Freesurfer November 2024

freesurfer@nmr.mgh.harvard.edu

40 participants
52 discussions

Re: [Freesurfer] Question on using thalseg_1.1.h5
by Georgios Argyropoulos 23 May '25

23 May '25

External Email - Use Caution Many thanks and apologies, Henry - I figured it out... I stupidly replaced your improved segmentation script in both the scripts and the bin directory instead of only replacing the former. many thanks for your time, much appreciated g

2 5

use and registration of FLAIR in recon-all and segmentHA
by Simone Cauzzo 04 Dec '24

04 Dec '24

External Email - Use Caution Hi all I am running Freesurfer 7.4 I use recon-all with the -FLAIRpial option. 1) I wonder whether the FLAIR to T1 registration is handled by recon-all or whether I need to supply a FLAIR image already registered to T1. 2) in case recon-all handles the registration, is there a way I can check the registration quality? which file should I use in freeview? 3) in case I already have a reliable FLAIR to T1 registration, is there a way to make recon-all skip the FLAIR to T1 registration? In addition, I would like to use segmentHA_T2.sh 4) in case recon-all handles the registration, which file can I give to segmentHA_T2 as additional scan? I guess I should select the FLAIR already registered to T1.. 5) Is there a reason why I should prefer a T2 image to a FLAIR for segmentHA_T2? Thank you Simone Cauzzo, PhD University of Padova

2 2

mri_coreg threads parallel processing clarification
by Hemond, Christopher 03 Dec '24

03 Dec '24

External Email - Use Caution Dear experts, Thanks in advance for any help you can provide. I’m using “mri_coreg” and trying to accelerate it with the “--threads” (and/or “--nthreads”) flags. However in the subsequent command feedback it looks like it is still using just one thread (see output below, “nthreads 1”; and also it is no faster). Am I doing something obviously wrong? There are no errors and it executes successfully… Not sure if relevant but I’m using this for nifty (.nii.gz) files, my command is: “mri_coreg --ref <path/to/ref.nii.gz> --mov <path/to/mov.nii.gz> --reg <path/to/registration.lta> --threads 10” I’m on MacOS running a recent dev download (freesurfer-macOS-darwin_arm64-dev-20241011), but I’ve tried it on 7.4.1 with no success either. … INFO: using NIfTI-1 sform (sform_code=1) Setting cras translation parameters to align volume centers Init matrix params -0.4553 -6.3123 39.4428 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 0.45535; 0.00000 1.00000 0.00000 6.31235; 0.00000 0.00000 1.00000 -39.44280; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt -0.4553 -6.3123 39.4428 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (2): 4 2 min = 2 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-07 linmintol 1.000e-03 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 3917.0000 mov gstd 0.9539 0.9539 0.7422 Smoothing mov … The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, transmission, re-transmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer.

2 2

Merging aparc+aseg and ThalamicNuclei
by Andrew M 01 Dec '24

01 Dec '24

External Email - Use Caution I'm looking to merge the aparc+aseg.mgz with outputs from additional seg steps such as ThalamicNuclei (e.g., ThalamicNuclei.v13.T1T2.FSvoxelSpace.mgz) I see in history there used to be a function mergeseg, but maybe doesn't exist anymore? I also found in freesurfer/7.4.1/trctrain/hcp separate subject folders which have aparc+aseg+thalnuc.nii.gz, which is exactly what I'm looking for, except not in the correct space (hoping to keep in the same space as the original aparg+aseg, which ThalamicNuclei.v13.T1T2.FSvoxelSpace.mgz is in). Thank you! Andrew

2 1

Pipeline for Transferring VBM Outputs to FreeSurfer and Parcellating with the Destrieux Atlas
by Safari, Nooshin (rvz7wf) 01 Dec '24

01 Dec '24

External Email - Use Caution Hi experts, I am working on transferring VBM output, which is in NIfTI format, to FreeSurfer space. I would like to follow this with parcellation using the Destrieux atlas, which is the standard with FreeSurfer. What is the pipeline to do this? Sincerely, Nooshin

