get that result. If the download worked, then remove any existing freesurfer installation  $ ls If you do not see a freesurfer subdirectory then skip the “rm” command $ rm -rf freesurfer Now unarchive the tar archive with, $ tar zxpf freesurfer-linux-centos6_x86_64-7.1.1.tar.gz You should now have a ./freesufer directory under $HOME.  With ls command you should see the fsfast and mni subdirectories there, $ ls freesurfer Try setting the environment again but with FREESURFER_HOME set to ./freesurfer under your HOME directory.  (Note there is no subdirectory with a version number when using the tar archive).$ export FREESURFER_HOME=$HOME/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh - R. On Sep 25, 2021, at 12:39, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        Installed freesurfer with the following errors. banikr2@banikr:~/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /usr/local/freesurfer/fsfast does not exist FREESURFER_HOME   /home/banikr2/freesurfer FSFAST_HOME       /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /home/banikr2/freesurfer/subjects MNI_DIR           /usr/local/freesurfer/mni WARNING: MINC_BIN_DIR '/usr/local/freesurfer/mni/bin' does not exist. WARNING: MINC_LIB_DIR '/usr/local/freesurfer/mni/lib' does not exist. FSL_DIR           /usr/local/fslI can run freeview with the following: banikr2@banikr:~/freesurfer$ freeviewIs the installation done correctly? Do the warnings compromise anything? Rana Banik_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1yT-3W8puyc22tRUcUsaIE2-_pk6AoYUs_nVRPvgfpeuPUvABxAH0wzC62hfxyAycAG9LAzP0fbeYgwV7ey4k-31gAAV43Ty4j2Nt_UzE5OsPUgOsxml0z0ZUDKqdXoM5xAUb7_Rx0WWdTUIGSCLqN7d5So9AWQflKTUVR9ddUEEMzTXE6HBTIcOvwjGPMyOyAGNAQp_0E4Er79sEgvLYnzDzK48vqeC7_ivSNebZjO2FFGasg49YnAPguWTvN0OyglixpRu82rlD0cT88xX0RQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Freesurfer installation error?
by Banik, Rana 25 Sep '21

25 Sep '21

External Email - Use Caution Installed freesurfer with the following errors. banikr2@banikr:~/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /usr/local/freesurfer/fsfast does not exist FREESURFER_HOME /home/banikr2/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/banikr2/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni WARNING: MINC_BIN_DIR '/usr/local/freesurfer/mni/bin' does not exist. WARNING: MINC_LIB_DIR '/usr/local/freesurfer/mni/lib' does not exist. FSL_DIR /usr/local/fsl I can run freeview with the following: banikr2@banikr:~/freesurfer$ freeview Is the installation done correctly? Do the warnings compromise anything? Rana Banik

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Freesurfer V6: aparcstats2table command python issues
by Miguel Ángel Rivas Fernández 24 Sep '21

24 Sep '21

External Email - Use Caution Dear Freesurfer experts, I am trying to use the aparcstats2table command (FSurfer V.6) in order to export the thickness measures but there should be an issue with my python version. This is the complete output: aparcstats2table --hemi lh --subjects 4166 --meas thickness --parc aparc.a2009s --tablefile thickness.txt Usage: python [options] python: error: no such option: --hemi Could you give me some suggestions to solve this problem? Thank you very much in advance. Best regards, -- *Miguel Ángel Rivas Fernández*

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lme_mass_F error
by Emmanuel Nwosu 24 Sep '21

24 Sep '21

External Email - Use Caution Dear All I am running the longitudinal post processing statistical analysis and this error comes up each time I run the lme_mass_F. Does anyone have an idea of why this is happening and how to resolve it. Any help will be appreciated *************************************************************************************************** F_lstats = lme_mass_F(tlstats,CM); Computing F statistics, degrees of freedom and P-values ... Error using lme_mass_F (line 92) The source code (/matlab filepath/lme_mass_F.m) for the parfor-loop that is trying to execute on the worker could not be found. Caused by: Undefined function 'fcdf' for input arguments of type 'double'. Error using remoteParallelFunction (line 84) Worker unable to find file. Undefined function 'fcdf' for input arguments of type 'double' **************************************************************************************************** Kind regards Emmanuel

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fsaverage nifti to gifti
by Tom Vanasse 24 Sep '21

