Freesurfer

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30070 discussions

Freesurfer 7.2 Virtualbox - 7z file password
by Michelle Diniz 24 Apr '23

24 Apr '23

External Email - Use Caution Hi guys, I've just installed the VirtualBox and also downloaded the virtual machine. Now, I need the password to extract the file. In the *wiki* instructions, I was oriented to send a mail to this list. Can you kindly send the password to me? Kind regards, -- Michelle Diniz Lopes

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Longitudinal TRACULA subject folder confusion
by Brendan Angelo 24 Apr '23

24 Apr '23

External Email - Use Caution Hello FreeSurfer devs, I am attempting to run a Longitudinal TRACULA analysis on 3 timepoints per subject using an HCP server. I have used the example dmrirc page (https://secure-web.cisco.com/1JykEBcpM6vAD_4qy69NGW33wNc83B-TuXM37yVrgXaTHo…) to create a configuration file to be fed into the trac-all command, but I am running into issues with the naming of folders containing each subject and their respective FS timepoints. I have attached my configuration file, as well as a log output from one subject run for reference, but the issues I am running into pertain to the directory names of each subject and the FS timepoint needed for the longitudinal analysis. When I follow the example configuration file, it notes that each subject should be listed for each number of timepoints that are being included (in this case, we have 3 timepoints for each subject, and they are stored as {subjID}_Y{0,2,4}). When running trac-all -prep while the FS directory is called 100_Y0, for example, this error appears: ERROR: cannot find /ifs/loni/faculty/thompson/four_d/bangelo/FS_DTI_longitudinal/100_Y0.long.100_Y0, where the FS_DTI_longitudinal directory contains all the completed FS recon-all runs for each subject and timepoint. However, after changing the FS directory name to match the name it is searching for, I am met with an additional error after mri_convert is called: ERROR: cannot find /ifs/loni/faculty/thompson/four_d/bangelo/FS_DTI_longitudinal/100_Y0 I am extremely confused by this, as the configuration file example does not reference having an additional directory for each time point, that isn’t the directory that contains the FS output from that timepoint. Is there a way to force the scripting to only look for 100_Y0, instead of 100_Y0.long.100_Y0? And what is this additional directory it is looking for? I know it is trying to find a folder of the same name that I have set in the baselist, but I am still confused why the baselist folder and the subject folder are different to the script. Any help with sorting this out and any additional information that can be provided about what directories the script is looking for and what they should contain would be extremely helpful. 1. FreeSurfer Version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2. Platform: CentOS version 6 or 7 (I’ve been told both versions when I asked) 3. uname -a: Linux c2002 2.6.32-696.23.1.el6.x86_64 #1 SMP Tue Mar 13 22:44:18 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux 4. Tracula log file is attached Thank you! Sincerely, Brendan Angelo Brendan Angelo, MS BRANCH Lab USC

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mri_convert --conform
by Giuseppe 24 Apr '23

24 Apr '23

External Email - Use Caution Hello, Could you please tell me which formula is used by the command "mri_convert --conform" to rescale the input image to 0-255. I could not find it. Thank you, Giuseppe

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trac-all and bedpostx/xfibres GPU
by Bennet Fauber 24 Apr '23

24 Apr '23

External Email - Use Caution bedpostx, which also uses xfibres, takes a very long time on a single CPU. It does not seem like xfibres can even use multiple CPUs. We have GPUs available, and prior work with FSL suggests that using the GPU cuts processing down from about a day to about 20 minutes. I found an article from Aug, 2017 suggesting that the `-jobs` flag be used to generate a file that would have commands that could be run in parallel. I cannot get that to do so. Running just `trac-all -jobs` results in $ trac-all -jobs job_scripts/trac-all-jobs.sh ERROR: run list is longer than subject ID list We have a config file to use with -c, $PWD/etc/configfile, and using it runs `trac-all -c $PWD/etc/configfile -bedp`, but the -c option seems to be mutually exclusive with the -jobs option. I found a reply from Prof Yendiki at https://secure-web.cisco.com/18kY7tFQx1qjx67wI-ayKRuY1CubuoBO8bPSilQmcfR7sm… which says > TRACULA just expects the output files of bedpostX, and does not care if they > were generated on GPUs or CPUs. Just provide the $subjectID/dmri directory > (created by the first step of trac-all) as the argument to either version of > bedpostX. After it's done, you can skip to the 3rd step of trac-all. May I confirm that the three steps for trac-all are properly represented by trac-all -prep -c ../configfile trac-all -bedp -c ../configfile trac-all -path -c ../configfile and that I can simply replace the -bedp line with a direct call to bedpostx_gpu and all the processing done by `trac-all -bedp` will be properly done? That is, I have my setup such that all work is rooted in the TRACULA directory, the output of the trac-all -prep is being routed to TRACULA/output/sub-10001 and there exists within that the dmri directory, running bedpostx_gpu sub-10001 from TRACULA/output/sub-10001 creates the dmri.bedpostX directory, and that is all that will be needed. Sorry to be dense about all this.

