Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

recon-all clinical : usage with contrast-enhanced T1-weighted images?
by Barbara Bellenberg 14 Jun '24

14 Jun '24

External Email - Use Caution Dear all, I would like to use the recon-all-clinical pipeline with Gadolinium contrast-enhanced 3D-T1 weighted images. Can you tell me if recon-all-clinical is suitable for this purpose? Thanks in adcance for your support! Barbara

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Probability density function
by Jingjing Liu 13 Jun '24

13 Jun '24

External Email - Use Caution Dear Freesurfer team, I am looking for the answer that where I can find the document of Probability density function in voxels of each brain volume after preprocessing. Because I need these indicators. Thank you so much in advance for your reply! Sincerely, Jingjing Liu

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BIANCA Sensitivity/Robustness to non-brain material in skull-strip
by CRISTIAN MOJICA 13 Jun '24

13 Jun '24

External Email - Use Caution Hello, I will be running BIANCA in FSL after some quality control with the requisite files to be listed in the Masterfile. I am examining my skull-strip files (in FLAIR space), and most skull strips still have some dura or black space occupied by CSF leftover. How sensitive is BIANCA to some leftover non-cortical material, or is anyone aware of an analysis that examines BIANCA's output as a function of thoroughness of skull strip, or (on the Freesurfer side) have suggestions for gcut or wsthresh parameters that are good for BIANCA? The skull strip was done in Freesurfer's recon-all process, then the resulting brainmask was registered into FLAIR space with FSL. Thanks in advance!

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PETSurfer: pvc'ed and scaled output nifti image
by Sneha Pandya 12 Jun '24

12 Jun '24

External Email - Use Caution Dear team, I am using mri_gtmpvc to obtain PVC'ed regional data which we will use as an input TAC to perform kinetic analysis. In addition, we are also doing static SUVR analysis (sum of frames from 60-90 mins) in which I am scaling input PET data with gray matter cerebellum. In the output folder I see that upon scaling (when using --save-input flag) we get a scaled input image which can be used as SUVR. However, is this scaled image also PVC corrected or just scaled? If not, then is it possible to get PVC'ed and scaled nifti image? Thank you, Sneha

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Does motion correction command mc-sess do censoring of high motion timepoints?
by Possidente, Thomas 12 Jun '24

12 Jun '24

External Email - Use Caution Hi there, I'm using this version of Freesurfer: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 I'm using mc-sess to run motion correction on some functional task and resting state data. I would like to perform censoring on high motion timepoints in order to reduce spurious correlations due to movement during connectivity analysis. My main question is: does mc-sess include censoring? If so, what are the threshold parameters? If not, are there any optional arguments to turn censoring on? If not, how do you recommend doing motion correction with censoring using Freesurfer? I know mc-sess uses AFNI's motion correction, just not sure if it utilizes censoring. Thank you, Tom

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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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