Freesurfer May 2024

freesurfer@nmr.mgh.harvard.edu

56 participants
69 discussions

Research Technician positions in the FreeSurfer lab
by Player, Allison A. Stevens 24 May '24

24 May '24

Hi everyone, If you or anyone you know is looking for entry-level Research Technician positions working with FreeSurfer and/or postmortem human brain MRI research, please feel free to check out or share some of the job openings in our lab: https://lcn.martinos.org/jobs/ We are also looking for more experienced individuals who are interested in lab management. Feel free to contact me (best to do with your resume attached)! Allison Stevens Lab Manager Lab for Computational Neuroimaging, FreeSurfer Development Team Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown, MA

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Recon-all -hires
by Schroder, Kirsten 24 May '24

24 May '24

External Email - Use Caution Dear FreeSurfer experts, I am currently conducting a research project in which I am using 7T MP2RAGE data. I have denoised all the images and have used the -hires flag in FreeSurfer version 6.0.1 but for one images the skull stripping is not great and there is still some skull left. I tried using different preflooding heights, as stated on the website, but this resulted in parts of the brain being cut off. I then tried to manually edit the brainmask.mgz using tkmedit but in every other slice the skull still remains (as seen in the attached image). Is there a way to fix this in tkmedit or do you have any other recommendations? I also wanted to ask if there is a way to bypass the bias correction step in the expert options file? And can the solutions to the two aforementioned issues also be applied to newer version of Free Surfer, specifically FreeSurfer version 7.4.x? Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a uname -a: Linux pc8-009.ion.ucl.ac.uk 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Mar 21 12:19:18 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux Thank you in advance. Kind regards, Kirsten

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squirrel data sharing format available in beta
by Gregory Book 24 May '24

24 May '24

External Email - Use Caution The squirrel data sharing format is now available in beta format and we're looking for public comment. The squirrel format is designed to use the minimum number of objects to describe all parts of neuroimaging analysis. From experiments and raw data to analysis methods and results, all information can be categorized into 10 object types. Using a hierarchical storage, the format can store any number of subjects, any number of imaging sessions, any number of visits, and any modality of data. It handles not just imaging data, but demographics, measures, vitals, and drugs. Simple to use, simple to share. * convert from DICOM to squirrel * convert from BIDS to squirrel * modify existing packages * packages are in 7zip format, and JSON is human readable * available for RHEL8, RHEL9, and Debian12/Ubuntu22 The squirrel utilities are in beta, so not all parts work, but we're looking for testers and feedback! Download the squirrel utils from https://secure-web.cisco.com/1WRNkvQPK4BOcCo4fgUYLyLTBlLdPW7fwixbJiXy16MAKL… Documentation and the squirrel specification: https://secure-web.cisco.com/1uAU1-QCnkUDsyb1PHsY1vqWB553FNwLN1raYY7xR1zBej…

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run_samseg: Optimizer: maximalDeformation is too small; stopping; killed
by Stefano Cerri 24 May '24

