Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Questions for FreeSurfer 7.3.2 recon-all process INCLUDING SynthSeg
by Yoonho Hwang 11 Dec '22

11 Dec '22

External Email - Use Caution Dear Bruce Fischl, Hi, I'm Yoonho. I know that new features, such as SynthSeg, SynthStrip, segment_subfields (beta version), etc, based on deep learning have been added after the FreeSurfer 7.3.2. Here I have questions (I read papers related to SynthSeg, SynthStrip, segment_subfields). 1. *In FreeSurfer 7.3.2, the recon-all function includes the mri_synthse function. Does the recon-all process include SynthSeg by default? Likewise, does SynthStrip have the same process by default?* 2. There are already processed files with FreeSurfer 7.2.0, *can we apply new functions (e.g., SynthSeg, SynthStrip, etc) to them?* 3. From SynthSeg related papers (e.g., Billot et al, 2021 and 2022), in the following quoted text, "Therefore, there is a clear need for a fast, accurate, and reproducible automated method, for segmentation of brain scans of *any contrast and resolution*, and that can adapt to a wide range of subject populations", Synthseg is said to be able to process MRI data of any contrast and resolution. *Does this also apply to data taken from other manufacturers (Siemens, GE, Philips) and protocols (FSPGR, MPRAGE, etc)?* Also, there are many studies that attempt to harmonize MRI data obtained from various sites. *If there are different parts such as MRI data acquisition time, manufacturer, and protocol, the harmonization can be solved using the SynthSeg function of FreeSurfer 7.3.2. (In other words, can we simply proceed with the recon-all process?)* Thank you for reading my long question Please let me know if there is anything you don't understand. Looking forward to your feedback. Thank you very much. Sincerely, Yoonho -- *Hwang, Yoonho* *Research professor* *Institute of Human Genomic Study,* *College of Medicine, Korea University* *#123, Jeokgeum-ro, Danwon-gu, Ansan-si, Gyeonggi-do, **15355, Republic of Korea.* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

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ERROR: fast_mat2vol: szvol inconsistent with mat2d nv
by stdp82＠virgilio.it 11 Dec '22

11 Dec '22

External Email - Use Caution I would extract the rs-fMRI timeseries from Yeo’s Network components. I’m running: preproc-sess -s ${1} -fsd rest -sliceorder up -surface self lhrh -fwhm 0 -per-run fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config fcseed-sess -s ${1} -cfg wm.config fcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config fcseed-sess -s ${1} -cfg vcsf.config mkanalysis-sess -analysis fc.noseed.surf.lh -surface self lh -fwhm 0 -notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten mkanalysis-sess -analysis fc.noseed.surf.rh -surface self rh -fwhm 0 -notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten The line below produced this error: selxavg3-sess -s ${1} -a fc.noseed.surf.lh -no-con-ok -svres Saving rho1 ERROR: fast_mat2vol: szvol inconsistent with mat2d nv = 151008, size(mat,2) = 142954 run 2 t= 1.6reading data ... 0.518631Temporally filteringSaving rho1 ERROR: fast_mat2vol: szvol inconsistent with mat2d nv = 151008, size(mat,2) = 142954 Found 0 voxels with corrected AR1 > 0.90Not WhiteningFound 8054 zero-valued voxelsComputing contrasts The res folder in fc.noseed.surf.lh or fc.noseed.surf.rh contains res-001.nii.gz 158KB res-002.nii.gz 158KB that cannot be opended. Thanks Stefano

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Biannual Boston Freesurfer Workshops
by Salar Dini, Elaheh 09 Dec '22

09 Dec '22

External Email - Use Caution Hello dear freesurfer developers, I am leaving this message on the board to ask about the possibility of resuming the Boston Freesurfer course in the near future. The last update that I'm seeing on the Freesurfer official website pertains to the Spring 2020 course which is the one before the pandemic hit. Are you planning on resuming the biannual workshops anytime soon? Thanks and all the best, Ela

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A TRACULA Question
by Salar Dini, Elaheh 09 Dec '22

