Freesurfer

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30080 discussions

Issue running recon-all
by Bhattarai, Kriti 24 Apr '19

24 Apr '19

External Email - Use Caution I am having issues running recon-all in my Mac. I have checked my permission and it is not a read-write issue. Also, I dont know any way to manually verify if I have build-stamp.txt. Could someone guide me if they have seen this before? Thanks! [cid:d493af7b-4924-4889-9844-15035836a8d4]

2 1

How to Display Specific Cortical Parcels (not the output of the recon-all) on Brain Surface
by Mahshid Fouladivanda 24 Apr '19

24 Apr '19

External Email - Use Caution Dear Freesurfer Experts, I have a predetermined cortical parcels in native space. I want to display them on brain surface, As shown in the last image of page bellow: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview I have loaded *.pial files (transferred to native space ) and then volume file (contains native space parcels not output of the recon-all) using freeview but it is not desired! Now, I have some question. First, is it possible to show determined parcels (not the output of the recon-all) on brain surface using freesurfer? Second, is my procedure correct? Then, how could I display determined parcels (not the output of the recon-all) on brain surface using freesurfer? Regards, Mahshid

2 1

FreeSurfer 6.0 disk image for VirtualBox?
by Gonzalo Rojas Costa 24 Apr '19

24 Apr '19

External Email - Use Caution Hi: Where can I find the FreeSurfer 6.0 disk image for VirtualBox? Sincerely, Gonzalo Rojas Costa

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recon-all error
by 1013364183 24 Apr '19

24 Apr '19

External Email - Use Caution Dear freesurfer We run the recon-all command of freesurfer, but when it runs to the randomSeed 0 step below, it will not run anymore, that is, the running terminal has been stuck in the following statement for more than 10 days.We want to ask why this happens? How should we solve this problem? The running statement is as follows: only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/filled.mgz... reading volume /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/brain.finalsurfs.mgz... reading volume /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/../mri/aseg.presurf.mgz... reading volume /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/wm.mgz... 1792 bright wm thresholded. 583658 bright non-wm voxels segmented. reading original surface position from /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/surf/lh.orig... computing class statistics... border white: 318655 voxels (1.90%) border gray 363634 voxels (2.17%) WM (109.0): 109.3 +- 4.5 [70.0 --> 110.0] GM (109.0) : 101.3 +- 17.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 92.2 (was 70) setting MAX_BORDER_WHITE to 114.5 (was 105) setting MIN_BORDER_WHITE to 110.0 (was 85) setting MAX_CSF to 35.0 (was 40) setting MAX_GRAY to 105.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 60.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 56.6 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.26 +- 0.11 (0.00-->2.25) (max @ vno 28887 --> 31618) face area

2 1

fswiki brainstem substructures: test data unavailable
by Fabian Peter Hammerle 24 Apr '19

24 Apr '19

External Email - Use Caution Hi, Section "6. Test data" of the article "Brainstem Substructures" at https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures mentions: > Processed data of a single subject (also used to demo the hippocampal subfield segmentation) is available here: > wget -c ftp://surfer.nmr.mgh.harvard.edu/pub/data/hipposubfields-testdata.tgz At the moment `/pub/data` does not contain the mentioned file `hipposubfields-testdata.tgz`. Is the testdata file still publically available at some url? I found `pub/data/archive/hipposubfields-testdata.tgz`. However, this archive appears to be outdated (modification date: 2015-06-12). Thank you, Fabian

1 0

LGI in QDEC menu please respond soon
by Avi Gharehgazlou 23 Apr '19

23 Apr '19

External Email - Use Caution Hi experts, To give more detail re my previous post.... I have created the .Qdecrc file in my Subjects directory and QDEC folder, which contains one line : MEASURE1 = pial_lgi . However, LGI is still not appearing in the drop down menu on QDEC. When I do command more ~/.Qdecrc it gives the following output: # This file is automatically generated by the application # If you change any lines or add new lines, note that all # coments and empty lines will be deleted. Every line has # to be in format: # key = value # Qdec1\Dialogs\ExitApplication = 0 Qdec1\Dialogs\SendErrorLog = 0 Qdec1\Geometry\MainPanelSize = 375 Qdec1\Geometry\MainPanelVisibility = 1 Qdec1\Geometry\SaveUserInterfaceGeometry = 1 Qdec1\Geometry\SecondaryPanelSize = 250 Qdec1\Geometry\SecondaryPanelVisibility = 0 Qdec1\Geometry\ViewPanelPosition = Right Qdec1\Geometry\WindowGeometry = 900x700+531+190 Qdec1\RunTime\MostRecentVersionLaunched = 1.5 Qdec1\RunTime\PrintTargetDPI = 100.000000 Qdec1\RunTime\ShowBalloonHelp = 1 Qdec1\RunTime\ShowSplashScreen = 1 Qdec1\RunTime\ToolbarFlatButtons = 1 Qdec1\RunTime\ToolbarFlatFrame = 1 Based on previous archives I think my .Qdecrc was not saved properly because the line in this file (MEASURE1 = pial_lgi) doesn't appear in the above output. I know I have to put this line in the above output, but I can't seem to figure out how. Will you please be able to tell me how I can do this? Thanks so much

