Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

How Can I Track Coordinates from NIfTI Raw Files
by 권용현 01 Jan '25

01 Jan '25

External Email - Use Caution Hello, I am conducting research using ECoG. I want to accurately track the location of electrodes. I am inputting data from a NIfTI file (size: 512, 512, 360, 1). I already know the exact electrode location within the NIfTI file, e.g., (182, 274, 260). The x, y, z values of this coordinate correspond to the raw fMRI scan, with x ranging from 0-512, y from 0-512, and z from 0-360. I extracted the --vox2ras matrix from the 001.mgz file using mri_info. I attempted to project the coordinates from the NIfTI file onto the generated pial surface, but I found a significant discrepancy. What I need is not Talairach coordinates, but a precise transformation of the electrode coordinates in the NIfTI space to their exact location on the subject's pial surface. How can I achieve this? Additionally, I noticed that the origin (0,0,0) of the generated pial surface does not align with the anterior commissure (AC). I am curious about the coordinate system of the final mesh – is it simply the voxel-based x, y, z system, or is it in the RAS coordinate system? Thank you. Best regards, Yonghyeon Gwon -- Yongheyon Gwon Interdisciplinary Program in Neuroscience, Seoul National University, Human Brain Function Laboratory, Seoul National University Hospital Seoul, Korea E-mail: gngyong(a)hbf.re.kr , gyh0321(a)naver.com Phone: +82-10-9706-3814

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FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data
by Michael Eyre 01 Jan '25

01 Jan '25

External Email - Use Caution Hello I'm processing 7T MP2RAGE data (0.65mm isotropic) with FreeSurfer 8.0.0-beta. I have processed 30 subjects successfully but am encountering two distinct issues for 3 subjects: 1. Stack smashing errors during topology correction for subjects with large defects (sub-06, sub-31): Copy*** stack smashing detected ***: terminated Command terminated by signal 6 This occurs in mris_fix_topology when processing defects with many vertices: sub-06: Left hemisphere, defect 0 with 22,492 vertices sub-31: Right hemisphere, defect 2 with 14,313 vertices sub-06 does not have any obvious brain abnormalities. sub-31 has some white matter abnormalities at the terminal zones of myelination (deep posterior white matter). 2. Normalization failure for another subject (sub-04): Copyerror: MRInormFindControlPoints: could not find enough control points error: MRInormFindControlPoints failed This subject has some very minor scattered white matter abnormalities (perivascular spaces). My recon-all command: export FS_ALLOW_DEEP=1 recon-all -all -subject ${SUBJECT} -sd ${WORK_PATH}/freesurfer8 -hires -i ${WORK_PATH}/${SUBJECT}_uni_masked.nii.gz -T2 ${WORK_PATH}/${SUBJECT}_t2w_registered.nii.gz -T2pial -expert ${EXPERT_FILE} -openmp 20 My EXPERT_FILE contains two lines: mris_inflate -n 100 mris_fix_topology -threads 1 Preprocessing: Data are processed with 3D Gibbs deringing, ANTS DenoiseImage, bias field correction and brain extraction prior to freesurfer. Approaches tried: I have tried running without the EXPERT_FILE, and also tried with additional recon-all flags -3T -gcut -norm1-n 4 -norm2-n 6, without success. Previous successful processing: The same subjects processed successfully with FreeSurfer 7.4.1. System info: Ubuntu 20.04, 64GB RAM, 20 CPUs. Subjects are running in serial not in parallel, and no other processes with significant memory or CPU use are running on the system at the same time. Any suggestions would be greatly appreciated. I have attached the recon-all.log files. Let me know if you need any additional information. Best wishes Mike Eyre Dr Michael Eyre Locum Consultant Paediatric Neurologist, Evelina London Children's Hospital Visiting Research Fellow, School of Biomedical Engineering & Imaging Sciences, King's College London St Thomas' Hospital London SE1 7EH

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Reliability of Optic Chiasm Volume Measurements in FreeSurfer
by Knut J Bjuland 01 Jan '25

01 Jan '25

External Email - Use Caution Dear FreeSurfer experts, I am examining the optic chiasm segmentation in FreeSurfer. How reliable is the volume measurement of the optic chiasm when using FreeSurfer? Best regards Knut Jørgen Bjuland

