Freesurfer December 2024

freesurfer@nmr.mgh.harvard.edu

45 participants
62 discussions

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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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

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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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Doing predictive models on freesurfer outputs
by Yunus Soleymani 24 Dec '24

24 Dec '24

External Email - Use Caution Hello FreeSurfer Developers, I have a general statistical question regarding regression models. Our team attempts to create predictive models based on FreeSurfer outputs such as volumes, thicknesses, and curvatures. The predictive variables we are using include several demographic and metabolic factors. We have adjusted our models to account for intracranial volume (ICV) in the population. Instead of simply dividing our outputs by the ICV, we found through our literature review that it is a better approach to include ICV as a covariate alongside our predictive variables in the model. However, we are concerned that including ICV in this manner leads to a significant increase in the R-squared (R²) value of our models due to the effect size provided by ICV. I would like to know whether this is a statistically significant issue, and if it is, how we should address it. Thanks again for your valuable help, Yunus

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Issues with MRI and PET Registration to fsaverage Template
by 문준호 23 Dec '24

23 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. # Freeview results ## Example 1 [image: image.png] ## Example 2 [image: image.png] ## Example 3 [image: image.png] # 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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preparing config file to run Tracula
by Barletta, Valeria 23 Dec '24

23 Dec '24

Dear Freesurfers, I am setting up the configuration file to run Tracula preproc. I have some doubts on certain variables... * pedir: on my DTI protocol I have "PhaseEncodingDirection": "j-",so I assume it is AP * epifactor : I took it from "EchoTrainLength": 48 * echospacing: shall I take it from "DwellTime": 2.5e-06? In which format should I write it in the file? Thank you, Valeria

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Feature associations between recon-all and synthseg
by Banerjee, Tania 21 Dec '24

21 Dec '24

External Email - Use Caution Hello, I am reaching out to seek guidance on associating brain features generated using SynthSeg (approximately 101 features for the whole brain) with those generated by Recon-All. Given the coarse nature of SynthSeg features, I assume that multiple features from Recon-All might correspond to a single region in SynthSeg. For example, one Synthseg feature is: ctx-lh-caudalmiddlefrontal How can I determine the set of features in recon-all that correspond to this region ctx-lh-caudalmiddlefrontal? Thank you in advance for your time and assistance. Thank you, Tania Banerjee

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Extracting just the eTIV from stats file.
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 20 Dec '24

20 Dec '24

External Email - Use Caution Hi guys, I need to extract the eTIV from a stats file Its like this: # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1667606.252292, mm^3 According to https://secure-web.cisco.com/176-9WTUemMQHEI2hQhkubecmphcM6MFO1hfMQO3SLSaZ4…, typing mri_segstats --subject subjid --etiv-only Doesn't work for FS7.1.1. Also the --etiv flag in mri_segstats doesn't seem to work either. And the --etiv flag in asegstats2table. I also tried figuring how its done in recon-all.log but just need the eTIV and no other stats. Whats the best FS command to do this in FS7.1.1? Victor Zeng Beth Israel Deaconess Medical Center PI: Keshavan, Lizano, Bolo -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://secure-web.cisco.com/1yhjz1Kw9vsKRZdR40nL-BcWzv765EAqKqrY3w1Srb8ikwW… for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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