24 May '24

External Email - Use Caution Hi Marie, The error message "Killed" is usually thrown when the device runs out of memory. Can you double-check that this is not the case? If you're on Ubuntu you can track your memory usage with the command ("htop" or "top"). The SAMSEG log you provided looks good to me. Stefano [Freesurfer] run_samseg: Optimizer: maximalDeformation is too small; stopping; killed <https://secure-web.cisco.com/114ojuev3dL_eHg7uTGqpjYcYMhO6cH4mJbsWSMTEvEoud…> Ringki Marie Siewert <https://secure-web.cisco.com/1K89zJlQ6eJrrX8555rwKUHZ19K0pqU4fGS0TjTv5M7vUg…> Wed, 22 May 2024 11:04:52 -0700 <https://secure-web.cisco.com/1kCmJa4nr649UKj0FFzt1TncfWCWs2wpdsUwdZgFIudtKe…> External Email - Use Caution Hello Freesurfer Developers, I'm a medical student training with Freesurfer for my doctor thesis. My goal is to measure the brain volumetry of patients via SAMSEG. Attached is my logfile for run_samseg. When i run the samseg command: run_samseg --input STRUCT_samseg.nii.gz --output ~/fsl_course_data/registrat/SamsegOutput --threads 3 where: STRUCT_samseg.nii.gz is a T1 w image of a normal human brain. It runs for a while an then gives me the message: *Optimizer: maximalDeformation is too small; stopping* *iterationNumber: 0* *Killed* and just stops. There the files created as samseg output: samseg.talairach.lta template_coregistered.mgz cost.txt template.lta template_transforms.mat, but not the stats file that estimates the volumetry of the brain. I've searched the forum but there weren't any similiar reports for this error. 1) FreeSurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 2) Plattform: Ubuntu 20.04.6 LTS 3) uname -a: Linux TABLET-TSKI5C88 5.15.146.1-microsoft-standard-WSL2 #1 SMP Thu Jan 11 04:09:03 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux 4) log as text file is attached Last but not least I want to thank you for all your hard work! I really appreciate all the advice and support you give. Have a nice day, Marie Script started on 2024-05-22 15:06:09+02:00 [TERM="xterm-256color" TTY="/dev/pts/0" COLUMNS="72" LINES="46"] -------- freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni FSL_DIR /home/ringki/fsl ]0;ringki@TABLET-TSKI5C88: ~/fsl_course_data/registration/SamsegOutput [01;32mringki@TABLET-TSKI5C88 [00m: [01;34m~/fsl_course_data/registration/SamsegOutput [00m$ run_samseg --input STRUCT_samseg.nii.gz --output ~/fsl_course_data/registration/ [A [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C [C SamsegOutput --threads 3 ##---------------------------------------------- Samsegment Options ##---------------------------------------------- output directory: /home/ringki/fsl_course_data/registration/SamsegOutput input images: STRUCT_samseg.nii.gz modelSpecifications: {'FreeSurferLabels': [0, 165, 258, 16, 24, 8, 47, 15, 259, 3, 42, 7, 46, 41, 2, 63, 54, 18, 53, 44, 17, 31, 5, 85, 60, 28, 14, 26, 12, 51, 62, 58, 77, 4, 30, 43, 52, 11, 49, 13, 50, 10, 80, 72], 'atlasFileName': '/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz', 'names': ['Unknown', 'Skull', 'Soft_Nonbrain_Tissue', 'Brain-Stem', 'CSF', 'Left-Cerebellum-Cortex', 'Right-Cerebellum-Cortex', '4th-Ventricle', 'Fluid_Inside_Eyes', 'Left-Cerebral-Cortex', 'Right-Cerebral-Cortex', 'Left-Cerebellum-White-Matter', 'Right-Cerebellum-White-Matter', 'Right-Cerebral-White-Matter', 'Left-Cerebral-White-Matter', 'Right-choroid-plexus', 'Right-Amygdala', 'Left-Amygdala', 'Right-Hippocampus', 'Right-Inf-Lat-Vent', 'Left-Hippocampus', 'Left-choroid-plexus', 'Left-Inf-Lat-Vent', 'Optic-Chiasm', 'Right-VentralDC', 'Left-VentralDC', '3rd-Ventricle', 'Left-Accumbens-area', 'Left-Putamen', 'Right-Putamen', 'Right-vessel', 'Right-Accumbens-area', 'WM-hypointensities', 'Left-Lateral-Ventricle', 'Left-vessel', 'Right-Lateral-Ventricle', 'Right-Pallidum', 'Left-Caudate', 'Right-Thalamus', 'Left-Pallidum', 'Right-Caudate', 'Left-Thalamus', 