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ACPC alignment and RF/B1 bias correction before processing
by Toshiharu Kamishikiryo 24 Apr '23

24 Apr '23

External Email - Use Caution Hello Freesurfer experts Would it be more accurate to apply ACPC alignment and RF/B1 bias correction to T1w.nii.gz before recon-all to improve pial estimation accuracy? Thanks in advance Regards Kamishikiryo Research Student

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How to extract TRACULA's fiber bundles in MNI template space
by Woo-Suk Tae 24 Apr '23

24 Apr '23

External Email - Use Caution Dear Freesurfer users. I'd like to know how to extract TRACULA's fiber bundles in MNI template space. Are there any command option for trac-all? or commands for already extracted tracks in native space? sincerely Woo-Suk, Tae Seou, Korea -- ---------------------------------------------------------------------------------------- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: wstae(a)korea.ac.kr, woosuk.tae(a)gmail.com, wo <woostae(a)naver.com>ostae(a)gmail.com ----------------------------------------------------------------------------------------

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TRACULA intensity normalization
by Silvia De Francesco 24 Apr '23

24 Apr '23

External Email - Use Caution Dear developers, Does TRACULA perform an intensity normalization of the DWI image, as recon-all do for the T1? Thanks, Silvia

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Re: [Freesurfer] free view crash report
by fsbuild 24 Apr '23

24 Apr '23

External Email - Use Caution If you are using a second monitor, then disconnect it so you are only using the primary laptop screen/monitor.   There have been issues displaying images properly when using multiple monitors with MacOS. If you have not tried running freeview directly from the command line, then please try the following. Open a new terminal window and run the bash shell, $ bash … prompt will change ... $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh … output with variable settings … Then see if freeview opens an empty window, $ freeview If that works, then quit freeview and try to display one of the existing volumes in the distribution, $ freeview $FREESURFER_HOME/subjects/bert/mri/brain.mgz If that works, then quit freeview and try to display your own surface/volume files. - R. On 4/20/23 12:24, Suman Nag (hulosom(a)gmail.com) wrote:         External Email - Use Caution         hi, i have downloaded 7.3.2 version on my macbook pro ,os 13.1. When i am trying to load volume from subjec > bert > T1.mgz or other .nii volume freeview crashing unexpectedly. below the error log,,please kindly  help.God bless.

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Re: [Freesurfer] freesurfer 5.3 license on ubuntu 22
by fsbuild 24 Apr '23

24 Apr '23

External Email - Use Caution The 5.3 release dates back to ~10 years ago when CentOS4 was current.  Because of changes to the crypt libraries since then (Ubuntu 22, CentOS8), it is no longer possible to decode a license for older versions of freesurfer on newer iterations of linux OS's.  Your alternative is to use Ubuntu 22 to host a container or VM, e.g., in VirtualBox, to run the version of the old OS you previously ran the 5.3 release under.  You can obtain copies of end of life'd OS iso images from the respective linux vendors web site - under OS archives or some similar title - in order to create a VM/container to run the old OS. - R. On Apr 23, 2023, at 21:59, Hadas, Itay <ihadas(a)health.ucsd.edu> wrote:        External Email - Use Caution        Hi,I am looking for workaround to run freesurfer 5.3 on ubuntu 22 - I get the ERROR: Invalid FreeSurfer license key found in license file $FREESURFER_HOME/license.txtother versions works fine.Thanks,Itay _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freesurfer 5.3 license on ubuntu 22
by Hadas, Itay 23 Apr '23

23 Apr '23

External Email - Use Caution Hi, I am looking for workaround to run freesurfer 5.3 on ubuntu 22 - I get the ERROR: Invalid FreeSurfer license key found in license file $FREESURFER_HOME/license.txt other versions works fine. Thanks, Itay

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