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Neuroimaging on the Shared Computing Cluster (SCC)

Neuroimaging on the Shared Computing Cluster (SCC). Dustin Clark clarkdc@bu.edu Research Computing Services Information Services & Technology Boston University. Goals. Learn how to use the SCC for neuroimaging analysis. Connect to the SCC Move data onto the SCC Unpack Data FreeSurfer

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Neuroimaging on the Shared Computing Cluster (SCC)

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  1. Neuroimaging on theShared Computing Cluster (SCC) Dustin Clarkclarkdc@bu.eduResearch Computing Services Information Services & Technology Boston University

  2. Information Services & Technology Goals Learn how to use the SCC for neuroimaging analysis • Connect to the SCC • Move data onto the SCC • Unpack Data • FreeSurfer • MRICron • Visualize Data • FreeSurfer • FSL • AFNI • Submit analyses for accelerated pre- & post-processing Image from https://www.stockunlimited.com/vector-illustration/circuit-board-brain-design_1948276.html

  3. Information Services & Technology Motivation • Run code that exceeds workstation capability • Optimization • Access to Professional Installations and of Software with Support • help@scc.bu.edu • Streamline Project & Pipeline Management • Storage – up to 800Gb free • Backup – up to 200Gb free • Collaboration • Connect with BU’s Cognitive Neuroimaging Center’s DICOM Server (under construction)

  4. Information Services & Technology Using the SCC • Linux • CentOS 6 • Networking • SSH • X-Forwarding • SFTP • Modules • Environment Variables • Parallel (Batch) Processing • qsub • OpenMP • GPU • Interactive Environments • VNC • OpenGL

  5. Information Services & Technology What Is The SCC? Public Network Public Network VPN Only >3PB SCC1 SCC2 GEO SCC4 File Storage Login Nodes Private Network Private Network Compute Nodes More than 580 nodes with ~14,000 CPUs and 268 GPUs

  6. Information Services & Technology What Is The SCC? • A Linux cluster with over 580 nodes, 14,000 processors, and 268 GPUs. Currently over 3 Petabytes of disk. • Located in Holyoke, MA at the Massachusetts Green High Performance Computing Center (MGHPCC), a collaboration between 5 major universities and the Commonwealth of Massachusetts. • Went into production in June, 2013 for Research Computing. Continues to be updated/expanded. • http://www.bu.edu/tech/support/research/computing-resources/scc/

  7. Information Services & Technology Connecting to the SCC Image sources on Image Sources Slide

  8. Information Services & Technology Connecting to the SCC Command Line Interfaces • Windows - MobaXtermhttp://www.bu.edu/tech/support/research/system-usage/getting-started/connect-ssh/#windows • Macintosh – Built-in Terminal applicationhttp://www.bu.edu/tech/support/research/system-usage/getting-started/connect-ssh/#apple • Linux – Terminal applicationhttp://www.bu.edu/tech/support/research/system-usage/getting-started/connect-ssh/#linux

  9. Information Services & Technology Connecting - Details • Software you need: • SSH Client – To log in to the SCC machines, such as scc1.bu.edu and then run commands • X Forwarding – Display graphics for those programs with a GUI interface (such as MATLAB) or that otherwise display images. • File Transfer – Transferring files between the SCC and your local machine using SFTP. • VNC – Advanced users only. Faster graphics:http://www.bu.edu/tech/support/research/system-usage/getting-started/remote-desktop-vnc/

  10. Information Services & Technology Using the SCC • Linux “Command Line” Environment – No menus or graphics unless in specific software packages. • Login Nodes - Interactive use, code development.General: scc1.bu.edu, scc2.bu.eduEarth & Environment Dept. Users: geo.bu.eduBUMC and Restricted Data Users: scc4.bu.edu • Compute Nodes – Run “Batch Jobs” on, both single and multi-processor.Names like scc-bc5.bu.edu

  11. Information Services & Technology Using the SCC - Basics • This tutorial is only going to introduce some basic Linux commands on the SCC. Please consider taking a fuller Linux tutorial from us or online if you end up using the SCC significantly. • We have on our web site some material for new users of Linux and the SCC at:http://www.bu.edu/tech/support/research/system-usage/getting-started/commands/

