Freesurfer June 2024

freesurfer@nmr.mgh.harvard.edu

47 participants
51 discussions

cluster area from mri_surfcluster and read_curv are inconstant
by wangzhiwei3233 12 Jun '24

12 Jun '24

External Email - Use Caution Dear Freesurfer experts, I got the area of a cluster by two methods, and found the results were inconstant. Method 1: During group level analysis, the individual surface was normalized to fsaverage. I exported the cluster area and label file by command mri_surfcluster. The command ws as followed: mri_surfcluster --in ./sig.nii.gz --subject fsaverage --hemi lh --centroid --annot aparc --thmin ${thp} --sign ${sigsignTemp} --no-adjust --minarea ${tharea} --sum area${tharea}.${sigsignTemp}${thp_infilename}.cluster.summary --o area${tharea}.${sigsignTemp}${thp_infilename}.cluster.nii.gz --ocn area${tharea}.${sigsignTemp}${thp_infilename}.ocn.nii.gz --olab $Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_area${tharea}.${sigsignTemp}${thp_infilename}/label Method 2: I calculated the cluster area using the label file outputed by mri_surfcluster via the matlab funciton read_curv. I did this to test the method for calculating the area of a label manually drawn by me. 1, I first got the area of each vertex by the command area = read_curv('../fsaverage/surf/lh.area'); 2, I red the IDs of vertices in the label file and added 1 3, I got area values of vertices in the label file and summed them. I found the areas calculated by the Method2 were much smaller(except one ROI) than the ones exported by mri_surfcluster as shown below. Area from Method 1： # ClusterNo Size(mm^2) NVtxs Annot 1 833.94 1999 postcentral 2 578.52 1300 precuneus 3 243.78 463 middletemporal 4 184.72 344 inferiorparietal 5 111.76 292 insula Area from Method 2： ClusterNumber Area(mm^2) NVtxs AnotomicalRegion 1637.39 1999 postcentral 2 480.44 1300 precuneus 3 140.37463 middletemporal 4 166.33344 inferiorparietal 5112.76292 insula What's the reason? Where did I do wrong in the method 2? Thanks. Best, zhiwei -- ----------------------------------------------- Zhiwei Wang（王志伟), Associate Investigator International Center for Primate Brain Research Center for Excellence in Brain and Intelligence Technology Institute of Neuroscience,Chinese Academy of Sciences Room 215, Building #5, 500 Qiangye Road, Shanghai, 201602,China

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Re: [Freesurfer] Help: when will the next version of FreeSurfer become available?
by fsbuild 11 Jun '24

11 Jun '24

External Email - Use Caution  We have no current reports about security issues with the FS release.   An address using the string fsbuild will email you directly so you can respond to only that address if you would like to report an issue.  Please check you spam folder.  PLEASE DO NOT POST AND/OR DISCUSS SECURITY ISSUES ON THE PUBLIC FREESURFER LIST. - R. On Jun 11, 2024, at 16:03, Tran, Kevin (NIH/NIMH) [E] <kevintran(a)mail.nih.gov> wrote:        External Email - Use Caution        Hi,We have been pressured by our IT Security team to address some of the vulnerabilities (e.g., OpenSSL) they found in FreeSurfer 7.4.1. I am wondering if you could share with us when would the next version of FreeSurfer become available?  Thanks,------------------------------Kevin TranData ScientistThe National Institutes of HealthNIMH, Laboratory of Brain and Cognition10 Center Drive, Room 4C215Bethesda MD 20892-1366kevintran@mail.nih.govWork:(301)435-4936 Cell:(301)755-3715_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Help: when will the next version of FreeSurfer become available?
by Tran, Kevin (NIH/NIMH) [E] 11 Jun '24

11 Jun '24

External Email - Use Caution Hi, We have been pressured by our IT Security team to address some of the vulnerabilities (e.g., OpenSSL) they found in FreeSurfer 7.4.1. I am wondering if you could share with us when would the next version of FreeSurfer become available? Thanks, ------------------------------ Kevin Tran Data Scientist The National Institutes of Health NIMH, Laboratory of Brain and Cognition 10 Center Drive, Room 4C215 Bethesda MD 20892-1366 kevintran(a)mail.nih.gov<mailto:kevintran@mail.nih.gov> Work:(301)435-4936 Cell:(301)755-3715