'non-WM-hypointensities', '5th-Ventricle'], 'colors': [[0, 0, 0, 0], [255, 165, 0, 255], [128, 128, 128, 255], [119, 159, 176, 255], [60, 60, 60, 255], [230, 148, 34, 255], [230, 148, 34, 255], [42, 204, 164, 255], [128, 0, 128, 255], [205, 62, 78, 255], [205, 62, 78, 255], [220, 248, 164, 255], [220, 248, 164, 255], [0, 225, 0, 255], [245, 245, 245, 255], [0, 200, 221, 255], [103, 255, 255, 255], [103, 255, 255, 255], [220, 216, 20, 255], [196, 58, 250, 255], [220, 216, 20, 255], [0, 200, 200, 255], [196, 58, 250, 255], [234, 169, 30, 255], [165, 42, 42, 255], [165, 42, 42, 255], [204, 182, 142, 255], [255, 165, 0, 255], [236, 13, 176, 255], [236, 13, 176, 255], [160, 32, 240, 255], [255, 165, 0, 255], [200, 70, 255, 255], [120, 18, 134, 255], [160, 32, 240, 255], [120, 18, 134, 255], [13, 48, 255, 255], [122, 186, 220, 255], [0, 118, 14, 255], [12, 48, 255, 255], [122, 186, 220, 255], [0, 118, 14, 255], [164, 108, 226, 255], [120, 190, 150, 255]], 'sharedGMMParameters': [GMMparameter(mergedName='Unknown', numberOfComponents=1, searchStrings=['Unknown', 'Skull']), GMMparameter(mergedName='GlobalWM', numberOfComponents=1, searchStrings=['White', 'Brain-Stem', 'VentralDC', 'Optic-Chiasm', 'Thalamus', 'Pallidum']), GMMparameter(mergedName='GlobalGM', numberOfComponents=1, searchStrings=['Cortex', 'Caudate', 'Hippocampus', 'Amygdala', 'Accumbens', 'hypointensities', 'Thalamus']), GMMparameter(mergedName='GlobalCSF_messy', numberOfComponents=1, searchStrings=['CSF', 'vessel', 'choroid-plexus', 'Fluid']), GMMparameter(mergedName='GlobalCSF_clean', numberOfComponents=1, searchStrings=['Ventricle', 'Inf-Lat-Vent', 'Fluid']), GMMparameter(mergedName='Putamen', numberOfComponents=1, searchStrings=['Putamen']), GMMparameter(mergedName='Soft', numberOfComponents=3, searchStrings=['Soft'])], 'useDiagonalCovarianceMatrices': True, 'maskingProbabilityThreshold': 0.5, 'maskingDistance': 10.0, 'K': 0.1, 'biasFieldSmoothingKernelSize': 50, 'whiteMatterAndCortexSmoothingSigma': 0} optimizationOptions: {'maximumNumberOfDeformationIterations': 20, 'absoluteCostPerVoxelDecreaseStopCriterion': 0.0001, 'verbose': False, 'maximalDeformationStopCriterion': 0.001, 'lineSearchMaximalDeformationIntervalStopCriterion': 0.001, 'maximalDeformationAppliedStopCriterion': 0.0, 'BFGSMaximumMemoryLength': 12, 'multiResolutionSpecification': [{'atlasFileName': '/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz', 'targetDownsampledVoxelSpacing': 2.0, 'maximumNumberOfIterations': 100, 'estimateBiasField': True}, {'atlasFileName': '/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz', 'targetDownsampledVoxelSpacing': 1.0, 'maximumNumberOfIterations': 100, 'estimateBiasField': True}]} Constructing image-to-world transform from header information (STRUCT_samseg.nii.gz) Read image: STRUCT_samseg.nii.gz Constructing image-to-world transform from header information (/usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii) Read image: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii performing affine atlas registration image: STRUCT_samseg.nii.gz template: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/template.nii Read mesh collection: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE min: 0 max: 644 robustMin: 0 robustMax: 514.041 histogram[ 0 ]: 14882 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.0422477 cumulativeHistogram[ 1 ]: 0.0422477 cumulativeHistogram[ 2 ]: 0.0422477 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 AFFINE min: 0 max: 644 robustMin: 0 robustMax: 514.041 histogram[ 0 ]: 14882 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.0422477 cumulativeHistogram[ 1 ]: 0.0422477 cumulativeHistogram[ 2 ]: 0.0422477 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 Read mesh collection: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: 0 max: 644 robustMin: 0 robustMax: 514.041 histogram[ 0 ]: 14882 