Freesurfer May 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
109 discussions

Approach for LR asymmetry analysis using ROIs?
by Silberfeld, Andrew 15 May '23

15 May '23

External Email - Use Caution Hello FS Community, I'm working on a study about left-right asymmetry and one of the experiments I'd like to do is to directly compare the average percent change between sides for each ROI when processed using a volumetric registration and when processed using FreeSurfer's surface-based approaches (same set of images). I'm hoping to characterize the degree to which both software produce consistent patterns of LR asymmetry for volume. However, I'm not sure what the best way is to implement a symmetrical registration with ROIs in FreeSurfer and I'm wondering what is recommended? For starters, the DK atlas/template is not feasible due to its inherent asymmetry, and I've considered a number of approaches but it feels like a challenge prohibits each one. What is the best way to go about doing this? I've considered the following ideas: 1. (Most ideally) I could import my already obtained symmetrical volumetric template/atlas into FreeSurfer, but my understanding is that making the .gca file requires multiple annotated subjects rather than a single annotated atlas, since FS uses probabilistic segmentations. 2. I've looked at the xhemi approach from Greve et al. 2013 but my impression from reading the documentation is that this gives results that differ based on whether the left hemisphere or right hemisphere is used and also that the final results are described for each vertex, rather than for each parcel which I need (although the original paper did do some ROI-analysis). 3. I've also thought about performing recon-all on each sample twice: once in the proper orientation and once more after flipping the LR orientation of each sample. From there I could compare the left hemi and the flipped-right hemi to each other which I think avoids the DK atlas bias. This feels similar to option 2 and so I'm not sure if this would give results that vary based on which hemisphere is used for analysis. Also the documentation says I would need to manually change lines in the text file, which is not an ideal solution for several hundred subjects, although this could be scripted. (https://secure-web.cisco.com/1b40CbQ8lToemytkQqJc49_lPSzSyb_qOkrmyKts2VtGlg…) Maybe I'm overthinking it. What is the best way to go about doing this? Thank you, Andrew

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mri_robust_register for mouse brain?
by Nadia Kane 15 May '23

15 May '23

External Email - Use Caution Hi, Can mri_robust_register be used for mouse brain atlas affine registration? What criteria need to be considered? Thanks, Nadia Nadia Kane Junior Imaging Specialist University Imaging Centers | University of Minnesota https://secure-web.cisco.com/1fMyxmsjafAHJa_lMbHaeJsspmhF-Q3odaixiH0gfbDn0g…

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Re: [Freesurfer] recon-all error: cannot find or read colortable_BARe: recon-all error: cannot find or read colortable_BA_thresh.txt_thresh.txt
by fsbuild 15 May '23

15 May '23

External Email - Use Caution We should have an update for this installed there soon. - R.

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recon-all error: cannot find or read /usr/local/freesurfer/dev//average/colortable_BA_thresh.txt
by Kelley, William 15 May '23

15 May '23

External Email - Use Caution Hello FreeSurfer Developers, Over the weekend I attempted to run a few mri images through recon-all on launchpad, but this morning I found the following error for each: ERROR: cannot find or read /usr/local/freesurfer/dev//average/colortable_BA_thresh.txt Here is the full recon-all command: recon-all -subjid $subject -all -brainstem-structures -no-isrunning I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this one? Also, I've attached one of the recon-all logs in case it's of any use. 1. FreeSurfer version: freesurfer-linux-centos7_x86_64-dev-20230515-068e824 2. Platform: CentOS 7 3. uname -a: Linux demeter.nmr.mgh.harvard.edu 3.10.0-1160.76.1.el7.x86_64 #1 SMP Wed Aug 10 16:21:17 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4. recon-all.log: see attached

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Reconstruction output differences with freesurfer 7.3.2 and 7.2.0
by Md Mahfuzur Rahman 15 May '23

15 May '23

External Email - Use Caution Dear Developers, I am trying to run 'recon-all' and then do some QC on the output. With 7.3.2 for skull stripping, I can fairly fix the brain mask with adjusting thresholds. But after fixing it, when I ran "recon-all -autorecon2 -autorecon3 -subjid <subject name>", the surface didn't change noticeably. However, I obtained noticeable changes with version 7.2.0. I am attaching a screenshot to make it understandable. Should there be output differences between 7.2.0 and 7.3.2? I was wondering if anyone has comments about which version one should rely on. Any help will be highly appreciated. Thank you. Regards, --- Mahfuz Md Mahfuzur Rahman, Ph.D. Postdoctoral Research Associate (AC) Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University Email: mahfuz.gsu(a)gmail.com, mrahman21(a)gsu.edu