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SAMSEG with recon-all
by Jones, Richard 11 Jun '24

11 Jun '24

External Email - Use Caution Hi, I have been looking to use SAMSEG to segment T1 and FLAIR images and then feed the segmentation results into the recon-all pipeline. The command I have been using is below:- /Applications/freesurfer/bin/samseg --t1w ./T1/Subjects/MP074.nii.gz --flair ./FLAIR/Subjects/MP074.nii.gz --hires --use-flair --normalization2 --fill --pallidum-separate --threads 4 --s MP074 --recon --refmode t1w The job completes without error and the segmentations look fine but when I look at the FLAIR images then images in the coreg and input folders in the subject directory are fine but when I look at the images in the mri directory while the FLAIR.prenorm.mgz looks fine the FLAIR.norm.mgz and FLAIR.mgz images are normalized T1 images with some of the neck clipped off and are indistinguishable from the nu.mgz image. The SAMSEG segmentation isn't affected since it uses the FLAIR image from the coreg directory but I'm assuming the issus with the FLAIr.norm and FLAIR images will have repercussions for the rest of the recon-all pipeline since I'm using the -use-flair option. Is that correct and is there a fix for this? I'm using a Mac Pro running version 12.6.8 (Monterey) of the Mc OS. I'm running version 7.4.0 of the Freesurfer software. I have attached the logfile and a pdf file showing some of the images. Richard

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Re: [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar
by Carina Obermüller 11 Jun '24