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Bug Report for Beta Version of FreeSurfer (8.0.0-beta)
by Zhang, Chaokai 31 Dec '24

31 Dec '24

External Email - Use Caution Hello FreeSurfer Developers, Happy New Year! I am currently using the latest beta version of FreeSurfer (freesurfer-linux-ubuntu22_x86_64-8.0.0-beta) and have been impressed by the significant acceleration in the recon-all process. However, I encountered an issue while performing a simple labelization on a T1-weighted sample using mri_watershed. When running the command: mri_watershed -LABEL T1.mgz T1_label.mgz I noticed that the output file (T1_label.mgz) is shifted and does not align with the original T1-weighted sample. To confirm, I ran the same command using the stable version (7.4.1), and the output aligned correctly with the T1-weighted sample. [cid:image001.png@01DB5BA1.780AAF30] This is just a bug report and does not require any assistance. I wanted to bring this to your attention. Thank you for your hard work and dedication to improving FreeSurfer. details of my system: 1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-8.0.0-beta 2) Platform: Ubuntu 24.04.1 LTS 3) uname -a: Linux Kai 5.15.167.4-microsoft-standard-WSL2 #1 SMP Tue Nov 5 00:21:55 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux Best regards, Chaokai

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Issues with MRI and PET Registration to fsaverage Template
by 문준호 30 Dec '24

30 Dec '24

External Email - Use Caution Hello, I am currently working on registering MRI and PET data from the ADNI dataset, processed using our custom preprocessing pipeline, to the fsaverage template. My goal is to align both the MRI and PET data to the fsaverage template. To achieve this, I followed these steps: Step 1: I used mri_coreg to create an LTA file for registering the MRI data to the fsaverage template. Then, I used mri_vol2vol to perform the registration of the MRI data to the fsaverage template. Commands Used: mri_coreg --mov $MRI_PATH --targ $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz --reg ${OUTPUT_DIR}/mri${num}_reg.lta mri_vol2vol --mov $MRI_PATH --targ $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz --reg ${OUTPUT_DIR}/mri${num}_reg.lta --o ${OUTPUT_DIR}/mri${num}_to_atlas.nii.gz Step 2: I used the LTA file generated in Step 1 and applied mri_vol2vol to register the PET data to the MRI data. Commands Used: mri_vol2vol --mov $PET_PATH --targ ${OUTPUT_DIR}/mri${num}_to_atlas .nii.gz --reg ${OUTPUT_DIR}/mri${num}_reg.lta --o ${OUTPUT_DIR}/pet${num}_to_atlas.nii.gz However, when visualizing the results using Freeview, I noticed that the registration of both the MRI and PET data to the fsaverage template is not accurate. (The MRI and PET data were successfully co-registered.) I have attached some images of the results and the output from the mri_info command for your reference. # mri_info results ## T1w MRI niiRead(): detected input as 64 bit double, reading in as 32 bit float Volume information for {my_mri_data} type: nii dimensions: 128 x 128 x 128 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 128.000 dof: 1 xstart: -64.0, xend: 64.0 ystart: -64.0, yend: 64.0 zstart: -64.0, zend: 64.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -13.0000 : x_a = -0.0000, y_a = 1.0000, z_a = -0.0000, c_a = 16.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 11.5000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -1.0000 -0.0000 0.0000 51.0000 -0.0000 1.0000 -0.0000 -47.5000 0.0000 0.0000 1.0000 -52.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 51.0000 -0.0000 1.0000 -0.0000 47.5000 -0.0000 -0.0000 1.0000 52.5000 -0.0000 -0.0000 -0.0000 1.0000 ## brain.mgz Volume information for /usr/local/freesurfer/7.4.1/subjects/fsaverage/mri/brain.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : /usr/local/freesurfer/7.4.1/subjects/fsaverage/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 128.0000 0.0000 0.0000 1.0000 -128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 128.0000 -0.0000 -0.0000 -1.0000 128.0000 -0.0000 1.0000 -0.0000 128.0000 -0.0000 -0.0000 -0.0000 1.0000 Could you please help me identify any potential issues with my approach or the commands I used? I would greatly appreciate any guidance you can provide. Thanks a lot! Best regards, Junho Moon

