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1 3dSkullStrip - AFNI program
https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dSkullStrip.html
AFNI program: 3dSkullStrip. Output of -help. Usage: A program to extract the brain from surrounding. tissue from MRI T1-weighted images.
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2 AFNI Tutorial #4-a: AFNI Commands - YouTube
https://www.youtube.com/watch?v=78lGrdmC9fg
Oct 31, 2019
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3 Chapter 1: AFNI Commands and uber_subject.py
https://andysbrainbook.readthedocs.io/en/latest/AFNI/AFNI_Short_Course/AFNI_Preprocessing/01_AFNI_Commands_uber_subject.html
The AFNI command to do this step is called 3dSkullStrip . ... to specify an additional flag, -h , to print the help; type 3dSkullStrip -h and press return.
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4 Module Details - LONI Pipeline
https://pipeline.loni.usc.edu/files/serverlib/view_workflow.php?file=/AFNI/Modules/3dSkullStrip.pipe
3dSkullStrip -input VOL -prefix VOL_PREFIX -ld 30 Use a denser mesh, in the cases where you have lots of csf between gyri. Also helps when some of the brain ...
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5 A Brief introduction to BEaST - AWS
http://rstudio-pubs-static.s3.amazonaws.com/8431_d05daa5d49aa4cada417b6afc8ffd295.html
My bottom line is, BEaST is a better alternative for BET, 3dSkullStrip and Freesurfer for brain extraction. It at least worth a try if the “main stream” ...
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6 AFNI 3dSkullStrip going wrong · Issue #554 · nipreps/mriqc
https://github.com/poldracklab/mriqc/issues/554
If that does not help, make sure that the skull-stripped volume has no ... Use it when parts of the frontal lobes get clipped See 3dSkullStrip -help for ...
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7 Brain extraction from MR images using a combination of ...
https://ieeexplore.ieee.org/document/8069542
Three common brain extraction methods (Brain Extraction Tool (BET), 3DSkullStrip and FreeSurfer) were used to provide the input segmentations.
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8 Automated brain extraction of multisequence MRI using ...
https://onlinelibrary.wiley.com/doi/pdf/10.1002/hbm.24750
Since BET, 3dSkullStrip, BSE, ROBEX, and BEaST have primarily been ... fees from Teva, grant support and lecture fees from Novartis and.
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9 Field of View Normalization in Multi-Site Brain MRI
https://scholar.harvard.edu/files/xda/files/s12021-018-9359-z.pdf
3dSkullStrip, FreeSurfer's HWA, BrainSuite's BSE, and MASS. ... Award for support to YO, Boston Children's Hospital and Harvard.
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10 Untitled
https://cds.ismrm.org/protected/17MProceedings/PDFfiles/5080.html
The five most common brain extraction methods (3dSkullStrip (AFNI)14, BET (FSL)15, ... can help to minimize error propagation to the final stage of cortical ...
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11 User's Guide Neuroimage Processing ToolKit (NPTK) - NITRC
https://www.nitrc.org/docman/view.php/80/230/user's%20guide
Skull-stripping using 3dSkullStrip ... 3dSkullStrip -input REFimage -prefix REFimageBrain ... see help spm_coreg, and help spm_reslice for more options.
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12 FSL Archives - JISCMail
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;bf53b064.0712
Hello, I would like to first people for the help with the fieldmapping suggestions. ... I have tried skull stripping using bet2, and AFNI's 3dSkullStrip, ...
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13 A Brief introduction to BEaST | The R-fMRI Network
http://rfmri.org/content/brief-introduction-beast
Hope it will be useful to help people start using BEaST. ... The most commonly used brain extraction packages like AFNI's 3dSkullStrip, ...
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14 AFNI & FMRI - MIT CBMM
https://cbmm.mit.edu/sites/default/files/documents/afni01_intro.pdf
Help the user (message board; consulting with NIH users). ▫ Until our patience expires ... 3dSkullStrip = remove “skull” from anatomical dataset.