  12. Information Services & Technology Using the SCC – ssh • From your ssh/terminal application on your tutorial workstation or your laptop or on a machine at home:ssh -l tuta0 scc1.bu.edu • “ssh” is the command you areissuing • “-l tuta0” is a “command line option” to specify your login name on the SCC • “scc1.bu.edu” is a “parameter” of the command • Make sure to hit the “Enter” key after every command

  13. Information Services & Technology Exercise 1: Connect to SCC (SSH) Windows/MobaXterm local_prompt% ssh tuta0@scc1.bu.edu Mac local_prompt%ssh –Y tuta0@scc1.bu.edu Linux local_prompt%ssh –X tuta0@scc1.bu.edu

  14. Information Services & Technology Using the SCC – the “prompt” • You should now see something like:[tuta0@scc1 ~]$ • This is what is called the “prompt” and indicates the system (the bash “shell” in particular) is ready to accept commands from you. “tuta0” is your login name. “scc1” is the machine you are on. “~” is the directory you are in – in Linux “~” is a shorthand for a person’s home directory.

  15. Information Services & Technology Exercise 2: X-Forwarding (Graphics) • Run the command xclock to see if graphics are working for you. [tuta0@scc1 ~]$ xclock • A window similar to the image on the right should come up. • Click the X in the upper right to close this window. • http://www.bu.edu/tech/support/research/system-usage/getting-started/x-forwarding/

  16. Information Services & Technology Using the SCC – pwd • Show the current “full path”, the directory you are in with its parent and all levels of grandparents up to the root directory (/). Items you type will be shown in bold:[tuta0@scc1 ~]$ pwd/usr2/collab/tuta0 • Here the command pwd “returns” (prints to your screen) the result “/usr2/collab/tuta0”

  17. Information Services & Technology Using the SCC – ls • List the contents of a directory:[tuta0@scc1 ~]$lsnewdir • Or with a command line option, asking for more details:[tuta0@scc1 ~]$ ls -l total 0 drwxr-xr-x 3 tuta0 adftest 512 Oct 28 16:03 newdir

  18. Information Services & Technology Using the SCC – mkdir • Create a new directory:[tuta0@scc1 ~]$mkdirneuroimaging • Creates a new directory (folder) to store files in within your home directory.

  19. Information Services & Technology Using the SCC - cd • Change directory to “newdir”:[tuta0@scc1 ~]$ cd neuroimaging • You can also move to other directories by giving a “full path” (a path starting with the / character) such as:[tuta0@scc1 newdir]$ cd /usr/local/bin/ • Type just cd anytime to go back to your home directory. [tuta0@scc1 newdir]$ cd [tuta0@scc1 ~]$ pwd /usr4/tutorial/tuta0 [tuta0@scc1 ~]$ cd neuroimaging

  20. Information Services & Technology SFTP File Transfer to/from the SCC • Graphical Applications • Windows – MobaXterm (Free), WinSCP (Free) • Mac – FileZilla (Free), Fetch (BU site license) • Command Line Applications • rsync • scp • http://www.bu.edu/tech/support/research/system-usage/getting-started/get-started-file-transfer/

  21. Information Services & Technology Exercise 3: Moving Data to SCC (SFTP) MobaXterm – Windows Fetch - macOS

  22. Information Services & Technology Exercise 3: SFTP File Transfer • Go to: https://www.nitrc.org/ir/ • Click 1000 Functional Connectomes > AnnArbor_sub00306 > MR Session > Download > Download Images • Go to SFTP session • Download to:/usr4/tutorial/tuta?/neuroimaging • Go to SSH session connected to the SCC and confirm file transfer worked with ls command: [tuta0@scc1 neuroimaging]$ ls AnnArbor_sub00306_2_1_2018_10_??_??.zip

  23. Information Services & Technology File Transfer Issues – dos2unix • Windows, Macs, and Linux in text files define “end of line” differently. To solve this issue, there is a utility called dos2unix. This is not an issue with binary files. • Transfer text file “example.txt” from Windows to Linux. Rewrite “example.txt” as a Linux style file.[tuta0@scc1 ~]$ dos2unix example.txt • https://linux.die.net/man/1/dos2unix

