Freesurfer July 2023

freesurfer@nmr.mgh.harvard.edu

93 participants
130 discussions

Password FS_7_2_0_ubuntu_18_04_06.ova
by Reinier Tack 20 Jul '23

20 Jul '23

External Email - Use Caution Good afternoon, I'm trying to broaden my neuroimaging software skills with Freesurfer and was hoping to do the online tutorial. However it asks me for a password when downloading the zipped file and said to email to receive the password. Would it be possible for me to obtain this password through this route? Kind regards, Reinier.

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pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Geng Liu 20 Jul '23

20 Jul '23

External Email - Use Caution Dear freesurfer developer: I am writing to ask for the pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z. Could you kindly provide it? Many Thanks! Best, ---------------------------------------------- Geng UESTC school of Life Science University Of Electronic Science and Technology of China Shahe Campus: No.4, Section 2, North Jianshe Road Chengdu, Sichuan, P.R China Zip/Postal Code:611731

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File Password
by Gabriel Nasrallah 19 Jul '23

19 Jul '23

External Email - Use Caution Hello, I would like to request the password to the file FS_7_2_0_ubuntu_18_04_06.ova.7z

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There is a marked difference between the left and right brain in the reproducibility of volume when 1416 recon-all runs are performed on the same subject
by 神保岳大 19 Jul '23

19 Jul '23

External Email - Use Caution Dear FreeSurfer team, We were interested in the reproducibility of multiple runs of recon-all and repeated recon-all 1416 times on the same subject. We then checked the left and right brain results for the volume obtained from the Aseg process. The right brain showed exactly the same volume, while the left brain showed a small variation. We thought that the variation in volume between the left and right brains would be the same. But why is this not the case in reality? The volume_attemps1416.csv is attached. For example, the Left-Lateral-Ventricle in this file has variation, but the Right-Lateral-Ventricle has no variation, as shown below. *Left-Lateral-Ventricle*12377.8 12375.9 12375.9 12380 12376.4 ... *Right-Lateral-Ventricle*7514.7 7514.7 7514.7 7514.7 7514.7 ... 1) FreeSufer vesion: 7.2.0 2) Platform: Red Hat Enterprise Linux 8.6 3) uname -a: Linux fn01sv01 4.18.0-372.36.1.el8_6.x86_64 #1 SMP Thu Nov 17 16:37:07 EST 2022 x86_64 x86_64 x86_64 GNU/Linux 4) volume_attemps1416.csv: Summarized results of 1416 aseg.stats.

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pass code for FS_7_2_0_ubuntu_18_04_06.ova
by Ramtilak Gattu 18 Jul '23

18 Jul '23

External Email - Use Caution Hi, Could I please get the pass code for FS_7_2_0_ubuntu_18_04_06.ova Thanks Regards Tilak

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Tracula statistics outputs for version 7.2
by King-Wai Chu 18 Jul '23

18 Jul '23

External Email - Use Caution Hi, Upon further examination of pathstats.byvoxel.txt and pathstats.overall.txt, I have 2 more questions. Since my previous 3 questions still have not been answered, I'm including them here so that they are all in one place. The 2 new questions are 4) and 5), my previous 3 questions are appended after. 4) I have noticed that the averages of AD, RD, MD and FA in pathstats.byvoxel.txt are exactly the same as the *_Avg_Center in pathstats.overall.txt. According to the tutorial, *_Avg_Center in pathstats.overall.txt is the "average over highest-probability path only" and the AD, RD, MD and FA in pathstats.byvoxel.txt is the value at the "position on the maximum a posteriori path". Does it mean that "highest-probability path only" and "position on the maximum a posteriori path" are the same or one of them should be changed to the other one? 5) Are the averages of AD_Avg, RD_Avg, MD_Avg and FA_Avg in pathstats.byvoxel.txt suppose to match *_Avg(average over the entire support of the path distribution) in pathstats.overall.txt? When I removed the duplicate points in pathstats.byvoxel.txt, the averages of AD_Avg, RD_Avg, MD_Avg and FA_Avg come very close to the value of *_Avg in pathstats.overall.txt I don't think I can calculate the averages by including the duplicate points in 4) but removing them in 5). Either including them in both or not at all. Questions from my previous email. 1) There are duplicate points in pathstats.byvoxel.txt, is it normal? I didn't try it on all 42 tractcs. For the few I've looked at, they all have duplicate points. I used the default setting in the config file to run trac-all. 2) When I do along-tract statistical analysis, sig.mgh and z.mgh are 1D files. When embed the sig.mgh and z.mgh statistical maps from the analysis into the template .trk (*.display.trk, which is 3D), it seems to me that sig.mgh and z.mgh don't have enough information to give *.display.trk the voxel values for the *.overlay.trk. There is no one-to-one voxel corresponding between sig.mgh and *.display.trk. What am I missing? Or what's the embedding process do? 3) When I convert .trk(*.overlay.trk, for example) to nii.gz or ascii using dmri_trk2trk or mri_convert the voxel values of the .trk file don't get converted into the .nii.gz or ascii file, only the x,y,z coordinates are converted. Is there a way to get the voxels values of the .trk file when converting to .nii.gz or ascii format? Thanks, King-Wai -- King-Wai Chu, Ph.D. Program Analyst Mental Illness Research, Education and Clinical Center (MIRECC, VISN3) James J. Peters Dept. of Veterans Administration Medical Center (OOMH) 130 W. Kingsbridge Road Bronx, NY 10468

