Freesurfer May 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

Unable to install Matlab runtime to run the SegmentHA function in Mac OS 12.4
by Isabella Leung 26 May '22

26 May '22

External Email - Use Caution Hello Freesurfer expert, I have installed Freesurfer 7.2.0 onto my personal Mac OS (Monterey 12.4). The Recon-all function works but when I try to run the segmentHA_T1.sh bert [SUBJECTS_DIR] It tells me to install the Matlab R2014b runtime. I have downloaded and installed Matlab R2014b but it still tells me that I need to install the "runtime". I have downloaded the "MCR_R2014b_maci64_installer" but it gets stuck when I try to install and won't let me get past the libjvm.dylib no matter how many times I click the "Allow Anyway" button in my system preferences. I'm not sure what to do. Is there a script that I can run that will allow me to install the matlab runtime without being blocked or is there another script that will allow me to run the Segment HA without the matlab runtime installed? Many thanks and looking forward to hearing from you. Best wishes, Isabella Isabella Leung Post-Doctorate Fellow in Clinical Research NICM Health Research Institute, Western Sydney University e. i.leung(a)westernsydney.edu.au<mailto:i.leung@westernsydney.edu.au> p. +61 403 234 141 w. nicm.edu.au<http://secure-web.cisco.com/1uOIvmC0uTfFg7SmaAz1IwHOiK7TEnE6msNrSYrR-CH8p-c…> NICM Health Research Institute is an initiative seeded by the Australian and NSW Governments at Western Sydney University Unit Coordinator for Evidence-Based Practice in Chinese Medicine School of Health Sciences, Western Sydney University e. i.leung(a)westernsydney.edu.au<mailto:i.leung@westernsydney.edu.au> p. +61 403 234 141 w. https://secure-web.cisco.com/1KD9C7FKKxu6CkI2KpA6OrtwoHRvxhZbQcTrrNzA4M12bC… ________________________________ [200106_N_Western_email_sig]

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Re: [Freesurfer] Starting a new project
by fsbuild 26 May '22

26 May '22

External Email - Use Caution Let me just add, the tar archive listed in your email, freesurfer-linux-ubuntu20_x86_64-7-dev.tar.gz, is the install image (and not the source code) from a *development* nightly build on Ubuntu 20 which has not been tested like a freesurfer release.    So if you are looking to start using freesurfer commands and binaries that are already built and organized as a distribution (from either the tar file or the installer files), then you should consider using the existing, stable 7.2.0 release (which you can get from https://secure-web.cisco.com/1_rhmCsv6clReJC6U3u5VnsAa0yDplUEXxuv…)  The 7.2.0 release does have Ubuntu 18 binaries and an installer available via the link above.  I believe those binaries should run on Ubuntu 20. Installed images of freesurfer (including Ubuntu 18 binaries) are available in various system images  including a container, a VM, and also you can run it under the Windows Subsystem for Linux (WSL).  We have some info about that here if you just want to get started trying the commands, https://secure-web.cisco.com/1IqL_pExkd0h4Ll0hp7UdgBqalAfNpw… - R. On May 25, 2022, at 11:04, Wighton, Paul <PWIGHTON(a)mgh.harvard.edu> wrote:Hi Raffaele, There is some info here:https://secure-web.cisco.com/1jX2JN3DbC9pyyC4owHwUw6NjslWwtqIy469L_okI… more details on compiling FreeSurfer from source, you can refer to this neurodocker template:https://secure-web.cisco.com/1MhxB7ki4bAZDqdV3wp-FI5cN2cML6D8AGhwL… documents exact versions of gcc, cmake, python etc. and is part of this pull request:https://secure-web.cisco.com/1_0UM5oyyHFaIx0f_htzbnRkOFE5SP_QXA0WGK… on behalf of Raffaele Di Natale <rdinatale@dieei.unict.it>Sent: Wednesday, May 25, 2022 10:33 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh..harvard.edu>Subject: [Freesurfer] Starting a new project         External Email - Use Caution        Hello FreeSurfer Developers, I'm attempting to develop new functions in the tool for my research activity and I wish to know if there is a guide about to start this kind of activity.1) freesurfer-linux-ubuntu20_x86_64-7-dev.tar.gz Raffaele Di Natale, PhD Contract ResearcherDIEEI, University of Catania+39 095738 2385 (Edificio 13)+39 095738 7903 (OpenLab)_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Ubuntu + Freesurfer VM passcode
by fsbuild 26 May '22

26 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 24, 2022, at 09:36, Sarah Dziura <sdziura(a)umd.edu> wrote:        External Email - Use Caution        Hi,Could I please get the passcode for unzipping the virtual image FS_7_2_0_Ubuntu_18_04_06.ova.7z?Thank you,Sarah-- Sarah L. Dziura, Ph.D.Postdoctoral Research AssociateDevelopmental Social Cognitive Neuroscience LabUniversity of Maryland, College ParkPronouns: she/her_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] ubuntu vm
by fsbuild 26 May '22

26 May '22

External Email - Use Caution Sending the info to your email shortly. On May 25, 2022, at 11:14, Sodoma, Matthew <matthew-sodoma(a)uiowa.edu> wrote:        External Email - Use Caution        Hello,I was looking to receive the passcode to unzip the virtual box file below:Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7zMatt_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer Course
by Kretzer, Svenja 26 May '22

