Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

XL defect in recon-all
by Devika K 31 Jan '20

31 Jan '20

External Email - Use Caution Hi, I am running recon-all on Freesurfer version 6. Few of my subject's have XL defect error as shown below. CORRECTING DEFECT 0 (vertices=18408, convex hull=3300, v0=0) XL defect detected... This has been running for more than a day. How can I fix this error? Please give me some commands to solve this issue. Looking forward to hearing from you Thanks and Regards Devika K

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Tuning WM threshold
by Wright, Paul 31 Jan '20

31 Jan '20

External Email - Use Caution Dear FreeSurfer experts I am a relative novice with FreeSurfer. I am reprocessing some older images with v6.0 that were previously processed with v5.3. In the newer batch, the GM-WM boundary is wider and the pial boundary is pushed out, but the newer version does a better job in the hippocampus. I am trying to figure out what parameters might differ between versions so I can get a cortical reconstruction as well as hippocampal segmentation. Both batches used plain vanilla recon-all -all. The attached figure shows v5.3 on top and v6.0 below, with aseg.mgz over T1.mgz. I used an example that as well as thin cortex in the new version, shows a hippocampal error in the older version. (The slices are aligned at the hippocampus, but the pitch is slightly different so they don't line up more superiorly.) >From the T1, it looks like the step that sets white matter to 110 is more aggressive in 6.0. I looked through recon-all.cmd and noticed both normalization steps include the -mprage flag in 6.0 not 5.3.Could this be the why the results differ? (The images are SPGR not MPRAGE.) Looking at help for mri_normalize it doesn't mention this flag or how to switch it off, so I'm stuck here. Of course, it might be something else, not the -mprage flag. I'd much appreciate any guidance from the list. Best wishes Paul Paul Wright, PhD<http://kclpure.kcl.ac.uk/portal/p.wright.html> Postdoctoral Researcher, Department of Neuroimaging King's College London Maurice Wohl Clinical Neuroscience Institute 125 Coldharbour Lane London SE5 8NU Desk: +44 20 7848 8579 Mobile: +44 7491 905754 Email: p.wright(a)kcl.ac.uk

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Re: [Freesurfer] Error Bad CPU
by fsbuild 30 Jan '20

30 Jan '20

External Email - Use Caution Hello Phillip, If you run the following command on that file - which is from the 6.0.0 freesurfer release, $ file /Applications/freesurfer/tktools/tkregister2.bin I think you will see that it reports it is a i386 binary - which is 32 bit - and cannot run on Catalina.  That is also why you get bad CPU type, % file tkregister2.bin tkregister2.bin: Mach-O executable i386 % ./tkregister2.bin ../tkregister2.bin: Bad CPU type in executable. The last version of MacOS that can run 32 bit binaries is 10.14, Mojave, but with Mac OS 10.15 (Catalina) none of the old 32 bit binaries will run.   So if you need to be compatible with running the 6.0.0 freesurfer release, then I suggest you look into reverting back to the previous version of the OS you were running before the upgrade, i.e., hopefully you made a backup before upgrading.  Or if you have 10.13 (High Sierra), 10.12 (Sierra), or older, etc., that would work as well. - R. On Jan 30, 2020, at 10:50, Philipp Barzyk <philipp.barzyk(a)uni-konstanz.de> wrote:       External Email - Use Caution        Tanks for the quick reply.what exactly do you mean by all FS executables? It happens for various commands I am using but they all work on my Imac.I am working from a 2019 macbook air using catalina, and installed it myself. The imac where it works is from 2013 and runs on Mojave.Greets,PhilippOn 30.01.20, 16:31, "Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote:   Hi Philipp   does this happen for all the FS executables? What kind of machine are you    trying it from and who installed it? Sounds like you are on a mac and    maybe trying to use a version installed for a different kind of computer   cheers   Bruce   On Thu, 30 Jan 2020, Philipp Barzyk    wrote:       External Email - Use Caution        Hello,I am new to freesurfer and currently analysing and working on fMRI Data formy master thesis. I’ve come to an issue, that I can’t seem to solve.The following error occurs and I cannot find a threat or forum entry thatsolves it. /Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type inexecutable.It would be great if you could help me figure out a solution. Thanks in advance,Philipp Barzyk_______________________________________________   Freesurfer mailing list   Freesurfer@nmr.mgh.harvard.edu   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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(no subject)
by fsbuild 30 Jan '20

30 Jan '20

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format bvalues bvectors tracula
by Renew Andrade 30 Jan '20

30 Jan '20

External Email - Use Caution Dear FreeSurfer experts:I have tried to run tracula -prep but I cannot get to no where for the moment. I keep receiving this error. I assumed numbers had to be aligned in rows and columns. But none either that or one space in between seems to work. I don't know what format means with respect to bvalues o bvectors. It is not clear enough to me in the tutorial how do I have to fix the issue. Sincerely, Andrade. root@andraderenew:/home/andraderenew# trac-all -prep -c '/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/dmrirc.IXI' Too many ('s. INFO: SUBJECTS_DIR is /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed INFO: Diffusion root is /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed Actual FREESURFER_HOME /usr/local/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /Applications/freesurfer trac-preproc -c /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/dmrirc.local -log /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.log -cmd /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections mié ene 29 17:42:22 CET 2020 mri_convert --bvec-voxel /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998725, -0.0503472, 0.00377193) j_ras = (-0.0504772, 0.994141, -0.0955763) k_ras = (-0.00106217, 0.0956448, 0.995415) writing to /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz... cp /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/bvec/gradients.txt /media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.bvecs ERROR: Must specify input table of b-values Linux andraderenew 5.0.0-37-generic #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at mié ene 29 17:42:22 CET 2020

