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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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re-running recon-all after aseg.presurf.mgz edits
by Alexopoulos, Dimitrios 17 Jul '23

17 Jul '23

External Email - Use Caution A few quick questions FS experts. I made manual edits on subcortical structures in outputs from FS6.0. Specifically, I made the edits on the aseg.presurf.mgz file. I then reran using: recon-all -s neo267e_nil -autorecon2-noaseg -autorecon3 Do the updated stats files aseg.stats and ?h.aparc.stats incorporate these changes? I ask b/c the mri_segstats cmdline below uses the aseg.mgz not aseg.presurf.mgz # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/pkg/freesurfer6.0/ASegStatsLUT.txt --subject neo267f_nil ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Can I use Freeview (tksurferfv) Tools on surface?
by Andy Kim 17 Jul '23

17 Jul '23

External Email - Use Caution Dear FreeSurfer Developers, Hi. I want to manually draw a rectangular ROI on flat map. I tried "PolyLine voxel draw" of ROI edit tool (https://secure-web.cisco.com/1uYpRPHzaQ-b275n3Qt2rqUmDAbInkPLAno41z_mXOvA9D…) On the other hand, unfortunately, it seems that it only works in 3d volume space. So, I tried "Path/Custom FIll" -> pointing 4 vertices of a rectangle -> "Make Closed Path". But this time, the vertices were not connected straight. The lines were zigzag. Could you tell me how to draw a rectangular ROI with straight lines. Furthermore, if possible, could you explain how zigzag lines form? Thank you in advance. Kind Regards, Andy (Junghyun) Kim

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some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz
by zlseu2109 17 Jul '23

17 Jul '23

External Email - Use Caution TO: freesurfer(a)nmr.mgh.harvard.edu FROM: zlseu2109(a)163.com SUBJECT: segmentation of thalamic nuclei error: some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz Hello FreeSurfer Developers, I’ve segmented thalamic nuclei via thalamic nuclei atlas and gained volume result of 25 subregions of each thalamus, but some subregions (eg. Right Pt) cannot be shown by load ThalamicNuclei.v13.T1.mgz in freeview. I'm attempting to use this thalamic nuclei atlas for functional ROIs analysis, using other softwares (eg.SPM). Could you provide .nii file of this atlas? Or can you help me show this missed thalamic subregions? Or how can I transform the file of thalamic nuclei atlas in FreeSurfer pipeline to .nii file. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-ubuntu20_x86_64-7.3.2 2) Platform: Ubuntu Release 20.04.6 (focal) | | zlseu2109 | | zlseu2109(a)163.com |

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can't generate 3D rendering
by Magang Visa 16 Jul '23

16 Jul '23

External Email - Use Caution Hello FreeSurfer Developers, i'm attempting to open a 3D freeview but i don't see the 3D rendering i'm using this code to open the file freeview T1.mgz norm.mgz brain.mgz aseg.mgz 1) FreeSurfer version:Version 7 Release is 7.4.1 2) Platform: CentOS thanks [image: image.png]

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