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17 participants
30130 discussions

Surface vertex tkr-ras to native T1 RAS without volume files
by Dipterix Wang 11 Apr '24

11 Apr '24

External Email - Use Caution Dear FreeSurfer devs, I'm writing a program in JavaScript that converts FreeSurfer surface (mesh) files to other formats, which require the vertices to sit in scanner RAS coordinates. Right now I'm relying on the FreeSurfer *brain.finalsurf.mgz* or *T1.mgz* file to obtain the Torig (vox to tkr-ras) and Norig (vox to scanner ras) matrices, and using these matrices to calculate the rigid transform. This approach requires the users to upload the mgz volume files (but I only need the transforms). Today I found that each binary surface file (e.g. lh.pial) has a little footer that starts with uint32 sequence `2 0 20`, followed by the meta information such as xras, yras, zras, and cras. For example: valid = 1 # volume info valid filename = ../mri/filled-pretess127.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 cras = -1.000000000000000e+00 -1.700000000000000e+01 1.900000000000000e+01 \u0000\u0000\u0000\u0003\u0000\u0000\u0000\u0000\u0000\u0000\u0001 From what I understand, cras is the xyz of the volume center, which is the translation from mesh vertices xyz (in tkr-ras) to native scanner RAS. I wonder if I can rely on this information to calculate the transform from tkr-ras to scan-ras, if so, where are the rotation matrices? (Affine/rigid transform is a 4x4 matrix, if cras is the translation, where are the first 3x3 elements, are those always identity matrices?) Best, - Dipterix

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Re: [Freesurfer] WMH-SynthSeg - Torch module not found
by Corinne Alison Donnay 11 Apr '24

11 Apr '24

External Email - Use Caution Hi Eugenio, Thanks for getting back to me – I had the newest version installed and still get the same error (pasted below). mri_WMHsynthseg --i flair_ax.nii.gz --o flair_ax_WML.nii.gz --threads -1 Arguments seem correct; loading Python packages... Traceback (most recent call last): File "/usr/local/apps/freesurfer/dev-2024-04-19/python/packages/WMHSynthSeg/inference.py", line 284, in <module> main() File "/usr/local/apps/freesurfer/dev-2024-04-19/python/packages/WMHSynthSeg/inference.py", line 76, in main import torch ModuleNotFoundError: No module named 'torch' I also installed FreeSurfer 7.4.1. Would you be able to expand on what you mean by “a way around this is installing FreeSurfer 7.4.1, and using its fspython to run the WMh-SynthSeg code”? I loaded FreeSurfer 7.4.1, and then changed the location of the model in inference.py and tried using FreeSurfer 7.4.1 fspython but now its missing the 'unet3d' module: [donnayca@cn4270 anat]$ module load freesurfer [-] Unloading freesurfer 7.4.1 on cn4270 [+] Loading freesurfer 7.4.1 on cn4270 [donnayca@cn4270 anat]$ fspython ../inference_cd.py --i flair_ax.nii.gz --o flair_ax_WML.nii.gz Arguments seem correct; loading Python packages... Traceback (most recent call last): File "../inference_cd.py", line 285, in <module> main() File "../inference_cd.py", line 79, in main from unet3d.model import UNet3D ModuleNotFoundError: No module named 'unet3d' [donnayca@cn4270 anat]$ fspython Python 3.8.13 (default, Apr 21 2022, 14:55:37) [GCC 8.3.1 20190311 (Red Hat 8.3.1-3)] on linux Type "help", "copyright", "credits" or "license" for more information. >>> exit() Thank you! Corinne From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Saturday, April 6, 2024 at 1:04 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] WMH-SynthSeg - Torch module not found Wrong answer: apparently this has been fixed in the latest dev; maybe try that? Cheers, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1dHOeDzqKyQVK1dVoIBFTpN8aJzkFmLHSyp5Kt30eRmYaZV… From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Date: Friday, April 5, 2024 at 3:58 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] WMH-SynthSeg - Torch module not found Dear Corinne, A bunch of libraries are currently broken in the development version; apologies for this. A way around this is installing FreeSurfer 7.4.1, and using its fspython to run the WMh-SynthSeg code. Apologies for the inconvenience! Cheers, /E PS: I just updated the wiki to include this information. -- Juan Eugenio Iglesias http://secure-web.cisco.com/1dHOeDzqKyQVK1dVoIBFTpN8aJzkFmLHSyp5Kt30eRmYaZV… From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Corinne Alison Donnay <corinne.donnay(a)linacre.ox.ac.uk> Date: Friday, April 5, 2024 at 12:43 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] WMH-SynthSeg - Torch module not found External Email - Use Caution Good Afternoon! I was working with my IT department to install the development version of FreeSurfer on our server so that I could use WMH-SynthSeg<https://secure-web.cisco.com/13uSpbM7Qfplsr0IlNG1yQzvDu3TL4ODjz8qdEUly_QzsK…>. IT installed development version 2024-04-14. After loading the freesurfer development module, and running source $FREESURFER_HOME/SetUpFreeSurfer.sh, I still get the following error: [cid:image001.png@01DA8B65.91CED520] Is there any way to fix this or figure out what is wrong? Thank you! Corinne