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.0422477 cumulativeHistogram[ 1 ]: 0.0422477 cumulativeHistogram[ 2 ]: 0.0422477 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 maximalDeformation=1.0000 minLogLikelihood=-0.7611 maximalDeformation=1.6862 minLogLikelihood=-0.7777 maximalDeformation=1.4750 minLogLikelihood=-0.7945 maximalDeformation=1.2925 minLogLikelihood=-0.8050 maximalDeformation=0.9504 minLogLikelihood=-0.8100 maximalDeformation=1.0036 minLogLikelihood=-0.8131 maximalDeformation=0.2880 minLogLikelihood=-0.8143 maximalDeformation=0.0198 minLogLikelihood=-0.8143 maximalDeformation=0.0000 minLogLikelihood=-0.8143 appliedScaling: 1.0160 Read mesh collection: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: 0 max: 644 robustMin: 0 robustMax: 514.041 histogram[ 0 ]: 14882 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.0422477 cumulativeHistogram[ 1 ]: 0.0422477 cumulativeHistogram[ 2 ]: 0.0422477 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 maximalDeformation=1.0000 minLogLikelihood=-0.8302 maximalDeformation=0.2745 minLogLikelihood=-0.8304 maximalDeformation=0.0976 minLogLikelihood=-0.8304 maximalDeformation=0.0656 minLogLikelihood=-0.8306 maximalDeformation=0.1658 minLogLikelihood=-0.8309 maximalDeformation=0.0092 minLogLikelihood=-0.8309 maximalDeformation=0.0000 minLogLikelihood=-0.8309 appliedScaling: 1.0033 Read mesh collection: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlasForAffineRegistration.txt.gz Transforming points Transforming points AFFINE L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 0 min: 0 max: 644 robustMin: 0 robustMax: 514.041 histogram[ 0 ]: 14882 histogram[ 1 ]: 0 histogram[ 2 ]: 0 histogram[ 3997 ]: 0 histogram[ 3998 ]: 0 histogram[ 3999 ]: 1 cumulativeHistogram[ 0 ]: 0.0422477 cumulativeHistogram[ 1 ]: 0.0422477 cumulativeHistogram[ 2 ]: 0.0422477 cumulativeHistogram[ 3997 ]: 0.999997 cumulativeHistogram[ 3998 ]: 0.999997 cumulativeHistogram[ 3999 ]: 1 maximalDeformation=0.7196 minLogLikelihood=-0.8348 maximalDeformation=0.0000 minLogLikelihood=-0.8348 appliedScaling: 1.0014 writing template transform to /home/ringki/fsl_course_data/registration/SamsegOutput/template.lta writing talairach transform to /home/ringki/fsl_course_data/registration/SamsegOutput/samseg.talairach.lta atlas registration complete: 0:00:25.938044 Constructing image-to-world transform from header information (STRUCT_samseg.nii.gz) Read image: STRUCT_samseg.nii.gz Read mesh collection: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points [1.015625 1.015625 1. ] Unknown Unknown (100%) Skull (100%) GlobalWM Brain-Stem (100%) Left-Cerebellum-White-Matter (100%) Right-Cerebellum-White-Matter (100%) Right-Cerebral-White-Matter (100%) Left-Cerebral-White-Matter (100%) Optic-Chiasm (100%) Right-VentralDC (100%) Left-VentralDC (100%) Right-Pallidum (100%) Right-Thalamus (50%) Left-Pallidum (100%) Left-Thalamus (50%) GlobalGM Left-Cerebellum-Cortex (100%) Right-Cerebellum-Cortex (100%) Left-Cerebral-Cortex (100%) Right-Cerebral-Cortex (100%) Right-Amygdala (100%) Left-Amygdala (100%) Right-Hippocampus (100%) Left-Hippocampus (100%) Left-Accumbens-area (100%) Right-Accumbens-area (100%) WM-hypointensities (100%) Left-Caudate (100%) Right-Thalamus (50%) Right-Caudate (100%) Left-Thalamus (50%) non-WM-hypointensities (100%) GlobalCSF_messy CSF (100%) Fluid_Inside_Eyes (50%) Right-choroid-plexus (100%) Left-choroid-plexus (100%) Right-vessel (100%) Left-vessel (100%) GlobalCSF_clean 4th-Ventricle (100%) Fluid_Inside_Eyes (50%) Right-Inf-Lat-Vent (100%) Left-Inf-Lat-Vent (100%) 3rd-Ventricle (100%) Left-Lateral-Ventricle (100%) Right-Lateral-Ventricle (100%) 5th-Ventricle (100%) Putamen Left-Putamen (100%) Right-Putamen (100%) Soft Soft_Nonbrain_Tissue (100%) ==================== { depth: 1 maximumNumberOfDeformationIterations: 20 absoluteCostPerVoxelDecreaseStopCriterion: 0.0001 verbose: False maximalDeformationStopCriterion: 