24 Sep '21

External Email - Use Caution Hello, I have a question regarding the conversion of functional fsaverage lh and rh files (created from the Yeo lab MNI to fsaverage projection software: https://secure-web.cisco.com/1nRJbdVDTJHwxxGMU9q1fmvcPt_Df0AIfr6uIaGGD96UkP…) to a *gifti file*. For example, 'rh.sub-13_ses-fmri1_task-awak_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold_cleaned.allSub_RF_ANTs_MNI152_orig_to_fsaverage.nii.gz' This is necessary because my end goal is to then transform that gifti file, using wb_command, to the fs_LR HCP surface. Any help would be greatly appreciated, Tom

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Error in Analyze: Couldn't open PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file.
by Fabiola Macruz 24 Sep '21

24 Sep '21

External Email - Use Caution Dear FreeSurfer experts: I am processing in qdec 25 subjects (each with 3 MRIs studies) and I have this terminal output: Error in Analyze: Couldn't open PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file. I have executed the following qcache command for each subject: long_mris_slopes --qdec qdecfile --meas thickness --hemi > lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time > months --fwhm 10 --qcache fsaverage --sd SUBJECTS_DIR All the bases subjects have the specific files after this cmd: lh.long.thickness-avg[pc1/rate/spc].fwhm0[5, 10, 15, 20, 25].fsaverage.mgh. However, the file that qdec asks for - is missing in all the bases subjects. I have also created a qdec/.Qdecrc file in the qdec directory that contains the following lines: MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc Could you please help out? I have found another person with exactly the same problem in the freesurfer forum and the person assisting him, couldn't explain why this happen. Just went around about a bunch of other things that could be and didnt solve the guy's problem. I honestly found the tutorials for longitudinal analysis in the website very frustrating and poorly explained. Even in regard to the .Qdecrc file that we need to create, it wasn't clear to me what extension it was and if we were only suppose to copy paste the following in any terminal editor: EASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc Thanks, Fabiola

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Re: [Freesurfer] freesurfer running error at start
by fsbuild 23 Sep '21