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15 AFNI 3DUnifize error - neuroimaging - Neurostars
https://neurostars.org/t/afni-3dunifize-error/23483
... installed. afni -help and 3dUnifize -help works well in b… ... various programs... afni : success suma : success 3dSkullStrip : success ...
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16 Documentation/Nightly/Modules/BVeR - Slicer Wiki
https://www.slicer.org/wiki/Documentation/Nightly/Modules/BVeR
... FreeSurfer, BEasT, 3DSkullStrip, ROBEX, OptiBET and many others. ... Assist in the total brain volume estimate also reducing the ...
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17 Beauchamp:AFNI Install - - OpenWetWare
https://openwetware.org/wiki/Beauchamp:AFNI_Install
Copy over a .cshrc file which will help you set up your path every time you open ... This will help if you get an error after running 3dSkullStrip and are ...
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18 Performance of the U-Net models and traditional approaches ...
https://www.researchgate.net/figure/Performance-of-the-U-Net-models-and-traditional-approaches-The-box-plot-shows-the-Dice_fig3_350456044
AFNI 3dSkullStrip missed identifying the brain in the superior . ... This work can help inform the design of future preclinical rodent imaging studies and ...
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19 Appendix — C-PAC 1.8.4 Beta documentation
https://fcp-indi.github.io/docs/latest/user/appendix
... the libgsl.so.0 software library required for some of their tools (3dSkullStrip, and 3dHist). ... If this returns a help page with a list of parameters, ...
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20 Tumor Segmentation - Knowledge Base - QMenta
https://support.qmenta.com/knowledge/tumor-segmentation
Skull Strip Parameters: Skull stripping is customizable in the BrainSuite (please refer here for more details) and AFNI's 3dSkullStrip case using different ...
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21 Archive - Google Code
https://code.google.com/archive/p/brainwhere/wikis/brainImagingGuide.wiki
some AFNI reference manuals contain information omitted from program help: ... skull stripping == === bet === === 3dautomask/3dSkullStrip ===.
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22 The better skullstrip in AFNI - Crash Log
https://blog.cogneurostats.com/2018/05/10/the-better-skullstrip-in-afni/
If you're an AFNI user, you probably use 3dSkullStrip, if you use FSL then it's BET, and of course Freesurfer has their own in recon-step 1.
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23 An Open Resource for Non-human Primate Imaging - Cell Press
https://www.cell.com/neuron/pdf/S0896-6273(18)30768-2.pdf
technologies to support in vivo examination of brain organization ... For example, in AFNI, the program ''3dSkullStrip'' with.
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24 AFNI Jazzercise Hints - Yumpu
https://www.yumpu.com/en/document/view/23266332/afni-jazzercise-hints
2. Use program 3dMean. Check out the 3dMean –help menu for further assistance. 3. The –help menus for 3dAutomask and 3dSkullStrip will help you ...
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25 U-net model for brain extraction: Trained on humans for ...
https://www.sciencedirect.com/science/article/pii/S1053811921002780
For instance, a new option '-monkey' has been developed to customize AFNI's widely-used 3dSkullStrip function, which improves its performance ...
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26 neuro/anat/t1w - brainlife
https://brainlife.io/datatype/58c33bcee13a50849b25879a
1.25mm_brain3dSkullStrip7tAC-PC ... It allows you to draw regions of interest which can aid lesion mapping and fMRI analysis. fiberNavigator.
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27 AFNI Nonlinear Transform - LRCN Wiki
http://polaris.ssc.uwo.ca/mediawiki/index.php/AFNI_Nonlinear_Transform
... the 3dQwarp help page): 3dUnifize -prefix anatT1_U -input anatT1+orig 3dSkullStrip -input anatT1_U+orig -prefix anatT1_US -niter 400 -ld ...
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28 s13742-016-0150-5.pdf - GigaScience
https://gigascience.biomedcentral.com/track/pdf/10.1186/s13742-016-0150-5.pdf
used to compare the performance of BET, 3dSkullStrip ... We would like to thank Dr. Simon Fristed Eskildsen for help with the.
