Freesurfer December 2023

freesurfer@nmr.mgh.harvard.edu

52 participants
65 discussions

Help with transform matrix for SEEG
by Hyunchul Lee 01 Jan '24

01 Jan '24

External Email - Use Caution Hello, I've just started using Freesurfer this week and I'm quite confused about coordinate systems. Specifically, I have SEEG electrode locations that have been digitized in MRI RAS space, and I'm trying to apply a transform matrix so that these electrodes will be registered with the same brain that I performed recon-all on using Freesurfer, so that I can do further analysis in MNE python. I understand that voxel space to MRI RAS space transform matrix is stored in vox2ras and the transform for voxel space to Freesurfer's surface RAS is in vox2ras_tkr of T1.mgz in my subject folder. Since the electrodes are in MRI RAS space, I am applying a transform matrix that is a matrix product of inverse(vox2ras) and vox2ras_tkr. However, this doesn't work out in real life, and I end up with electrodes half way outside the head. Am I using the correct matrices? Also, T1.affine appears similar to vox2ras but very slightly different. Just hoping that there would be an easier way.. Best regards, *Hyunchul Lee* MBBS PhD

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Clear background from command line
by Datta, Aditya 01 Jan '24

01 Jan '24

External Email - Use Caution Hi, Is there any way to clear background for a volume file from the command line. I am attempting to overlay electrodes onto a T1 image, and I would like for the background of the electrode files to be clear when they are loaded from a script. Thanks, Aditya Datta Staff Research Associate II UCLA Department of Neurosurgery 670 Charles E. Young Dr. South, CHS 63-360 Los Angeles , CA 90095 650-435-9337 ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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MEMPRAGE dura flags
by Akkoyunlu, Beyza 01 Jan '24

01 Jan '24

External Email - Use Caution Hi, I have longitudinal data with MEMPRAGE. I want to improve white-gray matter boundaries by using dura flag. But I’m a bit lost about how to do it. Your previous recommendations to use echoes with “mri_make_surfaces” function, yet the surfaces only needed-created in the base and long steps. Should I register the echoes to the respective anatomical’s long version and then use mri_make_surfaces? if not, do you have any suggestion about how to go for it? Thanks in advance Best, Beyza

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Cortical Thickness Measurement in Cortical Lesion ROI
by 李浩 01 Jan '24

01 Jan '24

External Email - Use Caution Dear Freesurfer Experts, I am currently engaged in a project where I need to measure the cortical thickness of a segmented cortical lesion (ROI) in the volume space. After running recon-all for my subjects, i employed 'mri_vol2surf' function to project my ROI from the native T1 space to indiviaul surface space. My command was as follows: mri_vol2surf —mov $chronic_CMI_volume_path/"$sub_base"_chronic-CMI_4-1.nii.gz --hemi rh --surf white --projfrac-avg -0.1 1 0.05 --interp nearest --o "$sub"_chronic-CMI_4-1_rh.mgh --regheader "$sub" --trgsubject “$sub” However, I encountered an issue where I could not locate the ROI in the individual surface space, as the values in "$sub"_chronic-CMI_4-1_rh.mgh were all zero. I suspect this might be due to a registration error or possibly the small size of my ROI (only 4 voxels). Do you have any suggestions on how to address this issue? Additionally, I am wondering whether it's possible to register the cortical thickness map from the surface space back to the individual volume space, then calculate the mean cortical thickness of my ROI there. Alternatively, is it feasible to convert the coordinates of my ROI's center point to the MNI152 coordinate and then surface-based coordinates and directly create an ROI in the surface space? Any feedback on these questions would be greatly appreciated. Thanks in advance. Bests, Hao Li

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Correlation Line Plot for FS Group Analysis
by Tejaswi D. Sudhakar 01 Jan '24

01 Jan '24

External Email - Use Caution Hello, I am to generate a plot to visualize the slopes between classes for group analysis. I would like to generate something similar to this freesurfer post: https://secure-web.cisco.com/10NQ6nNamVal7BE9lNMpStHRFgMjBEDJy0P_U59n_G56Yh… Is this available in freesurfer version 7? Thanks in advance, Tejaswi

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volumetric to surface using mri_vol2surf: tpl-MNI152NLin2009cAsym
by Lee, Jeungchan 01 Jan '24