23 Sep '21

External Email - Use Caution Your output shows you should you should be ready to work with freesurfer version 6.0 which is an older release from ~2017.  So people there may have used version 6 for quite some time.   If there was something missing on the system that freesurfer 6 needed to run, it’s probably been remedied by now.  If you are just starting out with freesurfer then I would not be too concerned with using version 6. Just keep in mind the current release is version 7.2.0 from this year (2021).  Browsing the 7.X release notes (at the top of the page) and comparing then with the 6.0 release notes (at the bottom of the page) can help you decide if version 7 offers improvements depending upon what you need to do - see  https://secure-web.cisco.com/1BDXGUYepZSu-OnlNwiqwjMw9yYjoVH9lFYYgCyki-ZNot8TkGmaIVwTD9K5BQZzvk4HPvMrJ70VW_4L4LS4YCgONmrFbWrWSrr1SNqCc5eBh9Dkgm6gXT5a6iILq6cs4QyT0bhqBlK3UNMV7iayEbLgUxXWayiDLf0uImbHIg44Fs9ZY3h23oKWKU68tDgSkNZQiHtSz7k_uP8qWWVg3p1hRr3Sl0vZBeZEb3O6d3rEVs_ugFAfUBbbHaE6ey9MK2zgpKB3RxWjRpsiRBloIdQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes.  For ongoing work it’s recommended to stick with the version of freesurfer you started with  -  see the “Important Note” on this page, https://secure-web.cisco.com/1PMV3hWYoa71yGCIFhXRqSneCKhKc1Kl4cv…. - R. On Sep 23, 2021, at 18:25, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        banikr2@banikr:~$ bashbanikr2@banikr:~$ export FREESURFER_HOME=/usr/local/freesurferbanikr2@banikr:~$ source SFREESURFER_HOME/SetUpFreeSurfer.shbash: SFREESURFER_HOME/SetUpFreeSurfer.sh: No such file or directoryInstead, I changed the command as: banikr2@banikr:~$ source /usr/local/freesurfer/SetUpFreeSurfer.shgives 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/freesurferFSFAST_HOME       /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/subjectsMNI_DIR           /usr/local/freesurfer/mniFSL_DIR           /usr/local/fslHow do I check the installation is done properly? FYI, I have used mri_convert from python script.Rana BanikFrom: fsbuild <fsbuild@contbay.com>Sent: Thursday, September 23, 2021 4:11 PMTo: 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 $FREESURFER_HOME/SetUpFreeSurfer.shThen you should see what the output reports for the freesurfer version.- R.On Sep 23, 2021, at 15:30, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        Hello, There is no directory called /7.2.0 rather the directory i am finding the files is: <pre>banikr2@banikr:/usr/local/freesurfer$ pwd/usr/local/freesurfer</pre>Trying the same in the /freesurfer folderRana BanikFrom: fsbuild <fsbuild@contbay.com>Sent: Wednesday, September 22, 2021 7:11 PMTo: 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 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 tree2) source’ing a shell init file to set PATH and other environment variables in order to run freesurfer commandsThere 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_Linux- 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_MacJust 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/7.2.0For that linux path using bash you would do,$ bash$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0$ source $FREESURFER_HOME/SetUpFreeSurfer.shWhen you run the source command to read the SetUpFreeSurfer script for the shell you are using, the version of freesurfer will get printed out automatically for you.Using the 7.2.0 linux release you would see the string between the dashes no matter what the absolute path is to FREESURFER_HOME on your system.tmp$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0tmp$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7.2.0/subjectsMNI_DIR           /usr/local/freesurfer/7.2.0/mniFSL_DIR           /usr/pubsw/packages/fsl/current… now run any freesurfer commands …- ROn Sep 22, 2021, at 18:04, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        Running freesurfer from terminal with the following error: banikr2@banikr:~/freesurfer/bin$ ./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/12K27iXExmAVdiVJTTUsxnZc3CWcIk9z0PWXun_LFxlG1Lp… 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(a)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 BanikGraduate StudentDept. of Biomedical Engineering Vanderbilt University, Nashville, TN_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1OK46XhJ4f_3Ospz1-ee0_xWo4bRUc2OoqTABw2Ah_pe27RdS-aW_pQibZAl974Pt0PYOjUCLJT08iSBJwOy6FkDfGIKfPAZJvrEb-GG4HlOoKmGJMj2V-gnQbGbxXbtVxxpQoXTWcLQn7m7cisnAWyh_xUTKuSmFr-ecgOAENC8xA_cpcBL982rkplEg2kgVAt--kwwzQSi8ocDZ5LOJkI5ulY2HiNfAIUe8X_dvuN797OzEM5V45r0DW-llL6qeJabxGSUsj3JljdC9xOCqmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1BELKLcx6vgPMRdbYs-4tYZraPJcxSMRMxvDPgZ6p3a19TxnKVgkfMht9L_2VlznjdQDFxez5HBbIyXgrXkWk_Lc6S2ghMN25SNzHEo5jakTOjKVR1vXcR2zKWVVmVYgvD31PbL99JuXSTXIQk2Jq1REbdeDeXUawe6UFm7-IxrcoCnkmlgYIaC8Dg2rlzCxHrbacEqizESsgVtSde41PUjRMLJOoveJOe7cYqS5ndpqfY9g1UorY4kIuVgJjDUmk4xXbl037m0GcYyizM05PpQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1O0Y-A9a1QmlEQo8otOOhFrUi49KsM6gWNLejHjGUSI2lsBAF750WEBRQIL3BLRG3LzGH8tJohR9HiYOH510la_I4CbO0Bq_k7GTRgavQJi1obMeez1PmtNNjxE03xvq-7MPKAzvFTzbr42gnRt4m16jvPXunP2CGUlLhkKCsdsOWg6JtunHvFcpTF4_nRShaXoL2GlH01XwQlbPKdWJGSd-pBEaTSFBpokVMrwTyqM2qeFYP6HlqTFqPCYI3zpFQ8hex_uoHo-zt9_e3TcCqmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Re: [Freesurfer] freesurfer running error at start
by fsbuild 23 Sep '21