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Issues with MRI and PET Registration to fsaverage Template
by 문준호 30 Dec '24

30 Dec '24

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Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data
by fsbuild 30 Dec '24

30 Dec '24

External Email - Use Caution  Signal 6 run time error indicates some kind of buffer overflow is expected to happen like the stack is going to be corrupted, and so the process is killed.  Please let us know the OS name and version you are running 8.0.0-beta on that produced the error, e.g., what installer you used.   If what you listed is not the full text of the error output in the log, then please include that as well.  A more detailed message could look something like, **** stack smashing detected ***: foo.out terminated**======= Backtrace: =========**<path>/libc.so.6(<symbol+offset>)Aborted* - R. On Dec 29, 2024, at 10:54, Michael Eyre <michael.eyre(a)kcl.ac.uk> wrote:        External Email - Use Caution        Hello I'm processing 7T MP2RAGE data (0.65mm isotropic) with FreeSurfer 8.0.0-beta. I have processed 30 subjects successfully but am encountering two distinct issues for 3 subjects: 1. Stack smashing errors during topology correction for subjects with large defects (sub-06, sub-31):Copy*** stack smashing detected ***: terminatedCommand terminated by signal 6 This occurs in mris_fix_topology when processing defects with many vertices: sub-06: Left hemisphere, defect 0 with 22,492 verticessub-31: Right hemisphere, defect 2 with 14,313 vertices sub-06 does not have any obvious brain abnormalities. sub-31 has some white matter abnormalities at the terminal zones of myelination (deep posterior white matter). 2. Normalization failure for another subject (sub-04):Copyerror: MRInormFindControlPoints: could not find enough control pointserror: MRInormFindControlPoints failed This subject has some very minor scattered white matter abnormalities (perivascular spaces). My recon-all command:export FS_ALLOW_DEEP=1recon-all -all -subject ${SUBJECT} -sd ${WORK_PATH}/freesurfer8 -hires -i ${WORK_PATH}/${SUBJECT}_uni_masked.nii.gz -T2 ${WORK_PATH}/${SUBJECT}_t2w_registered.nii.gz -T2pial -expert ${EXPERT_FILE} -openmp 20 My EXPERT_FILE contains two lines:mris_inflate -n 100mris_fix_topology -threads 1 Preprocessing: Data are processed with 3D Gibbs deringing, ANTS DenoiseImage, bias field correction and brain extraction prior to freesurfer. Approaches tried: I have tried running without the EXPERT_FILE, and also tried with additional recon-all flags -3T -gcut -norm1-n 4 -norm2-n 6, without success. Previous successful processing: The same subjects processed successfully with FreeSurfer 7.4.1. System info: Ubuntu 20.04, 64GB RAM, 20 CPUs. Subjects are running in serial not in parallel, and no other processes with significant memory or CPU use are running on the system at the same time. Any suggestions would be greatly appreciated. I have attached the recon-all.log files. Let me know if you need any additional information. Best wishes Mike Eyre Dr Michael Eyre Locum Consultant Paediatric Neurologist, Evelina London Children's HospitalVisiting Research Fellow, School of Biomedical Engineering & Imaging Sciences, King's College LondonSt Thomas' Hospital London SE1 7EH<sub-04_recon-all.log><sub-06_recon-all.log><sub-31_recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] freesurfer installation issues on debian
by fsbuild 27 Dec '24

27 Dec '24

External Email - Use Caution I’m assuming you tried to install the freesurfer 7.4.1 release deb package for Ubuntu 22 which is available via the link,https://secure-web.cisco.com/1-8cAL3HeYSqkGt1gxwntnID8i3xh2XIP7o3oNj46… libc message seems to indicate your version of Debian Linux uses a newer version of the system glibc compared to what was used to build freesurfer on Ubuntu 22 linux.  If you run this command on your Debian linux system, $ ldd --version … and it reports a version of 2.36 or higher, then you would need to revert to an older release of Debian linux that uses glibc 2.35 in order to install the freesurfer Ubuntu 22 7.4.1 package.  While Ubuntu Linux is a derivative of Debian Linux, the OS names/versions do not strictly overlap, i.e., the version of Debian Linux needs to match or be compatible with Ubuntu 22 Linux for the install to work.   The chart below shows Debian bookworm spans both Ubuntu 22 and Ubuntu 23 linux; you are likely running the newer bookworm version matching Ubuntu 23 which changed glibc to a version > 2.35 - R.

