Freesurfer January 2022

freesurfer@nmr.mgh.harvard.edu

69 participants
112 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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Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter
by Kang, Jee Won 25 Feb '22

25 Feb '22

External Email - Use Caution Hello all, Apologies for the delay in response! For the applications in my group's work, we are looking at ventricular volume, as well as white matter volume. To that degree, we are interested in whether there are any processing steps earlier in the pipeline that we can implement just to minimize the manual editing required - just anecdotally, there have been cases where lateral ventricle volume increases over 5% after making manual edits, and I was unable to identify if there was a common element to the subjects with ventricle problems. Thank you for your work on this! We really appreciate it. Thank you, Jee Won ________________________________________ Message: 2 Date: Tue, 4 Jan 2022 22:11:53 +0000 From: "Nadar, Priyanka (NIH/CC/OCRTME) [F]" <priyanka.nadar(a)nih.gov> Subject: Re: [Freesurfer] [EXTERNAL] Re: Ventricle segmentation issue - ventricle mislabeled as white matter To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MN2PR09MB5210A46F62E837624F830D51844A9(a)MN2PR09MB5210.namprd09.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution I am not part of Jee Won's team: just generally interested. For my work, I am looking at ventricular volume and so it would be good to not have to manually correct a large number of my scans. ________________________________ From: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Sent: Tuesday, January 4, 2022 1:19 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. Hi Jee Won and Priyanka, there are several things going on here. First, the original aseg (aseg.presurf.mgz) has these areas labeled as nothing (0); they show up as WM in aseg.mgz and aparc+aseg.mgz. Obviously, it would be good to have them properly labeled, but is this critical to your applications? Eg, are you looking at ventricular volume? On 12/21/2021 9:19 AM, Kang, Jee Won wrote: External Email - Use Caution Hello all, I found a very common error in our data while I was correcting recons. The lateral ventricles (usually the horns) are being misclassified as white matter in aseg.mgz. This happened in around 1/3 of our 108 subjects. We were able to fix this issue by manually filling in the ventricles in aseg.presurf.mgz and re-running Freesurfer with the command autorecon2-noaseg -autorecon3, but this is obviously quite a labor-intensive fix for a substantial portion of our data. This was also the only way to fix the segmentation - filling in the mislabeled areas as 255 in the wm.mgz did not fix the problem. I'm not sure why Freesurfer is having issues here, as the areas it is mislabeling have very distinct intensity boundaries - the T1 intensity is usually between 20 and 45 in the areas that are being mislabeled. I've attached a screenshot of a subject's aseg.presurf.mgz who had this ventricle segmentation issue, and you can see that a large portion of the right ventricle has just not been segmented properly; the intensity of the area in the aseg.presurf.mgz and wm.mgz volumes is just 0, and it was 41 (R cerebral white matter) in aseg.mgz. Would you be able to provide some insight into why this might have been happening, and what we could do in the future to prevent such extensive manual editing in the future? I can also say that this data was processed with a T2 image as well, and supplying that flag didn't help with the segmentation issue. Thank you, Jee Won _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1ZGRySYd-5iOMX55uEC_0An1dt-wqdEh2tYIkVApSE6ZYz…

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Recon-all reconstructed image coordinates
by Salar Dini, Elaheh 13 Feb '22

13 Feb '22

External Email - Use Caution Dear Freesurfer developers, In the link below, you see two brains belonging to the same subject: https://secure-web.cisco.com/13BPz3RKb4ouXjNEzLehwPZTK95KDfvYg0N-g887u-w7ft… [https://secure-web.cisco.com/1B08cXHTWamf2XLl-Do2M2Y2jFkmx7hn93F8dK1GfF1Mv6…<https://secure-web.cisco.com/13BPz3RKb4ouXjNEzLehwPZTK95KDfvYg0N-g887u-w7ft…> Screen Shot 2022-01-26 at 1.40.23 PM.png<https://secure-web.cisco.com/13BPz3RKb4ouXjNEzLehwPZTK95KDfvYg0N-g887u-w7ft…> Shared with Dropbox http://secure-web.cisco.com/1qgxtofGxpoR7Sqc5YpeFwa6ndZVhgCVEL8DwdalIfXi80q… while one of them is reconstructed with FS7.2, the other one is reconstructed with a pipeline that uses another code for extracting brain tissue (BET Mask) and then use FS6 for the remaining stages of the reconstruction. While the final result of both constructions matches in most aspects, they don't occupy the same coordinates in space. Is there a way that we can match the coordinates of each voxel for two images? Or in other words make them compatible. The Platform we use is CentOS7 . Thanks and all the best, Ela

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PETSurfer: error: MatrixReadTxT: could not scan value [1][1]
by Jennifer Bramen 10 Feb '22

10 Feb '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to analyze amyloid PET data using PETSurfer. I am trying to do kinetic modeling and I am on the MRTM1 step. I have tried this two ways (one using the wiki instructions and the other using the tutorial ROI-based approach) mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/km.hb.tac.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o mrtm1 --no-est-fwhm --nii.gz; done mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/gtm.nii.gz --mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o $PET_DIR/PREV_019/mrtm1.roi --nii.gz;done Both times I get this error: error: MatrixReadTxT: could not scan value [1][1] I have opened all of the .dat files using my text editor (nano) and they seem ok. I have tried this in other subjects and I get the same error. I searched the list and I cannot find any discussion regarding this error using mri_glmfit and PET data. Anything you can do to help me troubleshoot this error would be greatly appreciated!!! Attached is my time.dat file (I think this is the most likely culprit). Warm regards, Jennifer Bramen, PhD (she/her/hers) Senior Research Scientist, Neuroimaging Assistant Professor Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | Providence Saint John's Health Center

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lGI value aberrantly high, again
by Bernardoni, Fabio 04 Feb '22

04 Feb '22

External Email - Use Caution Dear all as some other posted before me, sometimes the computation of lGI fails with the message (see for example: https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiH…, https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9…, https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9…) 'lGI for vertex number 35901 of the outer mesh is 2.5958 ... remeasuring lGI value for vertex iV = 36001. It may take a few minutes. WARNING -- Problem for vertex iV = 36001, lGI value is aberrantly high (lGI=53.1127)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.' as many reported before me, computation of euler number gives 2, i.e. nothing wrong. another suggestion by marie schaer is to rerun recon-all -hemi ?h -autorecon2 -autorecon3 , with or without the -randomness option. The point is that the -randomness option seems to have no effect, the error occurs again in exactly the same place, with the exact same value (lGI=53.1127). I am using freesurfer 7.1. Has there been any development to solve this? Thank you in advance Fabio Bernardoni Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1xvuU9YpZrNAT8MBR8aeslCWdv2cNu-xhctWukMA-pgRDlf…; http://secure-web.cisco.com/18N9590xMz7PXy9R7etuq98MdgjKagN7Y04h0saKn6vRWYJ… +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswP… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswP… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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impact of defacing on eICV calculations
by Ritobrato Datta 04 Feb '22

04 Feb '22

External Email - Use Caution Hi All, I have inherited some T1 data that are defaced. If I run the defaced images through freesurfer, will that impact the eICV calculations ? Please let me know. Many thanks Ri

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Display PCC in cluster
by Andrei Bieger 04 Feb '22

04 Feb '22

External Email - Use Caution Hi, Douglas, I performed a group analysis and, after permutation, one cluster survived. How can I display this cluster over an inflated surface, but with colors representing the partial correlation coefficient? In other words, I would like to see the pcc.mgh file in an inflated surface, but only for those vertices belonging to the cluster. -- Andrei Bieger

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Freesurfer January 2022