Freesurfer April 2024

freesurfer@nmr.mgh.harvard.edu

54 participants
64 discussions

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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Question on using thalseg_1.1.h5
by Georgios Argyropoulos 08 Apr '24

08 Apr '24

External Email - Use Caution Dear Colleagues, Hope you're well. I have been trying to use the thalseg_1.1.h5 patch (MRI Segment Thalamic Nuclei CNN model v1.1 update). I use the following command: mri_segment_thalamic_nuclei_dti_cnn --t1 mri/norm.dwispace.mgz --aseg mri/aseg.dwispace.mgz --fa dmri/dtifit_FA.nii.gz --v1 dmri/dtifit_V1.nii.gz --o outputSegmentation.nii.gz --vol measuredVolumes.csv --model /usr/local/freesurfer/7.4.1/models/thalseg_1.1.h5 --threads 3 However, I have been encountering the following error message. I was wondering whether you may be able to help. many thanks georgios Using user-specified model: /usr/local/freesurfer/7.4.1/models/thalseg_1.1.h5 DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) Traceback (most recent call last): File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 2551, in <module> main() File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 164, in main predict( File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 258, in predict net = build_model(model_file_segmentation=path_model_segmentation, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 661, in build_model net = unet(nb_features=24, ^^^^^^^^^^^^^^^^^^^^ File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 942, in unet dec_model = conv_dec(nb_features, ^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/freesurfer/7.4.1/bin/mri_segment_thalamic_nuclei_dti_cnn", line 1125, in conv_dec input_shape = last_tensor.shape.as_list()[1:] ^^^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'shape' -- Georgios P. D. Argyropoulos PhD, CPsychol, FHEA Division of Psychology, Faculty of Natural Sciences; University of Stirling; FK9 4LA Scotland UK *Personal Website <https://secure-web.cisco.com/1bHuyxjaHSXaNhBW47ORm6M_ZgtAKVjOaFDyrDvTlvpzMG…>*

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WMH-SynthSeg - Torch module not found
by Corinne Alison Donnay 06 Apr '24

06 Apr '24

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@01DA8780.B1BD2E60] Is there any way to fix this or figure out what is wrong? Thank you! Corinne

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recon-all exits with errors
by William Graves 05 Apr '24

05 Apr '24

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Recon-All Clinical Stream: Image Output Observations in Creating ENIGMA QC Images
by Sam Sievertsen 05 Apr '24

05 Apr '24

External Email - Use Caution Good Afternoon, I hope this email finds you well! My name is Sam Sievertsen, the research coordinator for Dr. Jennifer Forsyth at the University of Washington. We are utilizing the recon-all clinical processing stream from FreeSurfer 7.4.1 on Rocky Linux (within our institutions HPC environment) to process subjects with decreased T1 image quality, and for whom previously processing with the standard recon-all pipeline resulted in missed grey matter during segmentation. Per recommendations in the bug reporting page, I have attached an example recon-all clinical log from this processing in case it is helpful. Following the recon-all clinical processing of these subjects, we are using an existing (ENIGMA cortical QC) pipeline to take screenshots of the external cortical reconstruction <https://secure-web.cisco.com/19i9TSlgNlNnONXLIpqTWX3BCSsnOf-EugV08XsKq72OGs…> / aparc+aseg segmentation overlaid on internal images <https://secure-web.cisco.com/13TQ3PwQQ9BI4s2aBpZBhunwgJsJT6-yH3IIqx3cliLqe4…> . We are able to successfully generate external (reconstruction) cortical QC images using the recon-all clinical output, but encounter an error when attempting to generate the internal (T1 with aparc+aseg.mgz overlay) QC images. Specifically, there is a conditional check within the internal QC image generation script linked above that halts the process if the Nx*Ny*Nz dimensions in the T1 image and the Nx*Ny*Nz dimensions in aparc+aseg.mgz do not align, which is where our process is throwing the error. Manual examination of the recon-all clinical image output (e.g., "native.mgz", "synthSR.norm.mgz", and "aparc+aseg.mgz") suggests that the aforementioned dimensions are all different in those images. Conversely, the dimensions in the processed images and segmentations (e.g., "orig_nu.mgz", "aparc+aseg.mgz") from the standard recon-all pipeline appear to be uniform (256) for those same subjects we are processing in this cohort. To hopefully assist with clarity, I have attached the script we are using ("func_make_corticalpngs_ENIGMA_QC.m") to construct these internal QC images, and example output files from the same subject using the standard recon-all pipeline output ("internalQC_standard_recon_all.txt") and recon-all clinical pipeline output ("internalQC_recon_all_clinical.txt"), which show a discrepancy in the aforementioned dimensions. Following up on the above information, I am wondering if "SynthSeg: to obtain a volumetric segmentation and linear registration to Talairach space"on the recon-all clinical page <https://secure-web.cisco.com/1ysMZeQggBLaLzKrZvbENqA_ienVNIRzPan5TKDtzxTjvk…> about registration to talairach space implies that the recon-all clinical output should have uniform dimensions, or if I am misunderstanding that and there is anything that stands out from this description that we may be doing incorrectly/that other users have encountered as well? Would also be very appreciative of any other suggestions you may have for attempting to troubleshoot this issue, thank you very much in advance for your time! Happy to answer any resulting questions or follow up with additional information should it be helpful. All the best, *Sam Sievertsen * Research Coordinator I Department of Psychology, GRaND Lab [image: logo]

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Support for GPU on Freesurfer
by Camargo, Aldo 04 Apr '24

04 Apr '24

External Email - Use Caution Hi there, I was wondering if there is support for GPU on FreeSurfer. I really would like to use it on GPU because is taking 9 hours per subject to recon-all. Thanks a lot and have a nice day, Aldo Camargo Senior Postdoctoral Fellow at the University of Maryland, Baltimore

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Re: [Freesurfer] Question about mris_compute_lgi error: /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission denied")
by fsbuild 03 Apr '24

03 Apr '24

External Email - Use Caution  The permissions on /scratch may not be set to allow you to write files there.  If it does not work from the terminal window to create a plain file there via the command, $ touch /scratch/foo - then you will get the same permission denied error. If the above fails, then you should contact whoever setup the machine, your IT department, etc. and ask them to provide write permission there. - R, Begin forwarded message:From: XinRan Wu <wxr1173199759(a)gmail.com> Subject: [Freesurfer] Question about mris_compute_lgi error: /scratch/tp94c480ef_a005_4f9a_85af_ab56b34400cd.load_mgh.m.mgh: Permission denied") Date: April 3, 2024 at 12:14:38 EDT To: freesurfer@nmr.mgh.harvard.edu Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> ERROR: could not open /scratch/

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Freesurfer April 2024