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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and solutions of working with very large datasets SUBMISSION PROCESS: The workshop seeks high quality, original, and unpublished work on algorithms, theory, and applications of machine learning in clinical neuroimaging related to big data, transfer learning, and data harmonization.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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Problems with recon-all -s soft and hard fallures
by Camerino, .I.L. (Ileana) 22 Apr '19

22 Apr '19

External Email - Use Caution Dear Freesurfer experts, I am running recon all from the terminal of a linux machine: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I tried recon all on an image dataset of small vessel disease patients. I tried the command on several subjects and I got the same outcome: a soft fallure. Please, find the recon all log in the attachment. Even though in the "recon all.log": it says: recon-all -s sub025 finished without errors, after checking the pial and white matter segmentations, very clear misplacement failures and part of dura mater are present (see attachment: segmenation misplacement and dura). I am also wandering how to avoid that white matter lesions are taken into the aseg segmentation? I checked the documentation and this kind of errors is not mentioned anywhere. Can be the case, that this error is due to the fact that these are clinical images? Can this problem be fixed? For sake of curiosity, I tried the recon all command on another dataset (stroke) and with these data I got an hard failure. recon all exited with errors: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0573, pval=0.0034 < threshold=0.0050). (see second recon all o35403143 with errors) Please, can anyone give me some ideas how to fix both errors? Thank you in advance Ileana

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Re: [Freesurfer] Lazy binding problem {Disarmed}
by fsbuild 21 Apr '19

21 Apr '19

External Email - Use Caution Hello Lingyan, You can download an updated Mac freesurfer distribution from the following link,https://drive.google.com/file/d/1v2WwPg68id42NqfMeBTI3zijjto69_C1/view… After the download, you can uncompress the freesurfer_Mac.zip archive and put the freesurfer tree anywhere as long as you change the FREESURFER_HOME environment variable to point to it.  Then you would run the freesurfer script to setup the environment using that location.  For example, you can put the ../freesurfer tree under your home directory which you always have privileges to read/write to. $ cd $HOME$ pwd/Users/lwang  <— I am making up this path for this example ... then uncompress the zip archive in to your home directory, here assuming the archive was downloaded into your Downloads folder, $ unzip -d $HOME  $HOME/Downloads/freesurfer_Mac.zip … then in Bourne shell or bash shell you could do….  $ export FREESURFER_HOME=$HOME/Mac/freesurfer … and then to setup the environment… $ source $FREESURFER_HOME/SetUpFreeSurfer.sh Then you should no longer see the lazy evaluation error or be concerned with doing an install that needs admin privileges or whether or not SIP is on/off..(Setup instructions for the environment are also here, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) - R. On Apr 19, 2019, at 15:17, Wang, Lingyan <Lingyan.Wang(a)bcm.edu> wrote:        External Email - Use Caution        Hi,I had this lazy binding problem described in the FS6 releasenotes and couldn't solve it. This is the error message I got when using @SUMA_Make_Spec_Fs:dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibAnd I've disabled SIP.When I tried use sudo -E fs_update, here is the message I got:Build is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c   Running this will update some of your freesurfer binaries. Shall I proceed? [y/n/Abort]: yrsync -zbrlv --progress --suffix=.1555625828_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesurferreceiving file list ... rsync: change_dir "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in pub) failed: No such file or directory (2)0 files to considersent 4 bytes  received 9 bytes  26.00 bytes/sectotal size is 0  speedup is 0.00rsync error: some files could not be transferred (code 23) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-51/rsync/main.c(1404) [receiver=2.6.9]The MacOS system is macOS Sierra 10.12.5 and freesurfer is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96cI was wondering if you have any suggestions to fix this problem. Many thanks!Wang, Lingyan Yau LabDepartment of NeuroscienceBaylor College of Medicine_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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