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Error Bad CPU
by Philipp Barzyk 30 Jan '20

30 Jan '20

External Email - Use Caution Hello, I am new to freesurfer and currently analysing and working on fMRI Data for my master thesis. I’ve come to an issue, that I can’t seem to solve. The following error occurs and I cannot find a threat or forum entry that solves it. /Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable. It would be great if you could help me figure out a solution. Thanks in advance, Philipp Barzyk

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Job opening: MRI Senior Research Specialist at OHIO STATE UNIVERSITY
by Xiangrui Li 29 Jan '20

29 Jan '20

External Email - Use Caution MRI Senior Research Specialist OHIO STATE UNIVERSITY The Center for Cognitive and Behavioral Brain Imaging <https://ccbbi.osu.edu/> (CCBBI), in the College of Arts and Sciences, seeks an MRI (Magnetic Resonance Imagining) Senior Research Specialist to join our team. The College of Arts and Sciences is the largest college and the academic heart of the university. The College hosts 81 majors. With 38 departments, 20+ world-class research centers, and more than 2,000 faculty and staff members, students have the unique opportunity to study with the best artists, scholars, and scientists in their field. The College values diversity and offers a supportive, open, and inclusive community. The CCBBI, directed by Dr. Ruchika Prakash, is a state-of-the art imaging center, housing a research- dedicated 3T Siemens Prisma scanner and supporting principal investigators across the university conducting scientific investigations related to human and animal imaging. The MRI Senior Research Specialist remains informed of the latest technical developments in the field of functional MRI, and communicates these developments to users of the facility, both in-person and through research seminars; meets frequently with center users to learn about current and future needs as pertaining to sequences or fMRI techniques; and actively engages in the development and use of novel fMRI techniques to improve the technical caliber of the center; provides technical support to current and new pilot and funded research projects at the center; assists center users to optimize MRI, fMRI, and DTI sequences for different experimental needs; works with users to develop custom-tailored sequences; participates in the teaching mission of the center and educates users in image acquisition, processing, and data analysis through comprehensible presentations in research seminars and user workshops; participates with other CCBBI staff in teaching the annual Introduction to fMRI course every spring; maintains proper functioning of the Siemens Prisma MRI system, including quality checks, and related hardware in the facility, and debugs any hardware problem(s), and interfaces with representatives of various hardware vendors to find solutions to problem(s); works with the CCBBI team to maintain and monitor the safety of the participants and the fMRI facility; position available for one year with the possibility of extension based on satisfactory performance and availability of funds. Successful candidates must have earned a Doctoral degree in MR physics, biomedical engineering, electrical engineering or related field; research experience in a technical field closely related to MRI, fMRI, and DTI; experience in managing MRI system(s). If you are interested in being considered for the position, review the full job description and qualifications and apply online at https://www.jobsatosu.com, under job listing #457097 and submit a cover letter detailing background and experiences, a CV, the expected date of availability, and the names and contact of three references. If you have questions about the position or the center, please contact Dr. Ruchika Prakash at prakash.30(a)osu.edu CCBBI Website: https://ccbbi.osu.edu/ *To build a diverse workforce, The Ohio State University encourages applications from all individuals. Ohio State is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to age, race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, or protected veteran status.*

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TRACULA Preprocessing Error
by Al Qadi, Ameen 29 Jan '20

29 Jan '20

External Email - Use Caution Hi Freesurfer Developers, I downloaded the Freesurfer tutorial data to run the TRACULA tutorial, and encountered a number of issues: 1. When running trac-all, I get the following error: trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial INFO: SUBJECTS_DIR is /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_recons INFO: Diffusion root is /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial Actual FREESURFER_HOME /usr/local/freesurfer ERROR: cannot find /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_recons/elmo.2005 I found the elmo.2005 directory in *diffusion_tutorial*, and not *diffusion_recons*. Unsure why this happened, I copied all the data from diffusion_tutorial to diffusion_recons. 2. After re-running trac-all, the following error appeared: mri_convert --bvec-voxel /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz ERROR: file /zstore/data/aalqadi/aalqadi/tutorial_data/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm does not exist trac-preproc exited with ERRORS at Tue 28 Jan 2020 10:21:41 PM UTC The issues with mri_convert stemmed from the failure to locate the * dwi_orig.nii.gz* file in diffusion_tutorial/elmo.2005/dmri/. The dmri subdirectory did not have the .gz file, so I was wondering if there was an issue with the tutorial data? (Couldn't find the .gz file anywhere else, re-downloaded the data and the same error showed up). Any guidance would be much appreciated. The log file for error #2 is attached. Best, Ameen -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi(a)icahn.mssm.edu

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Anatomicuts usage
by nayan wadhwani 29 Jan '20

29 Jan '20

External Email - Use Caution Hello FS users, I am trying to use Anatomicuts tool of freesurfer for macOS. Since I was not using ./dev version of freesufer so I am unable to set the environment for the tool and is it available for use or will be available with the new release itself. Thanks and Regards Nayan Wadhwani

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Re: [Freesurfer] Xl defect in Freesurfer
by Devika K 29 Jan '20

29 Jan '20

External Email - Use Caution Hi Freesurfer Team, I am running recon-all command in parallel. one of my subject's (recon-all.log file) is showing Xl defect and it has been in this step overnight and there is no further progress. PFA of recon-all.log file and recon-all-status.log file of the above-mentioned subject. The recon-all process for this subject is not terminated with an error, it's still running. Could you please help me to resolve this issue? Regards Devika K Research Scholar, Dept of EEE e: k_devika(a)cb.students.amrita.edu Amrita Vishwa Vidyapeetham Coimbatore, India

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Freesurfer January 2020