Freesurfer April 2023

freesurfer@nmr.mgh.harvard.edu

80 participants
105 discussions

The longitudinal Midlife in the U.S. (MIDUS) study is looking for postdoctoral researchers
by STACEY M SCHAEFER 26 Apr '23

26 Apr '23

External Email - Use Caution The MIDUS Affective Neuroscience Project team led by Dr. Stacey M. Schaefer at the University of Wisconsin-Madison’s Institute on Aging is seeking a postdoctoral scholar to analyze and publish on data from the national longitudinal Midlife in the US study. MIDUS is an NIA-supported study on aging explicitly focused on all the adult years (25-100+) with multiple longitudinal timepoints over the past +20 years. This is an opportunity to become part of a scientific community that is actively engaged with MIDUS and play a key role in analyzing neuroimaging data in relation to affective, psychophysiological, sociodemographic, behavioral, cognitive, biomarker, and environmental data with an emphasis on understanding the factors that are important for emotional wellbeing, brain health, and brain aging. For more information see: https://secure-web.cisco.com/191EwmVOBKe0a4n05j11zWFZF5tHg3ATL6HmuGKmYAjsUQ… Stacey M. Schaefer, Ph.D. Leader of the MIDUS Neuroscience Project & Co-Leader of the MIDUS Admin Core Institute on Aging 2245C Medical Sciences Center University of Wisconsin-Madison 1300 University Ave Madison, WI 53706 USA

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Freesurfer 7.2.0 release in Ubuntu 18d .ova.7z password
by Min Wang 26 Apr '23

26 Apr '23

External Email - Use Caution Greetings team Freesurfer, Following the instructions in your wiki page, I’m sending you to kindly provide me with the .7z password for the said file (Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7z). Thanks a lot in advance, Min Wang

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EasyReg for group-average template?
by AmirHussein Abdolalizadeh 26 Apr '23

26 Apr '23

External Email - Use Caution Dear Freesurfer users/experts, I am working on a research project that requires generating group-average templates from a large sample of data. I wonder about the possibility of using mri_easyreg for generating group-average templates. To my knowledge, the best current pipeline is based on using ANTs that 1) do not support GPU, 2) take ages to generate a template esp. from a large sample of data. I wanted to know, do you have any suggestions to use mri_easyreg for such purposes? I would greatly appreciate any suggestions or advice you can provide. Best, Amir

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Alternatives to Qdec
by 余卓远 26 Apr '23

26 Apr '23

External Email - Use Caution Dear experts, I was trying to use the Qdec script that came with Freesurfer to perform intergroup analysis of morphological data such as cortical surface area, but I found that the Qdec tool has been removed in version 7.2. Is there an alternative that can do the analysis as described above in version 7.2? Or should I download the previous version software? Kind regards, Zhuoyuan

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passcode to install freesurfer
by ANAIS LLORENS 25 Apr '23

25 Apr '23

External Email - Use Caution Hi I woud like the pass code to open FS_7_2_0_Ubuntu_18_04_06.ova.7z. Thank you! Anais

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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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Freesurfer April 2023