0.001 lineSearchMaximalDeformationIntervalStopCriterion: 0.001 maximalDeformationAppliedStopCriterion: 0.0 BFGSMaximumMemoryLength: 12 multiResolutionSpecification: { depth: 2 atlasFileName: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz targetDownsampledVoxelSpacing: 2.0 maximumNumberOfIterations: 100 estimateBiasField: True }, { depth: 2 atlasFileName: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz targetDownsampledVoxelSpacing: 1.0 maximumNumberOfIterations: 100 estimateBiasField: True } } ==================== Read mesh collection: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz Transforming points Transforming points iterationNumber: 0 EM converged! 1 0.398942 SLIDING FutureWarning: The default value of `n_init` will change from 10 to 'auto' in 1.4. Set the value of `n_init` explicitly to suppress the warning L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 blockNumber 0 efficiency: 126.7000 % relative size: 24.6395 % setup time: 1.2095 sec L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 blockNumber 1 efficiency: 128.3933 % relative size: 20.0000 % setup time: 0.6145 sec L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 blockNumber 2 efficiency: 127.1974 % relative size: 18.9204 % setup time: 0.6081 sec L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 blockNumber 3 efficiency: 122.7357 % relative size: 19.8431 % setup time: 0.5968 sec L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 blockNumber 4 efficiency: 127.1474 % relative size: 19.2977 % setup time: 0.6058 sec L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.001 MaximalDeformationStopCriterion: 0.001 MaximumNumberOfIterations: 20 Verbose: 0 blockNumber 5 efficiency: 126.6879 % relative size: 23.7617 % setup time: 0.6279 sec Total time spent: 1.3786 sec maximalDeformation=2.3455 Total time spent: 1.1736 sec maximalDeformation=1.3181 Total time spent: 1.1150 sec maximalDeformation=0.9837 Total time spent: 0.0030 sec maximalDeformation=0.0000 maximalDeformationApplied: 2.7207 ======================================================= iterationNumber: 1 EM converged! 1 0.398942 SLIDING ProbabilisticAtlas reusing warm optimizers!! Total time spent: 1.3099 sec maximalDeformation=0.9719 Total time spent: 1.3018 sec maximalDeformation=1.1376 Total time spent: 1.0990 sec maximalDeformation=1.0771 Total time spent: 0.0031 sec maximalDeformation=0.0000 maximalDeformationApplied: 1.8142 ======================================================= iterationNumber: 2 EM converged! 1 0.398942 SLIDING ProbabilisticAtlas reusing warm optimizers!! Total time spent: 1.4168 sec maximalDeformation=0.9816 Total time spent: 1.2834 sec maximalDeformation=0.7318 Total time spent: 1.0291 sec maximalDeformation=0.8476 Total time spent: 0.0031 sec maximalDeformation=0.0000 maximalDeformationApplied: 1.9384 ======================================================= iterationNumber: 3 EM converged! 1 0.398942 SLIDING ProbabilisticAtlas reusing warm optimizers!! Total time spent: 1.3210 sec maximalDeformation=0.7104 Total time spent: 1.0347 sec maximalDeformation=0.8439 Total time spent: 0.9609 sec maximalDeformation=0.5982 Total time spent: 0.0037 sec maximalDeformation=0.0000 maximalDeformationApplied: 1.7072 ======================================================= iterationNumber: 4 EM converged! 1 0.398942 SLIDING ProbabilisticAtlas reusing warm optimizers!! Total time spent: 1.2096 sec maximalDeformation=0.8494 Total time spent: 1.0121 sec maximalDeformation=0.7369 Total time spent: 0.9503 sec maximalDeformation=0.9738 Total time spent: 0.0030 sec maximalDeformation=0.0000 maximalDeformationApplied: 2.1911 ======================================================= iterationNumber: 5 EM converged! 