01 Jan '24

Hi Freesurfers, I was wondering if there is a registration matrix (from volumetric to surface) for MNI152NLIN2009cAsym template. I was not able to find any (relevant) dat files in $FREESURFER_HOME/average/. I have some data in that space and would like to map them on the surface for visualization. Thanks, jeungchan

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Re: [Freesurfer] Help (Freeview fails to launch)
by fsbuild 29 Dec '23

29 Dec '23

External Email - Use Caution Depending upon the state of a machine, there is no guarantee a list of "required" packages will encompass everything that needs to be installed/updated, or that a manual install will work.  So we neither recommend or support manual/piecemal installs, e.g., via the list below, instead of using the built-in linux package management tools. - R. On Dec 29, 2023, at 22:32, Kiyotaka Nemoto <kiyotaka(a)nemotos.net> wrote:        External Email - Use Caution        Dear Akira,I agree with R that installing FreeSurfer using the deb is preferred, but if you want to stick to tar.gz,below is the list of the packages to be installed when you install FreeSurfer using the deb package.So if you install these packages, you would be able to run freeview.Hope this helps,Kiyotakasudo apt install -y language-pack-en binutils libx11-dev gettext x11-apps \  perl make csh tcsh bash file bc gzip tar \  xorg xorg-dev xserver-xorg-video-intel libncurses5 libbsd0 libc6 libc6 \  libcom-err2 libcrypt1 libdrm2 libegl1 libexpat1 libffi7 libfontconfig1 \  libfreetype6 libgcc-s1 libgl1 libglib2.0-0 libglu1-mesa libglvnd0 libglx0 \  libgomp1 libgssapi-krb5-2 libice6 libjpeg62 libk5crypto3 libkeyutils1 \  libkrb5-3 libkrb5support0 libpcre3 libpng16-16 libquadmath0 libsm6 \  libstdc++6 libuuid1 libwayland-client0 libwayland-cursor0 libx11-6 \  libx11-xcb1 libxau6 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \  libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 \  libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 \  libxcb-xinput0 libxcb-xkb1 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 \  libxkbcommon-x11-0 libxkbcommon0 libxmu6 libxrender1 libxss1 libxt6 zlib1g  On Fri, Dec 29, 2023 at 12:14 PM fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution         That message could be the result of missing system libraries which the Ubuntu 22 FS 7.4.1 .deb package will try to automatically identify, download and install for you.  You can download the package via the link MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_u… the install can be done with,… cd to your Downloads to wherever the .deb file is …$ sudo apt install  ./freesurfer_ubuntu22-7.4.1_amd64.debIf the install succeeds, freesurfer will be under /usr/local/freesurfer/7.4.1 which is the path to use for the environment variable FREESURFER_HOME,$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1If they are not already set in your environment, you should also set,$ export XDG_RUNTIME_DIR=$HOME/.xdg$ export DISPLAY=:0- R.On Dec 27, 2023, at 23:17, Akira Kita <jorrydep9876(a)gmail.com> wrote:        External Email - Use Caution        I have installed FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tar archive freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz.Freeview fails to launch with the following error message:This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.  Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl,How can I solve this?　　　Akira_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web..cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Kiyot… Nemoto, M.D., Ph.D.Associate ProfessorDepartment of PsychiatryDivision of Clinical Medicine, Institute of MedicineUniversity of Tsukuba1-1-1 Tennodai Tsukuba, Ibaraki 305-8575, JapanE-mail: kiyotaka@nemotos.net_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Help (Freeview fails to launch)
by fsbuild 29 Dec '23

29 Dec '23

External Email - Use Caution  That message could be the result of missing system libraries which the Ubuntu 22 FS 7.4.1 .deb package will try to automatically identify, download and install for you.  You can download the package via the link https://secure-web.cisco.com/1t9e2mCgXLQVxO1_HRQVcGKF8xT7sodKwA6z… the install can be done with, … cd to your Downloads to wherever the .deb file is … $ sudo apt install  ./freesurfer_ubuntu22-7.4.1_amd64.deb If the install succeeds, freesurfer will be under /usr/local/freesurfer/7.4.1 which is the path to use for the environment variable FREESURFER_HOME, $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1 If they are not already set in your environment, you should also set, $ export XDG_RUNTIME_DIR=$HOME/.xdg $ export DISPLAY=:0 - R. On Dec 27, 2023, at 23:17, Akira Kita <jorrydep9876(a)gmail.com> wrote:        External Email - Use Caution        I have installed FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tar archive freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz.Freeview fails to launch with the following error message:This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.  Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl,How can I solve this?　　　Akira_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_easyreg error: No cortical labels found; does the segmentation include cortical parcels?
by r04458005＠ntu.edu.tw 29 Dec '23