26 May '22

External Email - Use Caution Dear all, I hope you are well. I am a PhD student studying neuroscience at King’s College London. My project is on adolescent neurodevelopmental growth trajectories and internalising symptoms. I’m using FreeSurfer and I believe I’d highly benefit from the course offered on your website. I was wondering whether you are offering a course September this year. Could you please let me know if there is one and if so, if you have spots available? Thank you very much, I look forward to hearing from you! All the best, Svenja

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using freeview7 to set manual paths
by Valeria Centanino 26 May '22

26 May '22

External Email - Use Caution Hello, I need to set manual paths on inflated surfaces, and I would like to use FreeView7, but I couldn't find any option to save the path after creating it. Could you please tell me if this is implemented in FreeView7 and, if yes, how can I do it? Thanks very much, Valeria

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mris_label2annotation issues with individualizing
by Deck,Benjamin 25 May '22

25 May '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to create annotation files from label files which have been estimated at the level of the individual. Therefore, some subjects may not have all ROIs. When attempting to take those label files and concatenate them into individual subject-specific annotation files I run into a few issues. The command I have used previously: mris_label2annot --s sub-DAEK --hemi lh \ --ctab /mnt/c/Users/Ben/Documents/GitHub/parcellationPipeline/li2019_to_dti/yeo2011nodesLUT.txt \ --a yeo2011nodes \ --surf orig \ --maxstatwinner \ --ldir-default stdout: subject sub-DAEK hemi lh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable /mnt/c/Users/Ben/Documents/GitHub/parcellationPipeline/li2019_to_dti/yeo2011nodesLUT.txt AnnotName yeo2011nodes nlables 0 1. The first issue is that -ldir and -ldir-default don't seem to work as anticipated. After reading many threads on the FS mailing list archives I saw that the LUT should have identical ROI IDs as the file names with the exception of the label file extension. Thus, my LUT looks like the following: * 0 Unknown 0 0 0 0 1 lh.Net_2_ROIs_1_lh 25 5 25 0 2 rh.Net_2_ROIs_1_rh 25 100 40 0 3 lh.Net_2_ROIs_2_lh 70 130 180 0 4 rh.Net_2_ROIs_2_rh 100 100 0 0 5 lh.Net_3_ROIs_1_lh 196 58 250 0 6 rh.Net_3_ROIs_1_rh 100 25 0 0 7 lh.Net_3_ROIs_2_lh 120 70 50 0 8 rh.Net_3_ROIs_2_rh 220 20 10 0 9 lh.Net_3_ROIs_3_lh 220 20 100 0 10 rh.Net_3_ROIs_3_rh 180 40 120 0 11 lh.Net_4_ROIs_1_lh 122 186 220 0 -----------------and so on. * When I list the dir from my subject's label directory the following is presented: i. lh.Net_10_ROIs_1_lh.label lh.Net_2_ROIs_1_lh.label lh.Net_13_ROIs_3_lh.label lh.Net_5_ROIs_1_lh.label rh.Net_2_ROIs_1_rh.label rh.Net_3_ROIs_3_rh.label ------------and so on. * However, when I provide the -l arg with the full path, the file is found and the nlabels arg in stdout is the number of -l args I supply. 1. The next issues is that if I go the route of -l args (there are 116 ROIs so this is not desirable) I receive issues because not all subjects have all the label files that the LUT file expects. Therefore the resulting annotation file has mislabeled ROIs. * Is there a way to force the unfound labels to unknown or a way to bypass this issue? * I recognize the one way to do this may be to create individual specific LUT files but that seems tedious and unnecessary if there is a better way that you all may be wiser to. 1. Another issue I have been running into is that if I even attempt to just remove the -l args where labels do not correspond exactly with the LUT file I have a number of overlapping label file vertices issues. * How do you recommend correcting for this, my best guess is some sort of thresholding scheme. However, these are functional networks so I am unsure what the best route for thresholding would be. Thanks so much for your help in advance! Ben

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ubuntu vm
by Sodoma, Matthew 25 May '22

25 May '22

External Email - Use Caution Hello, I was looking to receive the passcode to unzip the virtual box file below: Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1QpBVQUbsVdz-ntFx0QiYhbLcmY3KmbxxWUEnqMECp1b6U…> Matt

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Starting a new project
by Raffaele Di Natale 25 May '22

25 May '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to develop new functions in the tool for my research activity and I wish to know if there is a guide about to start this kind of activity. 1) freesurfer-linux-ubuntu20_x86_64-7-dev.tar.gz Raffaele Di Natale, PhD Contract Researcher DIEEI, University of Catania +39 095738 2385 (Edificio 13) +39 095738 7903 (OpenLab <http://secure-web.cisco.com/19HCh4dsz8VYs-eTR0dm-vPoxaUmxK1ULuABd3lg8agIWG7…>)

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Deface DICOM
by Victor Montal Blancafort 24 May '22

24 May '22

External Email - Use Caution Dear FS experts, I am using mri_deface to annon our data. Nevertheless, for a recent project, we were requested to share our DICOM original files, instad of .nii or .mgz. Thus, I was wondering if you know a simple way to deface T1 data inputing a DICOM and obtaining a series of DICOM as output? I have tried to 1) deface using mri_deface, 2) convert the .nii to dicom using the nifti2dicom utility and 3) correct DICOM info thats incorrecly parsed at step 2). However, such approach does not work correctly for all our data (it fails for several reasons, such as correctly storing acq direction, or dimensions when sampling from nifti 2 dicom). I have seen that @Doug has been working on a new deface utility (mideface) but it seems to work also only for .nii Any insight? Victor Montal

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Freesurfer May 2022