1 0.398942 SLIDING ProbabilisticAtlas reusing warm optimizers!! Total time spent: 1.2341 sec maximalDeformation=0.8784 Total time spent: 1.0890 sec maximalDeformation=0.6860 Total time spent: 0.9218 sec maximalDeformation=0.9306 Total time spent: 0.0028 sec maximalDeformation=0.0000 maximalDeformationApplied: 2.3352 ======================================================= iterationNumber: 6 EM converged! 1 0.398942 SLIDING ProbabilisticAtlas reusing warm optimizers!! Total time spent: 1.1320 sec maximalDeformation=0.8858 Total time spent: 1.0573 sec maximalDeformation=0.7423 Total time spent: 1.0033 sec maximalDeformation=0.5425 Total time spent: 0.0033 sec maximalDeformation=0.0000 maximalDeformationApplied: 1.8393 ======================================================= iterationNumber: 7 EM converged! 1 0.398942 SLIDING ProbabilisticAtlas reusing warm optimizers!! Total time spent: 1.0969 sec maximalDeformation=0.4317 Total time spent: 1.0330 sec maximalDeformation=0.2635 Total time spent: 0.8456 sec maximalDeformation=0.2330 Total time spent: 0.0031 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.7037 ======================================================= iterationNumber: 8 EM converged! 1 0.398942 SLIDING ProbabilisticAtlas reusing warm optimizers!! Total time spent: 1.1469 sec maximalDeformation=0.1336 Total time spent: 0.9835 sec maximalDeformation=0.1533 Total time spent: 0.9917 sec maximalDeformation=0.0903 Total time spent: 0.0038 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.2659 ======================================================= iterationNumber: 9 EM converged! 1 0.398942 SLIDING ProbabilisticAtlas reusing warm optimizers!! Total time spent: 1.1334 sec maximalDeformation=0.0820 Total time spent: 1.0976 sec maximalDeformation=0.1198 Total time spent: 0.8241 sec maximalDeformation=0.1144 Total time spent: 0.0030 sec maximalDeformation=0.0000 maximalDeformationApplied: 0.2500 ======================================================= Read mesh collection: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level1.txt.gz Read mesh collection: /usr/local/freesurfer/7.4.1/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz SLIDING L-BFGS BFGS-MaximumMemoryLength: 12 LineSearchMaximalDeformationIntervalStopCriterion: 0.005 MaximalDeformationStopCriterion: 0.005 Verbose: 1 [BRACKETING] Found a really good solution -- no need for zooming: 1 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 7.16011 ----------------------- [BRACKETING] Hit a really bad solution -- ready for zooming: 3.55517 [ZOOMING] Zooming with low=0 and high=3.55517 bisected: 1.77758 [ZOOMING] Found a good solution: 1.77758 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 1.33934 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.132102 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.109576 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.0715406 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.0258653 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.0195591 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.0061019 ----------------------- [BRACKETING] Found a really good solution -- no need for zooming: 0.00454179 ----------------------- Optimizer: maximalDeformation is too small; stopping iterationNumber: 0 Killed ]0;ringki@TABLET-TSKI5C88: ~/fsl_course_data/registration/SamsegOutput [01;32mringki@TABLET-TSKI5C88 [00m: [01;34m~/fsl_course_data/registration/SamsegOutput [00m$ ]0;ringki@TABLET-TSKI5C88: ~/fsl_course_data/registration/SamsegOutput [01;32mringki@TABLET-TSKI5C88 [00m: [01;34m~/fsl_course_data/registration/SamsegOutput [00m$ exit exit Script done on 2024-05-22 15:10:40+02:00 [COMMAND_EXIT_CODE="137"] _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1Bav4UyazUOOSSroLT9imHtZhddXReF_Ms-muXe5F9NPra… <https://secure-web.cisco.com/1Bav4UyazUOOSSroLT9imHtZhddXReF_Ms-muXe5F9NPra…> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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analyzing a picture of a brain with the presence of a cyst
by Vania Tsoneva 23 May '24