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Issues with MRI and PET Registration to fsaverage Template
by 문준호 27 Dec '24

27 Dec '24

External Email - Use Caution Hello, I am currently working on registering MRI and PET data from the ADNI dataset, processed using our custom preprocessing pipeline, to the fsaverage template. My goal is to align both the MRI and PET data to the fsaverage template. To achieve this, I followed these steps: *Step 1:* I used mri_coreg to create an LTA file for registering the MRI data to the fsaverage template. Then, I used mri_vol2vol to perform the registration of the MRI data to the fsaverage template. Commands Used: mri_coreg --mov $MRI_PATH --targ $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz --reg ${OUTPUT_DIR}/mri${num}_reg.lta mri_vol2vol --mov $MRI_PATH --targ $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz --reg ${OUTPUT_DIR}/mri${num}_reg.lta --o ${OUTPUT_DIR}/mri${num}_to_atlas.nii.gz *Step 2:* I used the LTA file generated in Step 1 and applied mri_vol2vol to register the PET data to the MRI data. Commands Used: mri_vol2vol --mov $PET_PATH --targ ${OUTPUT_DIR}/mri${num}_to_atlas .nii.gz --reg ${OUTPUT_DIR}/mri${num}_reg.lta --o ${OUTPUT_DIR}/pet${num}_to_atlas.nii.gz However, when visualizing the results using Freeview, I noticed that the registration of both the MRI and PET data to the fsaverage template is not accurate. (The MRI and PET data were successfully co-registered.) I have attached some images of the results and the output from the mri_info command for your reference. # mri_info results ## T1w MRI niiRead(): detected input as 64 bit double, reading in as 32 bit float Volume information for {my_mri_data} type: nii dimensions: 128 x 128 x 128 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 128.000 dof: 1 xstart: -64.0, xend: 64.0 ystart: -64.0, yend: 64.0 zstart: -64.0, zend: 64.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -13.0000 : x_a = -0.0000, y_a = 1.0000, z_a = -0.0000, c_a = 16.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 11.5000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -1.0000 -0.0000 0.0000 51.0000 -0.0000 1.0000 -0.0000 -47.5000 0.0000 0.0000 1.0000 -52.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 51.0000 -0.0000 1.0000 -0.0000 47.5000 -0.0000 -0.0000 1.0000 52.5000 -0.0000 -0.0000 -0.0000 1.0000 ## brain.mgz Volume information for /usr/local/freesurfer/7.4.1/subjects/fsaverage/mri/brain.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : /usr/local/freesurfer/7.4.1/subjects/fsaverage/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 128.0000 0.0000 0.0000 1.0000 -128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 128.0000 -0.0000 -0.0000 -1.0000 128.0000 -0.0000 1.0000 -0.0000 128.0000 -0.0000 -0.0000 -0.0000 1.0000 Could you please help me identify any potential issues with my approach or the commands I used? I would greatly appreciate any guidance you can provide. Thanks a lot! Best regards, Junho Moon

1 0

freesurfer installation issues on debian
by Misty 27 Dec '24

27 Dec '24

External Email - Use Caution Hello all, I have a debian machine running on debian "bookworm". I tried to install freesurfer ubuntu 7.4.1 deb package and had issues with dependencies. 1. Depends: language-pack-en but it is not installable 2. Depends: libc6 ( < 2.36) but 2.36-9+deb12u9 is to be stalled. For dependency issue 1, When I ran locale -a, here is what I got: " C C.utf8 en_us.utf8 POSIX " and file /etc/default/locale contains: LANG="en_US.UTF-8" And for dependency issue 2, When I run apt show -a libc6 packet libc6 version "2.36-9+deb12u9" already installed. So how do I resolve this discrepancy? Thanks!

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