Freesurfer December 2021

freesurfer@nmr.mgh.harvard.edu

56 participants
87 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] Spatial distance between regions
by Julie Ottoy 26 Jan '22

26 Jan '22

External Email - Use Caution Hi Doug, Just checking in with the question below. Does Freesurfer have such an option? Thanks, Julie On Tue, 14 Dec 2021 at 18:38, Julie Ottoy <julie.jj.ottoy(a)gmail.com> wrote: > Hello FreeSurfer team, > > I was wondering if there is a way to calculate a distance matrix between > atlas-based regions (e.g. between their centers of mass) in volumetric > space (MNI152) space? > > Thank you for the information! > Best regards > Julie >

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Ventricle segmentation issue - ventricle mislabeled as white matter
by Kang, Jee Won 04 Jan '22

04 Jan '22

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

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Making a Patch
by Alison McDonnell 04 Jan '22

04 Jan '22

External Email - Use Caution Hi Freesurfer, I am currently trying to make a patch to make a flat map. I make the relaxation cuts and circular cut in midline region but then when I try to remove the circle it removes everything but. I can't work out why this is happening as I was able to do it with the other hemisphere and have tried variations of cuts etc. Any advice would be appreciated. Thanks, Ali

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Possible to Specify Default Version of MATLAB for selxavg3-sess?
by Yadav, Shrikanth Muralidhar 02 Jan '22

02 Jan '22

Hello Freesurfer Developers, I am having trouble with my first level analysis using selxavg3-sess. I passed the -debug flag in my command and noticed that MATLAB 2021a was being used. However, the command worked as expected before MATLAB was updated from 2020b. Is there a way I can specify freesurfer (v6.0.0) to use a specific version of MATLAB? I tried passing the -octave flag but got the following error ERROR: cannot find /usr/local/freesurfer/stable5_1_0/matlab/ The full command: selxavg3-sess -s 002_S_0413_V1_fMRI -overwrite -a lh-FastADNI12state1 -no-preproc -force -debug Thank you Shrikanth

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Cohen´s D effect size
by Steve Petersen 02 Jan '22

02 Jan '22

External Email - Use Caution Dear Freesurfer experts, I am attempting to estimate the Cohen's D effect size of significant clusters using the suggested command <https://secure-web.cisco.com/1jHNDOrJJ6TcImjSXLGzeh59SUh27A8_HOdinuqzuimVg7…>: fscalc gamma.mgh div rstd.mgh -o cohensd.mgh Now, I get the cohensd.mgh file but I am not able to open this file. How can I see the particular effect size of each significant cluster included in the sig.cluster.summary file?. Thank you very much for your help! Best regards,

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Re: [Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala
by Laura Willers de Souza 02 Jan '22

02 Jan '22

External Email - Use Caution Dear Douglas, Thanks so much for your answer. Could you check if the following commands to perform ROI analysis with GLM are correct? 1. Create the table with the volumes of the hippocampal segmentation (1 command for each hemisphere - only replace lh with rh): asegstats2table --statsfile hipposubfields.lh.T1.v21.stats --fsgd CU_CI.fsgd \ --meas volume \ --all-segs \ --tablefile hipposubfields.lh.T1.v21.CU_CI.dat 2. GLM Analysis – DODS (1 command for each hemisphere - only replace lh with rh): mri_glmfit \ --table hipposubfields.lh.T1.v21.CU_CI.dat \ --fsgd CU_CI.fsgd dods \ --C group.diff.CU_CI.mtx \ --glmdir hipposubfields.lh.T1.v21.CU_CI.glmdir 3. Correction for multiple comparisons – FDR: mri_fdr --fdr .05 --pos --thfile --i contrast/lh.sig.mgh lh.mask.mgh hipposubfields.lh.T1.v21.CU_CI.mgh --no-log10p --i contrast/rh.sig.mgh rh.mask.mgh hipposubfields.rh.T1.v21.CU_CI.mgh --no-log10p Are these commands correct? Another question, in this type of analysis is image smoothing common? Like was done here https://secure-web.cisco.com/1ZjmO80yeIcvew54e44mv0-Yzru83V18CRkiga2XGIlA0l… Thank you so much again! Best regards, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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Freesurfer December 2021