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29 Function reference • afnir - Neuroconductor
https://neuroconductor.org/help/afnir/reference/index.html
AFNI 3dSkullStrip function. afni_3dTshift() tshift(). Convert AFNI File to NIFTI Image. afni_3dTstat() afni_3dtstat() tstat() Tstat(). AFNI 3dTstat function.
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30 Issue with running singularity image - Google Groups
https://groups.google.com/g/cpax_forum/c/G_9UMgTWjfE
3dSkullStrip -input ... 3dSkullStrip: error while loading shared libraries: libGL.so.1: cannot open shared object file: No ... Thank you again for your help.
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31 Automated template-derived brain extraction in animal MRI
https://www.nature.com/articles/s41598-019-48489-3
... “Brain-Extraction-Tool”, “3dSkullStrip”, “Primatologist-Toolbox”, “Rapid Automatic Tissue Segmentation” and “Robust automatic rodent ...
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32 [SOLVED]Install libgsl.so.0 package - Arch Linux Forums
https://bbs.archlinux.org/viewtopic.php?id=273137
3dSkullStrip: error while loading shared libraries: libgsl.so.0: cannot open ... You could probably get help from the AUR maintainer as they ...
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33 AFNI -- All Helps on One Page
http://www.grahamwideman.com/gw/brain/afni/alldocs_afni.htm
See the output of 'cdf -help' for documentation on the meanings of and ... Example: afni -niml -yesplugouts & suma -niml & 3dSkullStrip ...
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34 The CONP Privacy and De-identification Toolkit
https://conp.ca/wp-content/uploads/2022/02/CONP_De-identification_Toolkit_v1.0.3.pdf
guidance below seeks to help researchers prepare neuroscience ... https://www.mathworks.com/help/images ... ogram_help/3dSkullStrip.html.
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35 Skull Removal of brain using matlab - MathWorks
https://www.mathworks.com/matlabcentral/answers/86233-skull-removal-of-brain-using-matlab
and the part used for skull stripping is called 3dSkullStrip ... treasures in MATLAB Central and discover how the community can help you!
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36 Field of View Normalization in Multi-Site Brain MRI. - Abstract
https://europepmc.org/article/pmc/pmc7334884
We used 5 skull stripping tools: BET, 3dSkullStrip, BSE, HWA and MASS. ... Thrasher Research Fund Early Career Award for support to YO, Boston Children's ...
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37 CONP Privacy and De-identification Toolkit v1.0.2
https://training.incf.org/sites/default/files/2021-11/CONP_Privacy_and_Deidentification_Toolkit_v1.0.2.pdf
https://www.mathworks.com/help/image s/ref/dicomanon.html ... rogram_help/3dSkullStrip.html. Laboratory for. Computational. Neuroimaging's.
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38 067017v1.full.pdf - bioRxiv
https://www.biorxiv.org/content/10.1101/067017v1.full.pdf
3dSkullStrip is a modified version of BET that is ... We would like to thank Dr. Simon Fristed Eskildsen for help with the.
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39 preprocessed connectomes project repository of manually ...
https://academic.oup.com/gigascience/article/5/1/s13742-016-0150-5/2737425
3dSkullStrip is a modified version of BET that is incorporated in the AFNI toolkit ... We would like to thank Dr. Simon Fristed Eskildsen for help with the ...
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40 https://ruj.uj.edu.pl/xmlui/bitstream/handle/item/...
https://ruj.uj.edu.pl/xmlui/bitstream/handle/item/148071/step-by-step_dti.odt?sequence=2&isAllowed=y
If you need more help check out FSL Wiki: ... 3dSkullStrip -input T1.nii.gz -prefix T1_brain.nii.gz # skullstriping T1 #. # first try add -push to edge, eg.
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41 2D and 3D U-Nets for skull stripping in a large and ...
https://ojs.bibsys.no/index.php/NIK/article/view/836/707
3D or 3D+time) image will help subsequent segmentation algorithms in ... from Advanced Normalization Tools (ANTs) [9] and the 3dSkullStrip tool in AFNI.