29 Dec '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run the mri_easyreg and I used the following command: mri_easyreg --ref /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0 mm_T1.nii --flo /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/r002_T1W.nii --ref_seg /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0 mm_T1-1.nii --flo_seg /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/r002_T1W_synthseg.n ii --flo_reg /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/r002_T1W.nii --fwd_field /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/FWF.nii.gz --bak_field /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/BWF.nii.gz --threads -1 --affine_only ERROR: Error: Floating segmentation must be provided --flo_seg: command not found I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer_ubuntu22-7.4.1 2) Platform: Ubuntu 22.04.3 LTS Please help me. Thanks! -Edward

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Recon-all failing with pre-skullstripped input data (mri_em_register can't find brainmask.mgz)
by James Hengenius 29 Dec '23

29 Dec '23

External Email - Use Caution Hello FS experts, I downloaded some anatomical data. I have defaced full images and pre-skullstripped images for each participant. I tried the defaced images first, but FS skullstripping looks a little off (possibly because the defacing hides bits of the cranium in some images and causes problems in mri_watershed). So I would like to use the pre-skullstripped files as my initial inputs. I have placed the pre-skullstripped file for each participant in $SUBJECTS_DIR/$subjid/mri/orig/. Each participant's skullstripped input volume is named 001.mgz. I then submit the following command in a script to my slurm queue (after setting appropriate FS env vars), where the script input ${1} is the $subjid mentioned above: recon-all \ -subject ${1} \ -all \ -openmp 40 \ -noskullstrip The output log from FS ends with the following error. The function mri_em_register seems to be looking for brainmask.mgz, and fails to open it. If the input image is already extracted from the skull, do I need to manually call it brainmask.mgz rather than 001.mgz? Or am I missing something else in my function call (like order of flags)? Does -noskullstrip need to come before -openmp, for example? Thanks! Jim H. End of recon-all output: writing output to T1.mgz > 3D bias adjustment took 1 minutes and 20 seconds. > @#@FSTIME 2023:12:28:16:07:04 mri_normalize N 7 e 80.39 S 0.66 U 102.70 P > 128% M 581068 F 0 R 24411 W 0 c 32 w 229 I 0 O 0 L 1.00 1.38 9.22 > @#@FSLOADPOST 2023:12:28:16:08:25 mri_normalize N 7 1.99 1.66 8.64 > #------------------------------------- > #@# EM Registration Thu Dec 28 16:08:25 EST 2023 > /gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri > mri_em_register -uns 3 -mask brainmask.mgz nu.mgz > /home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca > transforms/talairach.lta > setting unknown_nbr_spacing = 3 > using MR volume brainmask.mgz to mask input volume... > == Number of threads available to mri_em_register for OpenMP = 40 == > reading 1 input volumes... > logging results to talairach.log > reading > '/home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca'... > GCAread took 0 minutes and 1 seconds. > average std = 7.2 using min determinant for regularization = 5.2 > 0 singular and 884 ill-conditioned covariance matrices regularized > reading 'nu.mgz'... > error: > > *mghRead(/gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri/brainmask.mgz, > -1): could not open file^@error: mri_em_register: could not open mask > volume brainmask.mgz.^@* > @#@FSTIME 2023:12:28:16:08:25 mri_em_register N 7 e 1.42 S 0.25 U 1.43 P > 118% M 446804 F 0 R 108260 W 0 c 2 w 56 I 0 O 0 L 1.99 1.66 8.64 > @#@FSLOADPOST 2023:12:28:16:08:26 mri_em_register N 7 1.99 1.66 8.64 > Linux nia0918.scinet.local 3.10.0-1160.102.1.el7.x86_64 #1 SMP Tue Oct 17 > 15:42:21 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux > recon-all -s 1000108_20252_2_0 exited with ERRORS at Thu Dec 28 16:08:26 > EST 2023 > For more details, see the log file > /gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/scripts/recon-all.log > To report a problem, see > http://secure-web.cisco.com/1ywN1tDbl7MCg8OnWFYEA2Vcf-TaEWXJQlDYsrE7jJo4KqF…

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Freesurfer December 2023