11 Jun '24

External Email - Use Caution Dear Antoine, Thank you so much again for your reply! I did as you said and it seems like the script is on my computer now, but I get this error: Could not find hipposubfields.rh.T1.v22.txt, skipping subject. For all files. The first few lines looked like this: carinaobermuller@MBP-di-Carina raw_data_freesurfer_Dec2023 % ConcatenateSubregionsResults.sh -f amygdalar-nuclei.lh.T1.v22.txt -f amygdalar-nuclei.rh.T1.v22.txt -f brainstem.v13.txt -f hipposubfields.lh.T1.v22.txt -f hipposubfields.rh.T1.v22.txt -s $PWD cmd: /Applications/freesurfer/7.4.1/bin/ConcatenateSubregionsResults.sh -f amygdalar-nuclei.lh.T1.v22.txt -f amygdalar-nuclei.rh.T1.v22.txt -f brainstem.v13.txt -f hipposubfields.lh.T1.v22.txt -f hipposubfields.rh.T1.v22.txt -s /Users/carinaobermuller/Documents/raw_data_freesurfer_Dec2023 Gathering results from: /Users/carinaobermuller/Documents/raw_data_freesurfer_Dec2023 Looking at files: amygdalar-nuclei.lh.T1.v22.txt amygdalar-nuclei.rh.T1.v22.txt brainstem.v13.txt hipposubfields.lh.T1.v22.txt hipposubfields.rh.T1.v22.txt Outputting results to: /Users/carinaobermuller/Documents/raw_data_freesurfer_Dec2023 Concatenating stats for file: amygdalar-nuclei.lh.T1.v22.txt Will write results to: amygdalar-nuclei.lh.T1.v22_concat.txt Working on subject: Raw_TP1 Could not find amygdalar-nuclei.lh.T1.v22.txt, skipping subject. Working on subject: Raw_TP2 Could not find amygdalar-nuclei.lh.T1.v22.txt, skipping subject. Working on subject: T1w_AoC1001_T1_reor Could not find amygdalar-nuclei.lh.T1.v22.txt, skipping subject. Working on subject: T1w_AoC1001_T2_reor Could not find amygdalar-nuclei.lh.T1.v22.txt, skipping subject. The files are in the “stats” folder of each subject folder. I am wondering if the script is calling the files from a different folder? Or am I doing something else wrong? Best wishes Carina Il giorno 24 mag 2024, alle ore 11:54, COSSA ANTOINE IDRS <antoine.cossa(a)servier.com> ha scritto: Dear Carina, I got the same problem at first, I thought it was coming from my computer. To resolve this, I simply downloaded the missing script file from here:https://secure-web.cisco.com/1P3_VeR3p4seMFU_4h_YDuZEeXwHEzHxThUx__-6W…, put it in the bin folder of FreeSurfer and rerun the source command (source $FREESURFER_HOME/SetUpFreeSurfer.sh). This should fix your issue. Kind regards, Antoine ________________________________ De : Carina Obermüller <carina.obermueller(a)live.at<mailto:carina.obermueller@live.at>> Envoyé : jeudi 23 mai 2024 17:01 À : COSSA ANTOINE IDRS <antoine.cossa(a)servier.com<mailto:antoine.cossa@servier.com>> Cc : Carina Obermüller <carina.obermueller(a)live.at<mailto:carina.obermueller@live.at>> Objet : Re: Group Stats for hipposubfields, brainstem and amygdalar CAUTION: This email originated from outside the company. Dear Antoine, Thank you so much for your quick reply 😊 I ran this command in the directory that contains the free surfer file structure of my data, but it showed me that the command doesn’t exist: ConcatenateSubregionsResults.sh -f amygdalar-nuclei.lh.T1.v22.stats -f amygdalar-nuclei.rh.T1.v22.stats -f brainstem.v13.stats -f hipposubfields.lh.T1.v22.stats -f hipposubfields.rh.T1.v22.stats -s $PWD Do you know where I am going wrong here? Kind regards Carina Il giorno 22 mag 2024, alle ore 16:36, COSSA ANTOINE IDRS <antoine.cossa(a)servier.com> ha scritto: Dear Carina, I think you can refer to this page : ConcatenateSubregionsResults - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1CUyxaHfBCZieKC2UZBS0ojCN-NyonuQwz4rUPZ-Bj_M__…> and use the ConcatenateSubregionsResults.sh command 😉 Kind regards, Antoine ________________________________ De : freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> de la part de Carina Obermüller <carina.obermueller(a)live.at<mailto:carina.obermueller@live.at>> Envoyé : mardi 21 mai 2024 13:45 À : freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Cc : Carina Obermüller <carina.obermueller(a)live.at<mailto:carina.obermueller@live.at>> Objet : [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar CAUTION: This email originated from outside the company. External Email - Use Caution Dear Freesurfer team, I am looking for a group stats command like the asegstats2table and aparcstats2table command for hipposubfields, brainstem and amygdalar, but I couldn’t find it in the archives. I remember it was mentioned in the recent Freesurfer course, but I can’t find it anymore. Could you help me out? Also more generally, is there an overview page of all the possible group stats commands? Thank you so much in advance for your reply! Sincerely, Carina _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1YC3Wkh9GsuoUgk2aLDNhZwQWnj050pY1okkYwzLmkGduw…<https://secure-web.cisco.com/1y0oaAj8_46msfz3eab9vNnk8YQrv2-9xR9bXASOV_MJuE…> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine athttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mas…<https://secure-web.cisco.com/1v_G4tfViUO0PitHCYTcVmk39R_yzC2VvNdgp58dPel26G…> <https://secure-web.cisco.com/15CClIlio2Fi86MEVXaEif15a6f-Blo3JBwfNOeSWmsV1-…<https://secure-web.cisco.com/1v_G4tfViUO0PitHCYTcVmk39R_yzC2VvNdgp58dPel26G…>> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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The Affective Neuroscience Project of the Midlife in the U.S. (MIDUS) study is recruiting a multimodal imaging scientist
by STACEY M SCHAEFER 11 Jun '24

11 Jun '24

External Email - Use Caution The Midlife in the U.S. (MIDUS; https://midus.wisc.edu/) Affective Neuroscience Project Team is excited to bring on an energetic and skilled Ph.D.-level scientist to join our dynamic team and ask questions within the national, longitudinal data to inform public health and wellbeing. The successful candidate will work in collaboration with members of the team to address critical scientific questions related to the factors contributing to brain mechanisms underlying emotional processes, cognitive decline, and brain aging with a goal of informing public health and social change to optimize emotional wellbeing and brain health. This position requires analytic thinking, expertise analyzing multimodal MRI data (e.g., structural MRI, task and resting state fMRI, diffusion weighted imaging, and perfusion imaging data), and the ability to apply technical innovation to neuroscience problems relevant to public health and wellbeing. The position is open to a qualified scientist with evidence of training in applying quantitative solutions to neuroscience imaging data and at least 2 years of post-doctoral experience. Please distribute this far and widely to anyone who may be interested and anywhere people might see it who have the skills and interests to work with our team. Please share with relevant neuroimaging, neuroscience, and psychology societies, departments, schools, and universities. Thanks very much! For more information on the position, please see: https://aging.wisc.edu/join-us/ https://jobs.wisc.edu/jobs/multimodal-imaging-scientist-madison-wisconsin-u… For more information on the MIDUS Affective Neuroscience team, please see: https://aging.wisc.edu/midus-affective-neuroscience-project/ Stacey M. Schaefer, Ph.D. Leader of the MIDUS Neuroscience Project & Co-Leader of the MIDUS Admin Core Institute on Aging 2245C Medical Sciences Center University of Wisconsin-Madison 1300 University Ave Madison, WI 53706 USA 608-265-3486