2 7

Putting LGI in drop down menu of QDEC
by Avi Gharehgazlou 23 Apr '19

23 Apr '19

External Email - Use Caution To give more detail re my previous post.... I have created the .Qdecrc file in my Subjects directory and QDEC folder, which contains one line : MEASURE1 = pial_lgi . However, LGI is still not appearing in the drop down menu on QDEC. When I do command more ~/.Qdecrc it gives the following output: # This file is automatically generated by the application # If you change any lines or add new lines, note that all # coments and empty lines will be deleted. Every line has # to be in format: # key = value # Qdec1\Dialogs\ExitApplication = 0 Qdec1\Dialogs\SendErrorLog = 0 Qdec1\Geometry\MainPanelSize = 375 Qdec1\Geometry\MainPanelVisibility = 1 Qdec1\Geometry\SaveUserInterfaceGeometry = 1 Qdec1\Geometry\SecondaryPanelSize = 250 Qdec1\Geometry\SecondaryPanelVisibility = 0 Qdec1\Geometry\ViewPanelPosition = Right Qdec1\Geometry\WindowGeometry = 900x700+531+190 Qdec1\RunTime\MostRecentVersionLaunched = 1.5 Qdec1\RunTime\PrintTargetDPI = 100.000000 Qdec1\RunTime\ShowBalloonHelp = 1 Qdec1\RunTime\ShowSplashScreen = 1 Qdec1\RunTime\ToolbarFlatButtons = 1 Qdec1\RunTime\ToolbarFlatFrame = 1 Based on previous archives I think my .Qdecrc was not saved properly because the line in this file (MEASURE1 = pial_lgi) doesn't appear in the above output. I know I have to put this line in the above output, but I can't seem to figure out how. Will you please be able to tell me how I can do this? Thanks so much Avi

1 0

Putting LGI in QDEC menu
by Avi Gharehgazlou 23 Apr '19

23 Apr '19

External Email - Use Caution Hi experts, I was able to put LGI in my QDEC drop down menu in the past by following instructions on FW wiki and archives. However, I am doing some more analyses now and unfortunately I can't seem to bring LGI in my QDEC repeating what I have done in the past: I made a .Qdecrc file with following text written in it: MEASURE1 = pial_lgi - I put this file in my Subject directory and QDEC folder and still LGI measure won't show up on QDEC... Will you please tell me what I have to do? Thanks so much, Avi

1 0

The 2nd International Workshop on Machine Learning in Clinical Neuroimaging (MLCN 2019): ENTERING THE ERA OF BIG DATA VIA TRANSFER LEARNING AND DATA HARMONIZATION
by MLCN Workshop 23 Apr '19

23 Apr '19

External Email - Use Caution Dear Colleagues,We are delighted to invite you to join us for the MLCN 2019 <https://mlcnws.com/> workshop as a satellite event of the MICCAI 2019 conference, Shenzhen, China. Call for Papers Recent advances in neuroimaging and machine learning provide an exceptional opportunity for investigators and physicians to discover complex relationships between brain, behaviors, and mental and neurological disorders. The MLCN 2019 workshop (https://mlcnws.com) as a satellite event of MICCAI 2019 (https://www.miccai2019.org) aims to bring together researchers in both theory and application from various fields in domains such as *e.g.* machine learning, neuroimaging, predictive clinical neuroscience, *etc.* Topics of interests include, but are not limited to: - Transfer learning in clinical neuroimaging - Model stability in transfer learning - Data prerequisites for successful transfer learning - Domain adaptation in neuroimaging - Data harmonization across sites - Data pooling – practical issues - Cross-domain learning in neuroimaging - Interpretability for transfer learning - Unsupervised methods for domain adaptation - Multi-site data analysis, from preprocessing to modeling - Big data in clinical neuroimaging - Scalable machine learning methods - Benefits, problems, and solutions of working with very large datasets SUBMISSION PROCESS: The workshop seeks high quality, original, and unpublished work on algorithms, theory, and applications of machine learning in clinical neuroimaging related to big data, transfer learning, and data harmonization. Papers should be submitted electronically in Springer Lecture Notes in Computer Science (LCNS) style ( https://www.springer.com/gp/computer-science/lncs/conference-proceedings-gu…) with up to 8-pages and using the CMT system at https://cmt3.research.microsoft.com/MLCN2019. The MLCN workshop uses a double-blind review process in the evaluation phase, thus authors must ensure anonymous submissions. Accepted papers will be published in a joint proceeding with the MICCAI 2019 conference. IMPORTANT DATES: - Paper submission deadline: July 1, 2019 (23:59 PST) - Notification of Acceptance: August 5, 2019 - Camera-ready Submission: August 12, 2019 - Workshop Date: October 13, 2019 Best regards, MLCN 2019 Organizing Committee <https://mlcnws.com/organization/>, Email: mlcnworkshop(a)gmail.com Website: https://mlcnws.com/ twitter: @MLCNworkshop <https://twitter.com/MLCNworkshop>

1 0

where to find label values of Hippocampus Segmentation v6.0
by Caroline Chwiesko 22 Apr '19

22 Apr '19

External Email - Use Caution Hello Freesurfer developers, this is just a quick question: where/with what function can I get all the label values that are included in lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz I want to replace the HIP labels in the Brainnetome segmentation with the freesurfer 6.0 ones, for this I need this information. I can not find it in the publication or in the freesurfer color LUT. Thank you very much in advance! Carolin

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