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42 AFNI - HPC Documentation - UIowa Wiki
https://wiki.uiowa.edu/display/hpcdocs/AFNI
NOTE: EVERYTHING BELOW HERE IS NOT RELEVANT OR NEEDED FOR AFNI BUILD THEY ARE NOTES THAT MAY HELP WITH OTHER BUILDS.
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43 A Macaque Brain Extraction Model Based on U-Net Combined ...
https://www.mdpi.com/2076-3425/12/2/260/htm
... 3dSkullStrip in AFNI [17,18,19], and the hybrid watershed algorithm (HWA) ... However, adding a relevant data training model may help the model improve ...
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44 The preprocessed connectomes project repository of manually ...
https://cyberleninka.org/article/n/785322
3dSkullStrip is a modified version of BET that is incorporated in the AFNI toolkit ... We would like to thank Dr. Simon Fristed Eskildsen for help with the ...
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45 The physiological effects of noninvasive brain stimulation ...
https://www.science.org/doi/10.1126/sciadv.aay2739
The brain representations in the figure panels were created with the help of the ... The structural images were skull-stripped using AFNI-3dSkullStrip, ...
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46 Development of Texture Weighted Fuzzy C-Means Algorithm ...
https://openprairie.sdstate.edu/cgi/viewcontent.cgi?article=3977&context=etd
their help to my thesis in the final defense. ... gave to me. Without their help, I could not continue my academic career. ... 3DSkullStrip by Smith et al.
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47 Deep MRI brain extraction: A 3D convolutional neural network ...
https://hci.iwr.uni-heidelberg.de/sites/default/files/publications/files/1721812507/kleesiek_16_deep.pdf
#:2162), ROBEX (v1.2), HWA (stable5) and 3dSkullStrip (AFNI_2011_ ... glioblastoma multiforme data. Med. Image Comput. Comput. Assist. Interv. 14,.
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48 diabetes mellitus and impaired glucose tolerance using multi ...
https://etheses.whiterose.ac.uk/24545/2/finalthesis_corrMED.pdf
Moshona who are always there for me, ready to support me in every possible way, ... AFNI's (204) 3dSkullStrip utilises a modified BET.
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49 A Library for fMRI Real-Time Processing Systems in Python ...
https://www.frontiersin.org/articles/10.3389/fnins.2022.834827/full
... (blue box in Figure 3), AFNI's 3dSkullStrip is used for brain extraction. ... A simulation analysis would help determine the necessary noise regressors ...
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50 Anxiety and the Neurobiology of Temporally Uncertain Threat ...
https://www.jneurosci.org/content/40/41/7949
... and brain-masked using 3dSkullStrip in AFNI (version 17.2.10) (Cox, 1996). ... On Uncertain Threat trials, this support was absent, ...
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51 Creating Masks In FSL - Andy's Brain Blog
http://andysbrainblog.blogspot.com/2012/11/creating-masks-in-fsl.html
Any help you can provide would be much appreciated! Thank you!! ... or you could use AFNI's 3dSkullStrip tool with the -avoid_eyes option.
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52 User`s Guide Neuroimage Processing ToolKit - StudyLib
https://studylib.net/doc/18646307/user-s-guide-neuroimage-processing-toolkit
Skull-stripping using 3dSkullStrip 4.2. ... rmeanEPIimage also referred to as rEPIimage % see help spm_coreg, and help spm_reslice for more options 4.2.3.
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53 Processing pipeline for image reconstructed fNIRS analysis ...
https://www.spiedigitallibrary.org/journals/neurophotonics/volume-8/issue-02/025010/Processing-pipeline-for-image-reconstructed-fNIRS-analysis-using-both-MRI/21002R.full
Thus, in this section, we describe steps in our pipeline to help ... has two options to generate the brain mask: 3dSkullstrip and ROBEX.
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54 Human-Object Interaction - OpenNeuro
https://openneuro.org/datasets/ds001235/
Each of the 12 subjects has 14 functional runs, as well as an anatomical scan that has been skull-stripped using AFNI's 3dSkullStrip.
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55 FCP-INDI/C-PAC: C-PAC Version 1.2.0 Beta | Zenodo
https://zenodo.org/record/1343648
... for both AFNI's 3dSkullStrip and FSL's BET for anatomical skull-stripping ... you can contact us here for user support and discussion: ...