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PetSurfer: Can kinetic modeling be applied to PET data with single frame?
by WONG Wan Wa 11 Apr '24

11 Apr '24

External Email - Use Caution Hi experts, As stated in the subject, can kinetic modeling be applied to PET data with only one frame? Or we just stop at ROI analysis without kinetic modeling? Best, Angel

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Probabilistic segmentation neonates
by Hamza Kebiri 10 Apr '24

10 Apr '24

External Email - Use Caution Hello, Is there a FreeSurfer tool to output a probabilistic tissue segmentation (gray/white matter proportions) tailored for the newborns (especially in the thalamus) ? Thank you very much. All the best, Hamza Kebiri

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NextBrain Segmentation PyTorch-GPU Compatibility Error
by AmirHussein Abdolalizadeh 10 Apr '24

10 Apr '24

External Email - Use Caution Hi, I'm using NextBrain segmentation tool on our cluster which has NVIDIA H100 GPUs and I'm getting this error: NVIDIA H100 with CUDA capability sm_90 is not compatible with the current PyTorch installation. The current PyTorch install supports CUDA capabilities sm_37 sm_50 sm_60 sm_70 sm_75 sm_80 sm_86. If you want to use the NVIDIA H100 GPU with PyTorch, please check the instructions at https://secure-web.cisco.com/1dXRtbKFFWRnAd7DYiR89C9QyPNuu24f97dyifrR_gDGXs… Should I contact our cluster managers in this regard or is there a specific workaround that can overcome this issue? Best, Amir

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Several faculty jobs at University of Chicago in Aging + Alzheimer's and related dementias
by Adam Martersteck 09 Apr '24

09 Apr '24

External Email - Use Caution *Apologies for cross-posting* The University of Chicago's Department of Neurology is recruiting several faculty members at any rank to join the Healthy Aging & Alzheimer’s Research Care (HAARC) Center. We welcome candidates with research interests that align with our mission including topics and methods such as digital biomarkers, blood-based biomarkers, imaging biomarkers (MRI, PET), large-dataset curation, social determinants of health, assessment of cognition, memory, psychosocial wellbeing, functional outcomes, neuropathologic, nonpharmacologic interventions, and implementation science. We are looking for (1) a tenure track faculty (any rank, with or without tenure), (2) a non-tenure track faculty (any rank), (3) a behavioral neurologist, and (4) a full professor of neuroimmunology to direct a program in neuroinflammation. Clinical neuropsychologists, behavioral neurologists, and cognitive neuroscientists with an interest in contributing to a collaborative multidisciplinary research center are encouraged to apply. We especially welcome applicants from URM groups, which are African American, Latino, Native American, Pacific Islanders, women, and individuals with disabilities. For more information see our website: https://secure-web.cisco.com/10L7_lboSnfTgH5hrqe1sUZtGSywMbqb47r96NhJAp4tK2… Tenure track faculty position: https://secure-web.cisco.com/1OeZ6fDc9_LaXQp8riD9fIo6-CzZ7ojZNXgL4wc93ARP8I… Non-tenure track faculty position: http://secure-web.cisco.com/17J6yWYJ2zsoku90RYF2YU_thqO3lxxSRJXfK4HSbPzjCan… Behavioral neurologist: https://secure-web.cisco.com/1ZT7et8OCIVgBMktDPuQAx1nX2C27i0IwlduDjDBH2QFZf… Tenured full professor in neuroimmunology, with endowed chair: https://secure-web.cisco.com/1aGaEvfSfHQUMYR0p_DyIC-4_q2Xse9-YUKKvf1BxySfjo… -- *Adam Martersteck, PhD * *(he/him)**Assistant Professor of Neurology* | The University of Chicago, Healthy Aging & Alzheimer's Research Care (HAARC) Center *Address *| 850 East 58th Street | Chicago, IL 60637 *Phone *| 773-795-1683 *Email *| martersteck(a)uchicago.edu