23 May '24

External Email - Use Caution Hello, can you help me with analyzing a photo of a brain with the presence of a cyst and does this patient have Alzheimer's? The makeup is from a scanner with contrast material . Thank you in advance and best regards! [image: image.png] [image: image.png] [image: image.png]

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Atlas Used in FreeSurfer for Segmentation of Fornix, Corpus Callosum, Hippocampus
by Ahsan Ali 22 May '24

22 May '24

External Email - Use Caution Dear FreeSurfer Team, After reviewing the literature, I have a question: which atlases are used in the segmentation of the fornix, corpus callosum, and hippocampus from magnetic resonance images using FreeSurfer? This is a significant question for me, and I would appreciate a clear and concise answer. Please provide some relevant references. With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552

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Re: [Freesurfer] fspalm error
by Stefano Delli Pizzi 22 May '24

22 May '24

External Email - Use Caution I have the same error that doesn't resolve with --mgh or mgz. warning: excluding contrast file /Volumes/mnu/MRI/XXX/NIFTI/FreeSurfer/rs-fMRI_AROMA/G3V0_Comparison/fc.MDseed.surf.rh/MD/G3V0_PALM.glmdir/group.effect/C.dat since it has multiple rows ERROR: for surface based analysis, input cannot be nii or nii.gz Thanks Stefano

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PhD candidate position - high-resolution imaging of the human claustrum
by Zaretskaya, Natalia (natalia.zaretskaya＠uni-graz.at) 22 May '24