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56 Automated Brain Masking of Fetal Functional MRI with Open ...
https://link.springer.com/article/10.1007/s12021-021-09528-5
Also, to aid in interpretation and benchmarking obtained evaluation ... The BET, 3dSkullStrip, and Anatomical U-Net masks do not adequately ...
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57 Ultrahigh-resolution microstructural diffusion tensor imaging ...
https://www.pnas.org/content/107/28/12687.full.pdf
(37) implemented in 3DSkullStrip (AFNI; National Institutes of Health). ... Gregory Sanchez for help with data collection and analysis.
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58 Neuroimaging Data Processing/Print version - Wikibooks
https://en.wikibooks.org/wiki/Neuroimaging_Data_Processing/Print_version
See the output of 'mris_convert -help' for examples. ie. mris_convert lh.pial ... 3dSkullStrip is a program in AFNI to extract the brain from surrounding ...
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59 An Open Resource for Non-human Primate Imaging
https://escholarship.org/content/qt87689223/qt87689223.pdf?t=qajntm
technologies to support in vivo examination of brain organization ... For example, in AFNI, the program ''3dSkullStrip'' with.
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60 Relationship to Gray Matter Volume | PLOS ONE
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075880
Conclusions The identified association between unit support and ... using AFNI's [45] 3dSkullStrip followed by manual editing to remove any ...
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61 Magnetic Resonance Imaging
https://daneshyari.com/article/preview/8159692.pdf
... and in turn, helps to improve the performance of the proposed method. ... method, called 3DSkullStrip, a program provided by the Anal-.
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62 Intelligent magnetic resonance imaging: application in fetal MRI.
https://repository.library.northeastern.edu/files/neu:cj82rk55g/fulltext.pdf
show the predicted brain masks using BET and 3dSkullStrip, respectively. The right ... learning process helping me not only in technical topics, ...
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63 Diffusion Imaging; Introduction, tutorials and background on ...
http://www.diffusion-imaging.com/2015/10/
Using the tensor information as show on the right will help ... Other skull stripping tools: 3dSkullStrip by AFNI, SPM, BrainSuite ...
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64 Brain Extraction in Multiple T1-Weighted Magnetic Resonance ...
https://latamt.ieeer9.org/index.php/transactions/article/download/6093/1449/82033
more efficient way, in order to support disease diagnosis, and the identification of pathologies ... 3) 3D Skull Stripping, or 3DSkullStrip, is part of AFNI.
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65 AFNI Jewel Box AKA Tool Box, Treasure Chest or ...
https://corpora.tika.apache.org/base/docs/govdocs1/570/570356.ppt
... and scripts; Most come with help output or menus that provide a reminder about their usage; ... 3dSkullStrip -input fred_anat+orig -prefix fred_strip \.
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66 Subjective Cognitive Decline Modifies the Relationship ...
https://www.cambridge.org/core/journals/journal-of-the-international-neuropsychological-society/article/subjective-cognitive-decline-modifies-the-relationship-between-cerebral-blood-flow-and-memory-function-in-cognitively-normal-older-adults/FA195B73B9F63E62450F510C1E775B3E
... cognitively normal older adults might help elucidate the underlying mechanisms of SCD and ... T1-weighted image was performed using AFNI's 3dSkullStrip.
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67 Processing pipeline for image reconstructed fNIRS analysis ...
https://digitalcommons.wustl.edu/cgi/viewcontent.cgi?article=12053&context=open_access_pubs
Thus, in this section, we describe steps in our pipeline to help ... mask: 3dSkullstrip and ROBEX.20 The 3dSkullstrip option performs well ...
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68 aici_applying_DL_models.pdf
https://mri.sbollmann.net/wp-content/uploads/2020/11/aici_applying_DL_models.pdf
AFNI 3DSkullStrip, Brainsuite. BSE, ROBEX and BEaST) ... 3DSkullStrip, BSE, and. ROBEX tend to overestimate ... For debugging it can help to “de-dockerize”.
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