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Issue with running recon-all
by hmarzban＠student.ubc.ca 15 May '23

15 May '23

External Email - Use Caution Dear developers, I am writing to report an issue I encountered while running recon-all on some subjects. Specifically, I received an error message stating "error: freadFloat: fread failed" for several of the subjects. Starting surface-based mapping Reading source registration /arc/project/3T/fsaverage/surf/lh.sphere.reg error: freadFloat: fread failed error: freadFloat: fread failed ... I am wondering if any of you have experienced this issue before, and if so, I would greatly appreciate any recommendations on how to proceed with resolving it. Thank you for your help. Hengameh

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Individualized subcortex atals generation with freesurfer derivatives
by bong516612 15 May '23

15 May '23

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EasyReg Troubleshoot - Killed
by Nadia Kane 12 May '23

12 May '23

External Email - Use Caution Hi, I'm working on applying deep learning in image registration for a master's project. The overarching goal was to use real tissue clearing lightsheet data to perform the image registration, but first created some synthetically deformed brains based on the Allen Brain Atlas and Lab2im algorithm <https://secure-web.cisco.com/15MqNxXe5KXHPIE2voNOwPZsAQlEcjvJ2VaFxWcPmWFuUF…>. However, I'm having some issues implementing the command in an Centos Linux 7 (Core) HPC environment. The command gets Killed, I'm wondering if you could provide some more insight? Thank you! I've set up my environment as follows: module load mamba mamba create -n freesurf # I named the environment freesurf conda activate freesurf mamba install tensorflow-gpu cuda-version=11.8 I've attached the easyreg.sh shell script that I run. Here's the output: (freesurfer) kanex161@agc02 [~/Documents/Thesis/code] % bash easyreg.sh 2023-05-09 11:19:32.374206: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2023-05-09 11:19:32.405672: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2023-05-09 11:19:32.405981: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. 2023-05-09 11:19:33.258226: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT [W interface.cpp:47] Warning: Loading nvfuser library failed with: Error in dlopen: libnvfuser_codegen.so: cannot open shared object file: No such file or directory (function LoadingNvfuserLibrary) using 1 thread Segmenting reference image Reading reference image Setting up segmentation net 2023-05-09 11:19:38.489093: E tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:266] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected 2023-05-09 11:19:38.489166: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:168] retrieving CUDA diagnostic information for host: agc02 2023-05-09 11:19:38.489202: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:175] hostname: agc02 2023-05-09 11:19:38.489460: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:199] libcuda reported version is: 470.103.1 2023-05-09 11:19:38.489502: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:203] kernel reported version is: 470.103.1 2023-05-09 11:19:38.489530: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:309] kernel version seems to match DSO: 470.103.1 Inference / segmentation easyreg.sh: line 8: 1108392 Killed ./mri_easyreg --ref /home/umii/kanex161/Documents/Thesis/data/outputs/atlas/atlas.nii.gz --flo /home/umii/kanex161/Documents/Thesis/data/outputs/lab2im/brains/brain_00.nii.gz --ref_seg /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/ref_seg.nii.gz --flo_seg /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/flo_seg.nii.gz --flo_reg /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/flo_reg.nii.gz --fwd_field /home/umii/kanex161/Documents/Thesis/data/outputs/easyreg/fwd_field.nii.gz

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password
by m.77 ms77 12 May '23

12 May '23

External Email - Use Caution Sorry, I have a problem. I am using FS_7_2_0_ubuntu_18_04_06.ova.7z on my virtual machine system but it wants a password to open it. What's the password of this file? Thank's

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recon-all for GM quantification
by Nikolaidou, Sofia 12 May '23

12 May '23

External Email - Use Caution Good afternoon, My name is Sofia and I work with Drs. Eva Ratai and Lilly Mujica-Parodi on the DCC project. I am reaching out to ask for your advice on a FreeSurfer question. I am using recon-all to try to quantify and compare GM volume and mean thickness among our subjects. In essence, I think I have all the necessary measurements in the outcome files titled aseg.stats and ?h.aparc.stats. Would you happen to know how I can customize the stream and reduce the processing time by taking out steps from the -all process? In other words, what would be the minimal set of steps that I have to run in order to acquire the above output files? Thank you in advance! Kindly, Sofia Sofia Nikolaidou | Clinical Research Coordinator MGH/HST Martinos Center for Biomedical Imaging 149 13th St, Charlestown, MA 02129 Phone: 617-417-4463 snikolaidou(a)mgh.harvard.edu

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Freesurfer May 2023