Freesurfer May 2024

freesurfer@nmr.mgh.harvard.edu

56 participants
69 discussions

Re: [Freesurfer] Question on using thalseg_1.1.h5
by Georgios Argyropoulos 23 May '25

23 May '25

External Email - Use Caution Many thanks and apologies, Henry - I figured it out... I stupidly replaced your improved segmentation script in both the scripts and the bin directory instead of only replacing the former. many thanks for your time, much appreciated g

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run_samseg: Optimizer: maximalDeformation is too small; stopping; killed
by Ringki Marie Siewert 08 Aug '24

08 Aug '24

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Recon-all for a common template
by Chen Yang 24 Jun '24

24 Jun '24

External Email - Use Caution Dear Freesurfer Developers, my data is from 50 preschoolers and I created my own group template from these kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti file (see attached). Then we'd like to process this group template in Freesurfer to reconstruct the cortical surfaces as the individual brain images. My question is, how can i do the recon-all with the template? Because I only have this template file I feel I don't have enough input files(?). Thanks in advance! Best regards, Chen -- Chen Yang PhD Student Independent Research Group 'Milestones of Early Childhood Development' Max Planck Institute for Human Cognitive and Brain Sciences Email:yangc@cbs.mpg.de

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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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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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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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mri_fuse_segmentation error: could not open file
by Tommaso Cusolito S319624 04 Jun '24

04 Jun '24

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to extract cortical thickness from a fifth scan using a template based on only the first four scans (obtained by following the longitudinal pipeline available at https://secure-web.cisco.com/1S7BQNmF9HghVT1XkcD-pYvMmoQDm0WTjg3-N1bP-4anPW…) Unfortunately, I don't have the option to run the longitudinal processing from scratch including the fifth scan as I no longer have access to the cross-sectionally processed single scan data (in format patient_scan#) for scans 1 through 4 but only to the folders generated by the recon-all function (in format patient_scan#.long.patient_template). I've made sure to generate .lta files (through mri_robust_register) for forwards and backwards transformations from s5 to template and to add the scan 5 to the "base-tps" file, but recon-all reports a later error when using the function mri_fuse_segmentations as I no longer have access to files for single scans (norm.mgz, aseg.mgz,aseg.auto_noCCseg.mgz). I acknowledge that the template data will be biased towards the first four scans but I was looking for a way to use the function on only data belonging to the "patient_scan#.long.patient_template" folders together with the fifth scan data "patient_s5". Has anyone tried using this course of action and found a viable solution? I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 2) Platform: 3.10.0-1160.92.1.el7.x86_64 3) uname -a: Linux krusty 3.10.0-1160.92.1.el7.x86_64 #1 SMP Tue Jun 20 11:48:01 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached

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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates
by Liliana Wu 03 Jun '24

03 Jun '24

External Email - Use Caution Thank you Douglas. That’s much clearer. I do however, have a subject without a gender disclosure. Would I set up my class and contrasts as: 5 classes: PatentientsMale, PatientsFemale, HCMale, HCFemale, HCNa then use contrast [0.5 0.5 -0.33 -0.33 -0.33 0 0 0 0 0 ...]? Best, Liliana

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