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Unequal size groups
by stdp82＠virgilio.it 11 Jun '24

11 Jun '24

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Fwd: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus
by Ahsan Ali 11 Jun '24

11 Jun '24

External Email - Use Caution Hello everyone, Could anyone please help me to know which Atlas is used in the segmentation of corpus callosum, hippocampus, and fornix using freeSurfer from Brian MR images. I have gone through the literature but couldn't find it. With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics (Biomedical Engineering Group) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552 ---------- Forwarded message --------- From: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> Date: Wed, May 22, 2024, 10:52 PM Subject: RE: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus To: Ahsan Ali <ahsan889960(a)gmail.com> Can you please post to the list so that others can answer? *From:* Ahsan Ali <ahsan889960(a)gmail.com> *Sent:* Wednesday, May 22, 2024 1:04 PM *To:* Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> *Subject:* Re: Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus * External Email - Use Caution * Dear sir, It is not clear from these papers to me. With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics (Biomedical Engineering Group) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552 On Wed, May 22, 2024, 8:19 PM Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> wrote: Mostly these: https://secure-web.cisco.com/1DKaAagv5wrZcn_HucsSWH8TG1zknHKvHLkGgJhoy1pwq5… <https://secure-web.cisco.com/1HR13_22Yz_9WpJjcigfRprjowpMV_nRs6XlxrY4Yb6j-e…> https://secure-web.cisco.com/1XuxKv5CEuHRfXAdPzciFLM-HiNv8hX8h1hN2vYlGz0J9u… <https://secure-web.cisco.com/1uYxJbJpTbAO8ILMWce1OXOAM2VlXwJ80ARMpic7_Y4CDC…> cheers Bruce *From:* Ahsan Ali <ahsan889960(a)gmail.com> *Sent:* Wednesday, May 22, 2024 4:31 AM *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>; Huang, Yujing <YHUANG43(a)mgh.harvard.edu>; Fischl, Bruce R.,PHD < BFISCHL(a)mgh.harvard.edu> *Subject:* Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus * External Email - Use Caution * Dear FreeSurfer Team, After reviewing the literature, I have a question: which atlases are used in the segmentation of the fornix, corpus callosum, and hippocampus from magnetic resonance images using FreeSurfer? This is a significant question for me, and I would appreciate a clear and concise answer. Please provide some relevant references. With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1OM4mcc50Qfe8k4W6OcHgaA943SBzfkdd7bNh8ZqMDtb9_… <https://secure-web.cisco.com/1N0MvKNFIBgTBpwH0_fE4Erq9GYA9l1dAIs9zS_j_cM3I1…> . The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1OM4mcc50Qfe8k4W6OcHgaA943SBzfkdd7bNh8ZqMDtb9_… .

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Intensity affected after using -c flag in mri_convert
by ERNEST KISSI 11 Jun '24

11 Jun '24

External Email - Use Caution Dear fresurfer team, Why does the use of conform flag (-c) in mri_convert affect the intensity of the image? I have an image with absolute intensity of 1000 and after using the conform flag in mri_convert, the intensity is around 98.1. why is there a different scale in the intensity after the use of the flag?

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Transformed geometry does not match
by Yasmine Salman 11 Jun '24

11 Jun '24

External Email - Use Caution Dear FreeSurfer developers, I am trying to run longitudinal recon-all -long command. For some subject the recon-all -long command does not work and the error message indicate that 'transformed geometry does not match". I checked and the initial recon-all finished without error as well as the recon-all -base. I also tried to re-run de base but it does not help. Knowing that recon-all -long command worked for the majority of my subjects, what can explain that it does not work for some of them ? And how can we solve that problem ? Thanks in advance for your help, Best, Yasmine

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