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Re: [Freesurfer] Tracula statistics outputs for version 7.2
by Alan Francis 18 Jul '23

18 Jul '23

External Email - Use Caution Hi King-Wai/ Chiara Thank you for your excellent suggestions. Chiara: I have made the changes you suggested. Can you please check if the config file looks workable? King-Wai - I made the change you suggested. But the problem still persists. I have attached the config file. best, Alan On Tue, Jul 18, 2023 at 12:26 PM King-Wai Chu <kingwai.chu(a)gmail.com> wrote: > Hi Alan, > > I think in your "set dcmlist", you are missing > /home/alanfrancis/IMAGING/DTI/ > before 109123 > It should be > set dcmlist = > /home/alanfrancis/IMAGING/DTI/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz > > Best, > > King-Wai > > On Tue, Jul 18, 2023 at 12:59 PM Alan Francis <alandarkenergy(a)gmail.com> > wrote: > >> Hi King-Wai: >> >> I have been running Tracula on 7T images and it keeps giving me an error. >> The error is as follows: >> >> copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_2 >> Unmatched '"'. >> >> I have attached my config file. Can you please let me know what I am >> doing wrong? >> >> Thanks, >> >> Alan >> -- >> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* >> >> >> >> *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of >> Neuroscience* >> *University of Texas, School of Medicine* >> >> *Rio Grande Valley* >> >> *Texas.* >> >> >> > > > -- > King-Wai Chu, Ph.D. > Program Analyst > Mental Illness Research, Education and Clinical Center (MIRECC, VISN3) > James J. Peters Dept. of Veterans Administration Medical Center (OOMH) > 130 W. Kingsbridge Road > Bronx, NY 10468 > -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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over-estimated brain volume based on (recon-all / recon-all-clinical) ?
by Yoonho Hwang 18 Jul '23

18 Jul '23

External Email - Use Caution Dear FS developers, Hi, I am very happy that we can use new features of FreeSurfer (e.g., recon-all-clinical.sh, SynthSeg, SynthSR, etc.) While using a variety of functions from FreeSurfer (v7.3.2 and v7.4.1), we would like to hear the answers to the following questions. 1-1. Compared to the recon-all stream, using SynthSeg seems to overestimate the volume in many subregions of the brain including eTIV? Can you explain why this happens? 1-2. The estimated volume of the entorhinal cortex is different between recon-all/SynthSeg and recon-all-clinical.sh. There is a 3-4 times difference. Can you tell me why the result is? 2. Can the functions (segment_subregions, segmentThalamicNuclei.sh, segmentBA.sh, segmentHA.sh, etc.) used in recon-all be used in recon-all-clinical.sh? Please let me know if there is anything you don't understand. Looking forward to your feedback. Thank you very much. Best, Yoonho -- *Hwang, Yoonho* *Research professor* *Institute of Human Genomic Study,* *College of Medicine, Korea University* *#123, Jeokgeum-ro, Danwon-gu, Ansan-si, Gyeonggi-do, **15355, Republic of Korea.* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

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how to manipulate values in m3z file
by Proulx, Jean Sebastien 17 Jul '23

17 Jul '23

External Email - Use Caution Hello, I produced an m3z warp file with mri_gradunwarp. Now I need to 0 out all displacement in the z direction, while keeping everything else the same since I need to combine multiple warps from images with different geometries. I see two strategies: (1) working directly on the m3z file I could not get mri_convert or mris_calc to do the trick. I thought I nailed it by manually editing the m3z file in freeview, but freeview saves the results in mgz format :-( Is there anything else I missed? (2) converting to mgz or nii timeseries, manupulate those and convert back to m3z mri_convert produced a nii file that freeview could not read and a single-frame mgz file that looks like some mishmash of the original 3-frame m3z. Any idea on how I can acheive my goal? A word on why would I want to do this silly thing. I have single-slice EPI and fov-matched higher-inplane-resolution single-slice GRE images. They have different within-slice gradient-non-linearity-related distortions. I want to undistort the GRE image then distort it to the EPI space. I need to zero out through-plane distortions to avoid displacing signal outside the imaging grid. Ignoring through-plane distortions should not be a problem for overlaying my GRE and EPI since, unlike within-plane distorsions, through-plane distortions are matched. Thanks a lot for the help and Have a very good day! Sebastien

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Freesurfer VM .7z Password
by Spencer Chandler 17 Jul '23

17 Jul '23

External Email - Use Caution Hello, I've downloaded the 7.2 Ubuntu virtual machine and its asking for a password to extract it. Is this something I can get? Thank you! -Spencer

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Freesurfer July 2023