2 1

FDG Pet: How do I create an 'SUVR Image'?
by Lai, Ian M. 01 Dec '24

01 Dec '24

External Email - Use Caution I am quite inexperienced with the technology but have been asked to use PETSurfer to create a 'SUVR Image' of an FDG Pet scan, where the number associated with intensity in the motion-corrected, partial volume corrected value is the SUVR value. >From what I understand, an indication of success would be that the values on the mgx.gm.nii.gz being on the scale of around 1-10, rather than in the thousands. I have tried to achieve this by adding the --rescale 7 8 46 47 flag to the partial volume correction step, but the numbers are still in the order of the thousands. Is there any way to manually rescale the file's intensities, dividing the entire file's intensities by the average value across the cerebellum? Thank you for your help, please let me know if my question is unclear. Ian

2 1

Recon-all failing
by Mark Wagshul 01 Dec '24

01 Dec '24

External Email - Use Caution Hi, I'm hoping someone can help with this strange error. Have been using recon-all on this dataset forever, and now all of a sudden it is completely failing just a few minutes into the processing. Attaching the recon-all.log file (had run a bunch of times, so only saved the last invocation in the file). It seems to get up to an mris_calc command to multiply the image by a scaling factor, but the number is missing. Here is the last bit of code where it fails: 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1410486/ones.mgz --i ./tmp.mri_nu_correct.mni.1410486/nu0.mgz --sum ./tmp.mri_nu_correct.mni.1410486/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1410486/output.mean.dat sysname Linux hostname mwagshul machine x86_64 user mwagshul whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1410486/ones.mgz Loading ./tmp.mri_nu_correct.mni.1410486/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.1410486/output.mean.dat mri_segstats done Missing parameters. Usage: bc inputImageFile inputSegmentationFile side PathToTrainingFiles outputSegmentationFile side = 0 (left side) or else (right side) mris_calc -o ./tmp.mri_nu_correct.mni.1410486/nu0.mgz ./tmp.mri_nu_correct.mni.1410486/nu0.mgz mul Segmentation fault (core dumped) Thanks so much in advance for any advice! Best, Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu<mailto:mark.wagshul@einsteinmed.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

2 1

FS version 8-beta
by Douglas N. Greve 01 Dec '24

01 Dec '24

Hi All, as some of you have figured out, we have a beta version of FS 8.0.0. Please give it a spin and let us know if you have any problems or concerns. The release notes are here https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes which I have copied below. One bug that we have already found is that you must set environment variable FS_ALLOW_DEEP to 1, eg, export FS_ALLOW_DEEP=1 (for bash) or setenv FS_ALLOW_DEEP 1 (for csh/tcsh) thanks doug * Now uses SynthSeg <https://surfer.nmr.mgh.harvard.edu/fswiki/SynthSeg>, SynthStrip <https://synthstrip.io>, and SynthMorph <https://synthmorph.io> (deep learning algorithms). These make recon-all more robust and much faster. Technically, SynthMorph <https://synthmorph.io> is not needed for recon-all to run, but the nonlinear registration can be used in multimodal analysis to map to the MNI152. * There is now DL automatic segmentation of regions that often cause errors in pial surface placement. These include the major sinuses (sagittal and transverse) as well as a spot between frontal and temporal lobes where the middle cerebral artery (MCA) and dura cause bright areas. * Several fixes in entorhinal cortex. First, the WM in EC is segmented using DL. The WM is often only 0.5mm thick and very hard to see; this often resulted in severe white surface areas in this location requiring manual editing to fix. The new surface now represents gyrus ambiens much better. Second, The white surface is extended to the front of amygdala. Third, the binary cortex of label now covers entorhinal cortex and parts of the temporal pole better allowing the pial surface to extend out to its true edge. * Some bugs where found in and around inferior frontal cortex causes the white surface to extend too far into basal ganglia. This has been fixed. This is above and beyond the issue reported in 7.3.2 below. * All the bug fixes described below are now turned on by default. * These changes will work with longitudinal with the caveat that the volumetric segmentation will not be fully longitudinal. The segmentation will be applied to the time point in the base space, but it will not (and cannot) be initialized with the base segmentation. Initial tests indicated that the change in power was minimal and mixed. * recon-all will now run in about 2h vs 8h on a single CPU. It will, however, required about 24GB of memory to run. * The use of SynthStrip <https://synthstrip.io> should make recon-all much more robust as the old skull stripping method often included extra cerebral tissue. * With synthseg, we are now supplying a segmentation-based total intracrainial volume (sTIV) along with the registration-based estimated TIV (eTIV) * We have applied v8 to several studies (aging, AD crossectional, AD longitudinnal, schizophrenia). There were no major changes in the ability to detect effects, and there was no interaction between effect and version. But let us know how it performs on your studies.