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Invitation to free symposium “What is brain connectivity?”
by Rullmann, Michael 09 Apr '24

09 Apr '24

Dear colleagues, On behalf of the <https://secure-web.cisco.com/1Da_DGXW57_rMCMeHTK5TADY_e9wv_LLc42BadYWVeAHWZ…> Molecular Connectivity Working Group, I am delighted to invite you to our next hybrid symposium with the title “What is brain connectivity?”, bringing together leading experts in the field of fMRI, DWI, EEG, and molecular imaging. <https://secure-web.cisco.com/13lW8OZnkl-8F1_iVwGP4PFs1RRaYQpkFZ82QPrnKzCBgz…> Registration is free (but places are limited - only 15 places left for in-person registration at the moment!). 📅 Date: May 3, 2024 🕒 Time: 9:00 am - 1:00 pm CEST 📍 Virtually + @TranslaTUM, University Hospital “Klinikum rechts der Isar”, Ismaninger Str. 22, Munich Key Highlights: · 🌐 Recognized experts · 🤝 Networking opportunities · 🎓 Virtual and on-site hybrid event · 📋 No registration fees Goal The symposium aims to identify a common denominator across modalities in the definition of macroscale brain connectivity. The event is supposed to provide a baseline for follow-up debates on standardized nomenclature for molecular connectivity. 🌐 For more information visit: <http://secure-web.cisco.com/12rjCoQpwDk0jBJ8kcmziUi1b5GHC6ZFLZEF6-2mtVjHiCh…> tinyurl.com/MCWGMunich2024 Registration: Registration for the symposium is open and free but obligatory. Places are limited so do not miss out on the opportunity to be a part of this event by securing your spot <https://secure-web.cisco.com/13lW8OZnkl-8F1_iVwGP4PFs1RRaYQpkFZ82QPrnKzCBgz…> here. NB: in-person registration closes on April 14th! Thanks to the sponsors <https://secure-web.cisco.com/1-fh2PS40b4Piodmmwh3PjcxUlGjw_kayQIYe4ivRH8PqQ…> Deutsche Forschungsgemeinschaft (DFG) - German Research Foundation, <https://secure-web.cisco.com/1kdcDe0OFt3LZUNYUb_gzPxVUoShr2oF_zGvBtSAYlTCLk…> Bruker (PMOD), <https://secure-web.cisco.com/10BxD1P26t9gzDB1fIiyhjRdv4NM1jjlLiOlxuVQMyC4FQ…> Curium Pharma, <https://secure-web.cisco.com/1wAgw3QOhqkL3u3eLWN-EOJ5Pw9Yaa8DvM-XjYPMQcRjZp…> Technical University of Munich for the support. Who we are The <https://secure-web.cisco.com/1Da_DGXW57_rMCMeHTK5TADY_e9wv_LLc42BadYWVeAHWZ…> Molecular Connectivity Working Group is an initiative of an international and interdisciplinary group of neuroimaging experts with background in biomedicine, health sciences, neuroscience, and physics. Our ultimate aim is to establish Molecular imaging as a tool to study brain Connectivity. Best Michael External Email - Use Caution

