Freesurfer April 2019

freesurfer@nmr.mgh.harvard.edu

99 participants
136 discussions

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

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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

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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>

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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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Projecting a subcortical label to the surface
by Nillo, Ryan Michael R 22 Apr '19

22 Apr '19

External Email - Use Caution Hello FreeSurfer users, I have a subcortical segmentation that I want to project to the nearest cortical vertex. Would I use the mri_vol2surf command to accomplish this, or do I need to convert the segmentation into a label, then project the label to the fsaverage cortical surface? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

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Re: [Freesurfer] Freeview update error
by fsbuild 22 Apr '19

22 Apr '19

External Email - Use Caution Hello Kelly, Do you have libfreetype installed on your system (which defines that symbol)? $ strings /usr/lib64/libfreetype.so.6 | grep -i ft_get_font_format FT_Get_Font_Format If not, you can install it with, $ sudo yum install freetype.x86_64 freetype-devel.x86_64 - R.On Apr 17, 2019, at 10:09, Kelly Vaughn <vaughnkellyann(a)gmail.com> wrote:libQt5XcbQpa.so.5: undefined symbol: FT_Get_Font_Format

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freeview and complex values
by shahin＠nmr.mgh.harvard.edu 22 Apr '19

22 Apr '19

Hi Surfers, I am trying to use freeview to present retinotopy mapping in subcortical regions. I need to show complex (real and imag) values generated by a retinotopy analysis in a 'color wheel' format (similar to what tksurfer does). Any hint? _____________________________________ Shahin Nasr Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129

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mri_surf2surf help
by Larson, Kathleen E 22 Apr '19

22 Apr '19

External Email - Use Caution Hello FreeSurfer developers, I'm having trouble running the command mri_surf2surf, and I haven't been able to find a fix in the message archives (a similar question has been asked, but I couldn't find the answer). I am trying to convert the pial and white matter surfaces for a series of subjects back to the anatomical space. I have computed the registration matrix to transform the surfaces, but am having trouble with the mri_surf2surf syntax. This is the command I am trying to run: mri_surf2surf --hemi lh --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --s <subjectID> and I get an error saying that --tval-xyz requires an input volume. (The syntax described on the website (https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat) is out of date.) I have tried to use rawavg.mgz as the input volume, but then I get an output that can only be read as a scalar overlay, and I need an actual surface. When I try to use a surface as the input, I get an error saying that the file type cannot identified. Do you have any suggestions for what I am doing wrong? Thank you, Kathleen Larson Department of Biomedical Engineering Vanderbilt University 304 Featheringill-Jacobs Hall (425)-894-2005

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mri_vol2surf error
by Nillo, Ryan Michael R 22 Apr '19

22 Apr '19

External Email - Use Caution Hello FS users, I am having a problem with mri_vol2surf. I want to project subcortical voxels onto the cortical surface. I found out that I can do this with the mri_vol2surf command. I am following the example given on the documentation, but I am getting this error: mri_vol2surf: could not read surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc//surf/lh.white. I am trying to project to the surface of the fsaverage. Does this error mean that FS is unable to find the fsaverage surface? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging

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thresholded cluster output data
by Peters, Douglas G 22 Apr '19

22 Apr '19

External Email - Use Caution Hi Everyone, I'm new to freesurfer, and I was wondering if there is a way to output clusterwise threshold from Freeview (or any other tool) to illustrate cluster size, location, and significance? I understand that mri_glmfit-sim outputs cluster data after multiple cluster correction, but I was wondering if there is a way to get a similar cluster output prior to running multiple cluster correction. Thank you, DP

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Freesurfer April 2019