Freesurfer October 2021

freesurfer@nmr.mgh.harvard.edu

81 participants
113 discussions

Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG
by Donatas Sederevicius 28 Aug '22

28 Aug '22

External Email - Use Caution A new pre-print paper comparing two FreeSurfer’s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selection of the processing method. https://www.biorxiv.org/content/10.1101/2020.10.13.335737v1

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NeuroImage: Reports: Call for papers for Special Issue on Replication findings in neuroimaging studies
by YAN Chao-Gan 25 Feb '22

25 Feb '22

External Email - Use Caution Replication is essential for progress in science. There are several reasons why findings may not replicate, including sampling variability, limited statistical power, cultural/population influences, and improvements in data acquisition and analysis methods. Replication studies are our best attempt at confirming or questioning the reliability of important findings. Replication studies also provide a crucial mechanism for reaching consensus about empirical support for or against a theory. Unfortunately, replication studies are difficult to publish, because many journals judge them as “lacking novelty.” For these reasons, we have created a special issue that highlights replication studies. We invite submissions that seek to replicate published neuroimaging studies, regardless of whether the initial results are confirmed. The primary criteria for acceptance are methodological and statistical rigor -- not conceptual novelty. Novel results are also welcomed, but authors must clearly state which analyses are replications and which are novel. Researchers may use their own collected data, original data from the to-be-replicated study, or publicly available data. We hope that this special issue will help highlight the importance of rigorous replication studies for ensuring progress in neuroimaging. *Submission instructions* The Neuroimage: Reports submission system is open for submissions to our Special Issue from *01 Oct 2021*. When submitting your manuscript please select the article type “*VSI: Replication*”. Please submit your manuscript before *01 Mar 2022.* All submissions deemed suitable to be sent for peer review will be reviewed by at least two independent reviewers. Once your manuscript is accepted, it will go into production, and will be simultaneously published in the current regular issue and pulled into the online Special Issue. Articles from this Special Issue will appear in different regular issues of the journal, though they will be clearly marked and branded as Special Issue articles. Please see an example here: https://secure-web.cisco.com/1CJkKxcFEBPguyPfb5m0Yr2MoiAzErZw3HYZKhuEAMSHET… Please ensure you read the Guide for Authors before writing your manuscript. The Guide for Authors and link to submit your manuscript is available on the Journal’s homepage at: https://secure-web.cisco.com/1VSgggrvcDPky-89wNR6lcPY0XqXuCfOZAX-r7Wa1HcuPp… Inquiries, including questions about appropriate topics, may be sent electronically to Dr. Yan Chao-Gan (ycg.yan(a)gmail.com) Best, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Principal Investigator Director, International Big-Data Center for Depression Research Director, Magnetic Resonance Imaging Research Center Institute of Psychology, Chinese Academy of Sciences 16 Lincui Road, Chaoyang District, Beijing 100101, China - Initiator <http://secure-web.cisco.com/1sqIAAZ4sZdTTXMKfxT5Aar2JR-7UiWQN4aQSU7ygjFTldr…>DPABI <http://secure-web.cisco.com/1oInECTabhfK3d2rurp29HORgmXMA7sq2SIDskuFNuKnDgO…> <http://secure-web.cisco.com/1sqIAAZ4sZdTTXMKfxT5Aar2JR-7UiWQN4aQSU7ygjFTldr…>, DPABISurf, <http://secure-web.cisco.com/1XPTEW4lBFtrlvcsygGbgiVdlAQ26ae4_S7nefApkjEds0k…>DPARSF <http://secure-web.cisco.com/1sqIAAZ4sZdTTXMKfxT5Aar2JR-7UiWQN4aQSU7ygjFTldr…>, and The R-fMRI Network <http://secure-web.cisco.com/1TCtydiq5Yh8xn1WXFHq0xSYHUMfBiOaJiSlkzkVhdXs_ms…> ( RFMRI.ORG <http://secure-web.cisco.com/1Y_OweFD7n8m7sSc_adhdgF-QyZ2_4q16Hw2t4tYSmw0HA2…>) http://secure-web.cisco.com/1p7GiR8RwAPykrvrU-kv5cEmnIMwRR95RSJmBn47-AcsD64… http://secure-web.cisco.com/1wC4UpbExTFsWuXE3IWRwjCjcBW1uPj-8MrNX4mlQzLH_o7…

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TRACULA error wrt to dwi_orig_las.1.bvals file
by juergen.haenggi＠upd.unibe.ch 07 Dec '21

07 Dec '21

External Email - Use Caution Dear TRACULA experts I try to run TRACULA FS7.2 on a Linux machine and get the following error (see below). A similar problem has already been reported in the archives, but I found no solution. https://secure-web.cisco.com/15ekCi1WQB-CkH0WPGgECXGvPn99_mRmsow_C5M9nEA423… Because the file "dwi_orig_las.1.bvals“ was renamed to „dwi_orig_las.bvals“ earlier in the run mv -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals it cannot be found by awk and as a result, I guess, the index.txt file is empty and therefore eddy_openmp terminated. How can I fix this problem? The terminal output, log and config files are attached. Thank you for any advise in advance Regards Jürgen —————— error ———— awk: fatal: cannot open file `/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals' for reading (No such file or directory) eddy_openmp --imain=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz --mask=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs --bvals=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals --acqp=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/acqp.txt --index=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt --data_is_shelled --out=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi EddyInputError: Error when attempting to read --index file /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt Terminating program Linux upd-159253 4.15.0-147-lowlatency #151-Ubuntu SMP PREEMPT Fri Jun 18 20:06:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Oct 27 13:41:49 CEST 2021 upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test> ——————