23 Sep '21

External Email - Use Caution 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 $FREESURFER_HOME/SetUpFreeSurfer.sh Then you should see what the output reports for the freesurfer version. - R. On Sep 23, 2021, at 15:30, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        Hello, There is no directory called /7.2.0 rather the directory i am finding the files is: <pre>banikr2@banikr:/usr/local/freesurfer$ pwd/usr/local/freesurfer</pre>Trying the same in the /freesurfer folderRana BanikFrom: fsbuild <fsbuild@contbay.com>Sent: Wednesday, September 22, 2021 7:11 PMTo: 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 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 tree2) source’ing a shell init file to set PATH and other environment variables in order to run freesurfer commandsThere 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_Linux- 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_MacJust 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/7.2.0For that linux path using bash you would do,$ bash$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0$ source $FREESURFER_HOME/SetUpFreeSurfer.shWhen you run the source command to read the SetUpFreeSurfer script for the shell you are using, the version of freesurfer will get printed out automatically for you.Using the 7.2.0 linux release you would see the string between the dashes no matter what the absolute path is to FREESURFER_HOME on your system.tmp$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0tmp$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7.2.0/subjectsMNI_DIR           /usr/local/freesurfer/7.2.0/mniFSL_DIR           /usr/pubsw/packages/fsl/current… now run any freesurfer commands …- ROn Sep 22, 2021, at 18:04, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        Running freesurfer from terminal with the following error: banikr2@banikr:~/freesurfer/bin$ ./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/1BX9WO2ZIUDU9BmWuM0YkMFQ5KPQ0N_6lDMeyaiAbyQnDa-… 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(a)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 BanikGraduate StudentDept. of Biomedical Engineering Vanderbilt University, Nashville, TN_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1OK46XhJ4f_3Ospz1-ee0_xWo4bRUc2OoqTABw2Ah_pe27RdS-aW_pQibZAl974Pt0PYOjUCLJT08iSBJwOy6FkDfGIKfPAZJvrEb-GG4HlOoKmGJMj2V-gnQbGbxXbtVxxpQoXTWcLQn7m7cisnAWyh_xUTKuSmFr-ecgOAENC8xA_cpcBL982rkplEg2kgVAt--kwwzQSi8ocDZ5LOJkI5ulY2HiNfAIUe8X_dvuN797OzEM5V45r0DW-llL6qeJabxGSUsj3JljdC9xOCqmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1BELKLcx6vgPMRdbYs-4tYZraPJcxSMRMxvDPgZ6p3a19TxnKVgkfMht9L_2VlznjdQDFxez5HBbIyXgrXkWk_Lc6S2ghMN25SNzHEo5jakTOjKVR1vXcR2zKWVVmVYgvD31PbL99JuXSTXIQk2Jq1REbdeDeXUawe6UFm7-IxrcoCnkmlgYIaC8Dg2rlzCxHrbacEqizESsgVtSde41PUjRMLJOoveJOe7cYqS5ndpqfY9g1UorY4kIuVgJjDUmk4xXbl037m0GcYyizM05PpQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Customising overlay
by Worker, Amanda 23 Sep '21

23 Sep '21

External Email - Use Caution Dear FreeSurfer Developers, I am attempting to create some figures which display regional (Destrieux atlas) values which are typically in the range of 0-10. I would like to have an inflated brain with those regional values overlaid, for both patients and healthy controls. In total there will be four independent figures. The problem I am having is that the range of values is different for each overlay e.g. overlay 1 regional value range from 0-3, overlay 2 regional values range from 0-8, which means that the colour scales are on different scales. I would like to find a way to manually set the scale to 0-10 for each overlay, regardless of the actual values that exist within the overlay file. I am currently using the below command to load the overlay and then manually configuring the colour scale via the custom option, but I cannot add a point that is outside the range of values that exist in that overlay. I hope this makes sense and I would appreciate any advice you can give on how to achieve consistent colour scales for different overlays. freeview -f /software/system/freesurfer/freesurfer-6.0.0/subjects/fsaverage/surf/rh.inflated:overlay=rh_pcnt_neg_control_01.mgz:overlay_method=linearopaque:overlay_threshold=0,5,10 Kind regards, Amanda

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Re: [Freesurfer] freesurfer running error at start
by fsbuild 23 Sep '21

23 Sep '21

External Email - Use Caution 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 tree2) 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,https://secure-web.cisco.com/1U_tQcIreV6NPEuFeulfUWAOPFCaUe8vUQglXkIl… and the Mac,https://secure-web.cisco.com/1lLrW0TVmBeBE-XNNGyud8WDh5s2-DkWIjI41lqr-K… 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/7.2.0tmp$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7.2.0/subjectsMNI_DIR           /usr/local/freesurfer/7.2.0/mniFSL_DIR           /usr/pubsw/packages/fsl/current … now run any freesurfer commands … - R On Sep 22, 2021, at 18:04, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        Running freesurfer from terminal with the following error: banikr2@banikr:~/freesurfer/bin$ ./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:   http://secure-web.cisco.com/12yYZnrgAMX9gDsyIH0PviXj24zc_BpPcACqoCQE3uVFASO… 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(a)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 BanikGraduate StudentDept. of Biomedical Engineering Vanderbilt University, Nashville, TN_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1OK46XhJ4f_3Ospz1-ee0_xWo4bRUc2OoqTABw2Ah_pe27RdS-aW_pQibZAl974Pt0PYOjUCLJT08iSBJwOy6FkDfGIKfPAZJvrEb-GG4HlOoKmGJMj2V-gnQbGbxXbtVxxpQoXTWcLQn7m7cisnAWyh_xUTKuSmFr-ecgOAENC8xA_cpcBL982rkplEg2kgVAt--kwwzQSi8ocDZ5LOJkI5ulY2HiNfAIUe8X_dvuN797OzEM5V45r0DW-llL6qeJabxGSUsj3JljdC9xOCqmQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Freesurfer September 2021