09 Dec '22

External Email - Use Caution Dear Anastasia, Thanks for your support in the past few months. I got an error message in -prep step: "Exception caught: itk::ExceptionObject (0x8a1e880) Location: "unknown" File: /home1/zs24/sandbox/build/ITKv5-install/include/ITK-5.0/itkSmoothingRecursiveGaussianImageFilter.hxx Line: 229 Description: itk::ERROR: SmoothingRecursiveGaussianImageFilter(0x8a1dd00): The number of pixels along dimension 2 is less than 4. This filter requires a minimum of four pixels along the dimension to be processed. ConvertTransformFile 3 /home1/es2263/TRACULA/subjects_dir/37/dmri/xfms/diff2syn0GenericAffine.mat /home1/es2263/TRACULA/subjects_dir/37/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras file /home1/es2263/TRACULA/subjects_dir/37/dmri/xfms/diff2syn0GenericAffine.mat does not exist . Linux ursapet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Oct 20 23:31:04 EDT 2022" I am attaching a log file too. Do you have a guess why this happened and how we can address it? One possibility is that we don't have all the dMRI sequence slices (like 300 out of 1600 are missing). Thanks for your time and help, Ela

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VM Password
by Mao, Andrew 08 Dec '22

08 Dec '22

External Email - Use Caution Hi, I'd like to request access to the Freesurfer VM. Thanks, Andrew Mao

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using FS7.2 tracula with FS6.0 outputs
by Alexopoulos, Dimitrios 08 Dec '22

08 Dec '22

External Email - Use Caution HI, we have run a cohort of 200 subjects through FS6.0 (including tracula) with good results. Is it possible to use the FS6.0 outputs (aparc+aseg, etc.) to run these data though only the updated tracula pipeline in 7.2? Jim ________________________________ 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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ma_ca_register is not called anymore in version 7.3.2
by Kilian M Pohl 08 Dec '22

08 Dec '22

External Email - Use Caution Hi , I have used the following call starting at Freesurfer 5.3 /usr/local/tools/freesurfer/bin/recon-all -norandomness -openmp 4 -sd LAB_S01541/standard/20180307_4541_03072018/structural/freesurfer7 -autorecon1 -noskullstrip -no-isrunning -s LAB_S01541_standard_20180307_4541_03072018 -rng-seed 1234 It is still working with Freesurfer 7.1.1 but we now tried updating to 7.3 and it is failing (on the same case). Looking at the recon-all.log it seem that ma_ca_register is not called anymore so that I get the following error message ERROR: cannot find or read transforms/talairach.m3z (see attached recon-all .log) Do I have to add flags ? I need to run with -noskullstrip Best, Kilian -- Kilian M. Pohl, Ph.D. Associate Professor Department of Psychiatry & Behavioral Sciences Stanford University 401 Quarry Road Stanford, CA 94305-5717 https://secure-web.cisco.com/18F69KCiyMWMSCouFYLrT3r9PgA1L7oUNzDa59-gQWUTsS…

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Regarding MRI Understanding.
by Rahul Sharma 07 Dec '22

07 Dec '22

External Email - Use Caution Hello everyone, I am very new to this neuroimaging and belongs to technical background. Could anyone provide me any source or material for understanding MRI scans and the neuroimaging tools such as Freesurfer or FSL. Eagerly waiting for your reply.

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Request for Assistance
by MANSON ERIC NAAB 07 Dec '22

07 Dec '22

External Email - Use Caution Dear Sir/Madam, I am Eric Naab, a Ph.D. student at the University of Ghana, and currently doing my research at the University of Ghana MRI Medical Center. The title of my research is "Optimization of Pulse Sequence Protocols for Magnetic Resonance Imaging of the Brain". I am working with a *1.5T MRI Philips scanner* and I intend to use the *FreeSufer software* for the first time*.* I would be very glad if you could provide me with the specific recommended protocol for imaging and any other assistance that could help me with my research. Thank you Counting on your usual cooperation.

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password request for file FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Daniele Ranieri 07 Dec '22

07 Dec '22

External Email - Use Caution Hello FreeSurfer, I downloaded VM from the official website: FS_7_2_0_ubuntu_18_04_06.ova.7z but I need the password to successfully open the compressed package. I hope that is the right place for this request. Thank you for your time.

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