22 May '24

External Email - Use Caution Dear colleagues, I would greatly appreciate if you could forward this job announcement to potentially interested candidates. The Visual Neuroscience Lab (PI: Natalia Zaretskaya) at the Institute of Psychology, University of Graz jointly with the fMRI Lab (PI: Christian Windischberger) at MR Center of Excellence, Medical University of Vienna are looking for a doctoral candidate to join us in the project dedicated to high-resolution imaging of the human claustrum, one of the most mysterious and least studied areas of the human brain. You will join the Vienna-based part of the team and will be involved in piloting and conducting experiments using 7 Tesla MRI. You will find further details and the official job advertisement text below. --- Visual Neuroscience Lab (PI: Natalia Zaretskaya) at the Institute of Psychology, University of Graz jointly with the fMRI Lab (PI: Christian Windischberger) at MR Center of Excellence, Medical University of Vienna is looking for a Doctoral Candidate within the framework of the FWF funded project "High-resolution imaging of the human claustrum" (Project-Assistant; 30 hours a week; fixed-term employment initially for 1 year with a possibility of extension for up to 4 years in total) Project description The project is dedicated to investigating the claustrum, one of the most mysterious structures of the human brain. It is led by the PI Natalia Zaretskaya in Graz and the co-PI Christian Windischberger in Vienna. You will join the Vienna-based part of the team and will be involved in piloting and conducting experiments using 7 Tesla MRI. Project-related publications: * Adam Coates, Natalia Zaretskaya, High-resolution dataset of manual claustrum segmentation, Data in Brief, Volume 54, 2024, https://secure-web.cisco.com/1zeq_ipnEfhXQWA1cKbf1_H6iUzhhXoee44VMGbemOb2mp… * Adam Coates, David Linhardt, Christian Windischberger, Anja Ischebeck, Natalia Zaretskaya, High-resolution 7T fMRI reveals the visual sensory zone of the human claustrum, bioRxiv 2023.09.18.558213; https://secure-web.cisco.com/1XoozScW5lqeJFO6PKFmaXkaXPux1aUn48UIO7n1abH2yi… Your duties * Participation in planning, preparing and conducting 7T fMRI experiments in Vienna, data analysis * Participation in scientific conferences and workshops * Preparing scientific manuscripts and publications * Contribution to supervising Bachelor and Master's theses * Writing and submitting a doctoral dissertation at the end of the project Your profile * Master's degree or diploma in neuroscience, physics, biomedical engineering, computer science or similar fields * Interest in the topic of the project and in vision/neuroscience research in general * Sound knowledge in conducting (f)MRI experiments and analyzing (f)MRI data, preferably at ultrahigh magnetic field * Excellent programming skills (MATLAB, Python, Linux shell, etc.) * Excellent English skills * Excellent organizational, communication and social skills, independence, reliability * Preferably sound knowledge of the visual system More information is available at https://secure-web.cisco.com/1QSEqOWvfyj3Fn-k_qchrTdPC3oPy2SGg1xDUvzx9ueGD8… , http://secure-web.cisco.com/13ejGmNm191wKTEtay0FeS3AMK97XGb6RNkQtfnvjwL2i2Z… and https://secure-web.cisco.com/1Fhf-9nVXOL71lbQuy8a0pzO-PeLa-akgsFsMyolBxJ-LY… Salary Salary scheme is according to the FWF scale for doctoral candidates. The minimum salary according to the FWF is currently EUR 2,684.10 gross/month. Expected position start: 1.10.2024 (negotiable) Application will be accepted until 13.07.2024 or until the position is filled. Application documents: * Motivation Letter * CV * Relevant diplomas/graduation certificates with grade transcripts * Contact information of two referees who would be willing to provide a reference letter upon request Application documents should be sent to Natalia.Zaretskaya(a)uni-graz.at<mailto:Natalia.Zaretskaya@uni-graz.at> -- Ass.-Prof. PD Dr. Natalia Zaretskaya Department of Psychology, University of Graz BioTechMed-Graz Universitaetsplatz 2 8010 Graz Austria +43 316 380 - 5117 natalia.zaretskaya(a)uni-graz.at<mailto:natalia.zaretskaya@uni-graz.at> https://secure-web.cisco.com/1QSEqOWvfyj3Fn-k_qchrTdPC3oPy2SGg1xDUvzx9ueGD8…

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Group Stats for hipposubfields, brainstem and amygdalar
by Carina Obermüller 21 May '24

21 May '24

External Email - Use Caution Dear Freesurfer team, I am looking for a group stats command like the asegstats2table and aparcstats2table command for hipposubfields, brainstem and amygdalar, but I couldn’t find it in the archives. I remember it was mentioned in the recent Freesurfer course, but I can’t find it anymore. Could you help me out? Also more generally, is there an overview page of all the possible group stats commands? Thank you so much in advance for your reply! Sincerely, Carina

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how to resolve recon-all stopping at fill step
by Dong, Yilei 20 May '24

20 May '24

External Email - Use Caution Dear FreeSurfer developers, Apologies for emailing once again about how to resolve the recon-all stopping exactly at the fill step. I understand this may have to do with specific issues on UCSD's computer cluster, but if UCSD's cluster is not having the most up-to-date version of the FreeSurfer module, would it make a difference if I asked UCSD's supercomputer team to update the module version, so that the entire processing stream may be able to run all the way for 1 subject? Would it also make a difference if I increased the number of cores for 1 subject from 1 to 2? Sincerely, Yilei

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Freesurfer May 2024