Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Re: [Freesurfer] recon-all mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied error
by fsbuild 27 Sep '21

27 Sep '21

External Email - Use Caution OK - fill out the form on this page and download the license.txt file, https://secure-web.cisco.com/1x188geQEK3Rrhy9C_TF54vhIgmM9qi1beEnk0Zgdzy4QT… You can copy license.txt to your home directory, e.g., if it’s in your Downloads folder from downloading via the browser, $ cp $HOME/Downloads/license.txt  $HOME/. Then you can set the environment variable FS_LICENSE to it’s location, $ export FS_LICENSE=$HOME/license.txt … check it is readable … $ cat $FS_LICENSE You can put the license.txt anywhere just as long as FS_LICENSE is set to point to it. Then try your commands again. - R.. On Sep 26, 2021, at 14:10, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        I installed freesurfer here: banikr2@banikr:~$ which freesurfer /usr/local/freesurfer/bin/freesurferI am getting the following error while running recon-all:banikr2@banikr:~$ export SUBJECT_DIR=/home/banikr2/273_p banikr2@banikr:~$ recon-all -s sub273 -i 273_p/273_MR.nii mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551I found this from previous troubleshoot emails of freesurfer here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/10nZ_VGLWCVDFmlydatYBlFkdXTaJEnvkpD2O… I performed accordingly. Any suggestions?Rana Banik_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1OG3BAo0lmU7cE8cn9LvmHGOEYJzbtbgtwdIvUeIwpOy9kXhVQ-h2j_LveMzWwYTkZ2AqEE8r0GJeWpLjEPOHdUK_hrAe6A9nF9duhTCbe1ACFFJzElxg8IrW7vAtVlSF1RXP7Dr0UUnskPRn4eZT5x9kfwr2t9JxN_OGawnuSTnvIK_SWF89JiymqD7T0csS5MzLGkbeUHy_l-JCJTAYaDIaRkN2AG8adtZhWjjaeeAKbBu14kofu7r8rX6JautSUQCIP5jw9zJhJVfqIlHAOQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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WM or Pial edits to correct surfaces
by Alexopoulos, Dimitrios 27 Sep '21

27 Sep '21

External Email - Use Caution Hi users, We're having some issues with running some of our 2-3yo data (0.8mm isotropic) through FS7 with and without the -hires flag. There are persistent issues with the frontal lobe regions where the pial has not extended to outer surface as illustrated below. The WM surface contour look reasonable but the pial has underestimated the outer cortex resulting in an incorrect surface (below). I don't think control points will work (low intensity values in the 50-60s), and no WM to add to the WM.mgz. Any suggestion on how to push the pial surface out to capture the cortical surface?? Thx. Jim [cid:image004.png@01D752FB.04011E10] [cid:image005.jpg@01D752FB.04011E10] [cid:image001.png@01D752F8.E6507AC0] [cid:image002.png@01D752F8.E6507AC0] [cid:image006.png@01D752FB.04011E10][cid:image007.jpg@01D752FB.04011E10] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Different volume measurements Freesurfer V7.1.1
by özenç taşkın 27 Sep '21

27 Sep '21

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Re: [Freesurfer] Converting MNI to RAS on fsaverage
by Douglas N. Greve 27 Sep '21

27 Sep '21

No, the RAS in fsaverage is in MNI305 space, so no need to do the conversion. On 9/27/2021 11:22 AM, Kennedy, Bryan wrote: > Good morning, > > We are trying to conduct a meta-analysis by mapping reported MNI > dimensions (by others) on fsaverage. I know that I have to use the > following conversion: > > MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' > > in which, > > Norig = [-1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 > -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 > 0.00000 1.00000] > Torig = [-1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 > -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 > 0.00000 1.00000] > > When I checked TalXFM, it was just the identity maxtrix (in > fsaverage/mri/transforms/talairach.xfm). So, > > RAS = inv(Norig)*Torig*MNI; > > But based on that, MNI and RAS would be the same coordinates. For > instance: > > MNI(16 -67 39) -> RAS(16 -67 39) > > Are we missing something? Do these numbers make sense to you? > > Thanks in advance, > Bryan > >

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Re: [Freesurfer] recon-all mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied error
by fsbuild 26 Sep '21

26 Sep '21

External Email - Use Caution Hello Rana, Looks like you are missing a capital S at the end of SUBJECT or it’s SUBJECTS_DIR instead of SUBJECT_DIR. $ export SUBJECTS_DIR=/home/banikr2/273_p So the default SUBJECTS_DIR, /usr/local/freesurfer/subjects, ended up getting used, and you do not have permission to write there. - R. On Sep 26, 2021, at 14:10, Banik, Rana <rana.banik(a)vanderbilt.edu> wrote:        External Email - Use Caution                External Email - Use Caution        I installed freesurfer here: banikr2@banikr:~$ which freesurfer /usr/local/freesurfer/bin/freesurferI am getting the following error while running recon-all:banikr2@banikr:~$ export SUBJECT_DIR=/home/banikr2/273_p banikr2@banikr:~$ recon-all -s sub273 -i 273_p/273_MR.nii mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551I found this from previous troubleshoot emails of freesurfer here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1gXITlegvJK1p_-l14FbolcoT9opnCLyCP3dD… I performed accordingly. Any suggestions?Rana Banik_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1OG3BAo0lmU7cE8cn9LvmHGOEYJzbtbgtwdIvUeIwpOy9kXhVQ-h2j_LveMzWwYTkZ2AqEE8r0GJeWpLjEPOHdUK_hrAe6A9nF9duhTCbe1ACFFJzElxg8IrW7vAtVlSF1RXP7Dr0UUnskPRn4eZT5x9kfwr2t9JxN_OGawnuSTnvIK_SWF89JiymqD7T0csS5MzLGkbeUHy_l-JCJTAYaDIaRkN2AG8adtZhWjjaeeAKbBu14kofu7r8rX6JautSUQCIP5jw9zJhJVfqIlHAOQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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recon-all mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied error
by Banik, Rana 26 Sep '21

26 Sep '21

External Email - Use Caution I installed freesurfer here: banikr2@banikr:~$ which freesurfer /usr/local/freesurfer/bin/freesurfer I am getting the following error while running recon-all: banikr2@banikr:~$ export SUBJECT_DIR=/home/banikr2/273_p banikr2@banikr:~$ recon-all -s sub273 -i 273_p/273_MR.nii mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/sub273': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/sub273/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 I found this from previous troubleshoot emails of freesurfer here: https://secure-web.cisco.com/1bocVcL-uht7sTBBGDhGvGZzup63MHVzmcTNCz1auLpZYP… which I performed accordingly. Any suggestions? Rana Banik

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Freesurfer V7.1.1: recon-all meet the problem: set: No match
by 胡浩宇 26 Sep '21

26 Sep '21

External Email - Use Caution Dear Freesurfer experts, I'm a novice in using Freesurfer and I'm trying to run recon-all command to try if I can use Freesurfer to deal with the MRI data. Here is my codes: "export SUBJECTS_DIR=hcp/data/100206 mkdir -p subject1 recon-all -s sub_try -i T1w/*.nii -sd project/subject1/ -all" The codes are in quotes, in which 100206 stands for a folder containing T1w folder that have a .nii file, and project stands for the folder I want to store my result. But when I tried to run this script, I got the feedback "set: No match" and I don't know why. Could you please give me some suggestions to solve this problem? Thank you very much! Best regards, Blue

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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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