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recon-all exits with errors
by William Graves 08 Apr '24

08 Apr '24

External Email - Use Caution Dear FreeSurfer Developers, I’m trying to run recon-all as a pre-processing step in the AFNI resting-state analysis pipline, using the command: recon-all -subject $subj -i $anat_cm -all -parallel So far it has successfully run on about 20 participants in my sample, but for the current participant it’s now suddenly throwing this error: PIDs (691564 691567) completed and logs appended. Linux demeter 6.2.0-26-generic #26~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Jul 13 16:27:29 UTC 2 x86_64 x86_64 x86_64 GNU/Linux recon-all -s R21-24 exited with ERRORS at Fri Apr 5 16:29:23 EDT 2024 I searched through the log file, tried Googling the error, and searched your email list archive, but couldn’t find anything to address this. The log file is attached, along with: 1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 2) Platform: Ubuntu 22.04.3 LTS I’d appreciate any help or advice you could give! Best, Will --- William W. Graves, Ph.D. Associate Professor, Department of Psychology Rutgers, The State University of New Jersey Smith Hall, Room 337 101 Warren Street, Newark, NJ 07102 http://secure-web.cisco.com/1j9r5gk2jDdMnViAisDWP_vqMXxEmt7r1AWEWqCgjw6_9jX…

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Easyreg > cortical parcels missing after SynthSeg with --parc option ?
by r04458005＠ntu.edu.tw 08 Apr '24

08 Apr '24

External Email - Use Caution Hello Freesurfer Developpers, I attempted to run mri_easyreg (Freesurfer 7.4) between two images. After I ran mri-easyreg adding these images (--ref_seg --flo_reg), I get again the > no cortical parcels. The following is the command I used and the error code. What did I do wong? Any hints? Thanks in advance for your help. Best, Edward mri_easyreg --ref /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0 mm_T1_scalp_trip.nii --flo /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only/pre_042_0000 .nii.gz --ref_seg /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0 mm_T1_scalp_trip_synthseg.nii --flo_seg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042 /pre_042_0000_synthseg.nii.gz --ref_reg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042 /pre_042_ref_reg.nii.gz --flo_reg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042 /pre_042_flo_reg.nii.gz --fwd_field /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042 /pre_042_FWF.nii.gz --bak_field /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042 /pre_042_BWF.nii.gz 2024-03-31 15:50:23.731218: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-03-31 15:50:23.752531: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-03-31 15:50:23.752807: 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 AVX_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. 2024-03-31 15:50:24.041622: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT using 1 thread Segmentation of reference image already exists; reading from disk Error: No cortical labels found; does the segmentation include cortical parcels?

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Lesion extraction !
by Martin Juneja 08 Apr '24

08 Apr '24

External Email - Use Caution Dear FS experts, I am trying to extract lesion volume from my structural MRI/FLAIR data of brain tumor patients using run_samseg program. Here, I am attaching my output colored in red overlapped on ground truth colored in blue. As you can see it misses identification of some portion of the lesion (non overlapped region) but instead gives some voxels which are not part of the lesion at all. I tried different lesion thresholds 0.95, default 0.30 and 0.1. In all the cases, results are very similar i.e. a chunk of lesion voxels are always missing and there are some unwanted voxels that get identified. I was wondering (a) how can this issue be fixed; (b) or, maybe run_samseg is not designed for tumor patients and it will work only for MS patients. In addition, I tried mri_WMHsynthseg pipeline, but it stops after about a minute: >> mri_WMHsynthseg --i BRAINIX_NIFTI_T1.nii.gz --o WMH_Out.nii Arguments seem correct; loading Python packages... Using cpu Using 1 thread(s) Preparing model and loading weights Working on image 1 of 1: BRAINIX_NIFTI_T1.nii.gz Loading input volume and normalizing to [0,1] Upscaling to target resolution Pushing data through the CNN Killed: 9 I would greatly appreciate any help. Thanks. [image: Lesion_Location.png]

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