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Tracula 7.2 using older structural outputs
by Alexopoulos, Dimitrios 21 Nov '21

21 Nov '21

External Email - Use Caution HI, Can you run Tracula 7.2 using older structural outputs generated with FS 6.0 and 7.1.1? 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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TRACULA configuration file for bash
by Alvarado,Luis R 21 Nov '21

21 Nov '21

External Email - Use Caution Hi FS and TRACULA experts, I have a simple question. Do I need to replace: setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_tutorial/fs with: export SUBJECTS_DIR $TUTORIAL_DATA/diffusion_tutorial/fs inside the TRACULA configuration file, if my shell is bash? or should I leave that alone? Best, Luis R. Alvarado Graduate Student Fellow Department of Anatomical Sciences and Neurobiology University of Louisville Kentucky Spinal Cord Injury Research Center 220 Abraham Flexner Way, Suite 1500 Louisville, KY 40202

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Tracula -- Segmentation Fault
by Kaplan, Elizabeth 19 Nov '21

19 Nov '21

External Email - Use Caution I ran recon-all on a group of three subjects, followed by trac-all -prep This process exited with errors: Segmentation fault Original DWI and T1 images appear normal, with no large distortions or missing voxels. My configuration file and trac-all.log are attached below. Any guidance is appreciated! -- [image: Brown logo] *Elizabeth Kaplan '22* *She / Her / Hers* Sc.B. Candidate Cognitive Neuroscience B.A. Candidate Contemplative Studies 69 Brown St Mail #4391 Providence, RI 02912

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mri_label2label issues
by Trisanna Sprung-Much 08 Nov '21

08 Nov '21

External Email - Use Caution Hi there I created labels on surfaces of subjects (chimp) registered to a particular volumetric template. The labels were created on the surfaces in Freeview using Freesurfer 7.1. Since creating these labels, I improved the intensity inhomogeneity in the scans and re-ran the surfaces. When I try to use mri_label2label to transpose the labels to the new surfaces of each subject, the labels do not fall exactly where they should. In fact, the surfaces themselves have a slight translation in them (see snapshot). I assume this is because my registration to the template that I did prior to running recon-all is differing somehow between the 2 groups. However, I thought that this should not matter since mri_label2label --regmethod surface is using the sphere.reg to fsaverage. I am wondering if there is anything I can do to improve mri_label2label to avoid editing the labels manually? Thank you for your time, Trisanna -- Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute

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Aseg and wm edits? + white/pial overlap near subcortical structures
by Kang, Jee Won 08 Nov '21

08 Nov '21

External Email - Use Caution Hello all, ? There are two topics I would appreciate your expert advice on: Topic 1: Aseg and wm edits I was going through the wiki and the archive of past inquiries and was unable to find a clear answer to whether you can make aseg edits and wm edits, and then re-run in Freesurfer at the same time. Furthermore, I was just a little unclear as to how exactly to perform aseg edits. According to this post: https://secure-web.cisco.com/1RxWuWDKVwztKCLSwXj6z1drGBPyh2kvn_19UWiYuyqKvR…,<https://secure-web.cisco.com/1RxWuWDKVwztKCLSwXj6z1drGBPyh2kvn_19UWiYuyqKvR…> you are supposed to edit aseg.manedit.mgz, and only make edits to wm.mgz if segmentation is still incorrect after re-running. The command suggested to be used is recon-all -s subject -autorecon2 -nogcareg -nocanorm -nocareg -autorecon3. However, according to this post: https://secure-web.cisco.com/12Lq8z3kDRX5hmVV3-U_tQM9lMGELV_rZuE0w7MEaZ6-3f… and the wiki page it references here: https://secure-web.cisco.com/1Ktb4SEXIjUqckJnfQRhLq0dVZmG77-DlcegK4GTCJhXvP…,<https://secure-web.cisco.com/1Ktb4SEXIjUqckJnfQRhLq0dVZmG77-DlcegK4GTCJhXvP…> you are supposed to edit aseg.presurf.mgz, and doesn't mention whether aseg edits are compatible with wm.mgz edits. The command these posts say you should run is recon-all -autorecon2-noaseg -autorecon3 -s subject, and this is also listed in the "OtherUsefulFlags" table. My questions are: 1) Does it matter which volume, aseg.presurf.mgz or aseg.manedit.mgz that you edit? 2) What is the proper command to use for re-running with aseg edits? 3) Can you make edits to wm.mgz and aseg edits and re-run with both edits being taken into account? For some background into why I've been looking into editing aseg segmentations, we have a sizeable portion of our data for whom the lateral ventricles are being mislabeled as wm (for some this is quite mild, for others it is pretty extensive). I know the -big-ventricles flag is an option, but we are not looking to re-run all of our subject with it at this time, as we have 100+ subjects. Topic 2: White/pial overlap near subcortical structures Sometimes, the pial surface near the subcortical structures will "pull back" too much, I've attached an example image. This "pull back" sometimes appears after I've re-run the subject after making wm edits, when it was not present in before re-running. In the attached example image, the original pial surface before re-running is in blue, the new pial surface is in red. The original white surface is in green, the new white surface is in yellow. I have the aparc+aseg.mgz and wm.mgz visible. As shown in the image, this "pull back" will often end up exclude a chunk of voxels from the aseg and aparc+aseg, even if there are wm.mgz voxels filled in that area. How important is it to fix errors in this area in general, and would aseg edits be appropriate since wm edits don't seem to address the problem? Thank you for your insight into these topics! Sincerely, Jee Won

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Freesurfer October 2021