4 7

Problems with recon-all on M4 iMac
by Torben Ellegaard Lund 27 Nov '24

27 Nov '24

External Email - Use Caution Dear FreeSurfer Developers, I am trying to run the recon-all pipeline on some MP2RAGE images, which have been regularised using the robust reconstruction, in order to avoid the salt and pepper noise in the background. I am running the beta-version of FS 8, and have followed the instructions, including "export FS_ALLOW_DEEP=1”. Synthstrip runs extremely slow, but finishes. I also get a lot of other mgz images : ls /Volumes/SanDiskSSD1/Freesurfer/subjetcs/sub-0271/mri T1.mgz mri_nu_correct.mni.log orig rawavg.mgz synthseg.rca.mgz tmp.mri_mcadura_seg.50836 aseg.auto_noCCseg.mgz nu.mgz orig.mgz rawavg2orig.lta synthstrip.mgz transforms But after a while the job crashes with the message: Node: 'unet/unet_bn_down_0/FusedBatchNormV3' 2 root error(s) found. (0) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] [[unet/unet_conv_downarm_2_1/BiasAdd/_44]] (1) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] 0 successful operations. 0 derived errors ignored. [Op:__inference_predict_function_1146] Installation details: 1) FreeSurfer version: MacOS X darwin arm64 (64b) PKG installer 2) Platform:macOS Séquoia version Version 15.1.1 32GB RAM 3) uname -a: Darwin iMac-Fam-Lund.local 24.1.0 Darwin Kernel Version 24.1.0: Thu Nov 14 18:19:02 PST 2024; root:xnu-11215.41.3~13/RELEASE_ARM64_T8132 arm64 4) recon-all.log: see attached I am new to Freesurfer, and really hope you can help. Best Torben Lund Torben Ellegaard Lund Associate Professor, PhD Center of Functionally Integrative Neuroscience (CFIN) Aarhus University Aarhus University Hospital Palle Juul Jensens Boulevard 99 J117 krydspunkt J117 8200 Aarhus N Denmark

1 0

Questions on Using recon-all-clinical for Cortical Thickness Analysis
by 王又劼 26 Nov '24

26 Nov '24

External Email - Use Caution Hello, I have longitudinal imaging data for some participants. Due to the data collection protocol, the T1w image from the first timepoint (TP1) is a clinical sequence (e.g., slice thickness of 5mm or 6.5mm), while subsequent timepoints collected 3D T1w images with a slice thickness of 1mm. My study focuses on analyzing cortical thickness changes in participants over time. I have the following questions: I plan to use recon-all-clinical to analyze the clinical T1w data. However, I noticed that the official documentation mentions that slice thickness significantly impacts cortical thickness estimation. Are there any acceptable methods for comparing cortical thickness changes across different timepoints for the same participants? Can the results of recon-all-clinical be used in FreeSurfer's longitudinal workflow? I have searched archived mails and reviewed studies citing articles related to recon-all-clinical but have not found relevant answers. I would greatly appreciate any help on this matter.

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer November 2024