  24. Information Services & Technology Exercise 4: unzip [tuta0@scc1 neuroimaging]$ unzip AnnArbor_sub00306_2_1_2018_10_??_??.zip [tuta0@scc1 neuroimaging]$ ls AnnArbor_sub00306/ SCANS [tuta0@scc1 neuroimaging]$ ls AnnArbor_sub00306/SCANS/AnnArbor_sub00306_ AnnArbor_sub00306_anat_mprage_anonymized.nii.gz/ AnnArbor_sub00306_anat_mprage_skullstripped.nii.gz/ AnnArbor_sub00306_func_rest.nii.gz/ [tuta0@scc1 neuroimaging]$ ls AnnArbor_sub00306/SCANS/AnnArbor_sub00306_anat_mprage_anonymized.nii.gz/NIfTI/ NIfTI_catalog.xml scan_mprage_anonymized.nii.gz [tuta0@scc1 neuroimaging]$ cd AnnArbor_sub00306/SCANS/AnnArbor_sub00306_anat_mprage_anonymized.nii.gz/NIfTI/ [tuta0@scc1 NIfTI]$ Press ‘Tab’ to Autocomplete existing directories and files when typing on the command prompt Continue typing desired directory to autocomplete with ‘Tab’ again until reaching final directory ‘NIfTI/’

  25. Information Services & Technology Check-In • Introduced Command Line Interfaces • Terminal, MobaXterm • Connected to SCC • SSH • Checked Graphics on SCC • X-Forwarding • xclock • Navigated SCC with Linux Commands • pwd, ls, mkdir, cd • Moved Brain Scans to SCC • SFTP • Uncompressed Brain Scans on SCC • unzip • Next: Visualizing Brain Scans on SCC Image sources on Image Sources Slide

  26. Information Services & Technology Exercise 5: Visualizing Brain Scans Loading Software on the SCC: Modules • Modules is a tool that organizes the environment variables of your command line interface, or shell, for quick and easy setup of installed software • A shortcut for activating, or sourcing, installed software on the SCC [tuta0@scc1 NIfTI]$ module list No Modulefiles Currently Loaded. [tuta0@scc1 NIfTI]$ module avail ... [tuta0@scc1 NIfTI$ moduleavail /share/module/bioinformatics: 1.0/1.0 EIGENSOFT/EIGENSOFT-4.2_gnu447 ... [tuta0@scc1 NIfTI]$ moduleavail | grepfreesurfer ... freesurfer/5.3.0-hcp freesurfer/6.0

  27. Information Services & Technology Exercise 5: Visualizing Brain Scans [tuta0@scc1 NIfTI]$ module load freesurfer/6.0 -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /share/pkg/freesurfer/6.0/install FSFAST_HOME /share/pkg/freesurfer/6.0/install/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /share/pkg/freesurfer/6.0/install/subjects MNI_DIR /share/pkg/freesurfer/6.0/install/mni [tuta0@scc1 ~]$ echo $SUBJECTS_DIR /share/pkg/freesurfer/6.0/install/subjects [tuta0@scc1 NIfTI]$ module list Currently Loaded Modulefiles: 1) freesurfer/6.0 [tuta0@scc1 NIfTI]$ freeview-v scan_mprage_anonymized.nii.gz [tuta0@scc1 NIfTI]$ cd [tuta0@scc1 ~]$ freeview -v neuroimaging/AnnArbor_sub00306/SCANS/AnnArbor_sub00306_anat_mprage_anonymized.nii.gz/NIfTI/scan_mprage_anonymized.nii.gz [tuta0@scc1 ~]$ tksurferfsaveragelh inflated

  28. Information Services & Technology Exercise 6: VirtualGL/OpenGL • VirtualGL is a program that allows OpenGL hardware accelerated rendering of 3D graphics through remote access. • Only accessible through Interactive Graphics Jobs on the SCC: qvgl [tuta0@scc1 ~]$ qvgl -P tutorial ================================================================== You must run 'vncpasswd' once before launching a vnc session ================================================================== [tuta0@scc1 ~]$ vncpasswd Password: <use SCC Login Password> [tuta0@scc1 ~]$ qvgl-P tutorial Waiting for immediate job to be scheduled. on your local workstation run: sshtuta0@scc-v01.bu.edu -L XXXX:localhost:5907 then execute vncviewer to connect to localhostportXXXX vncviewerlocalhost:XXXX to run an OpenGL application on a hardware GPU use vglrun command for example: vglrun glxinfo to quit the job please run: qdel 3934339 Legend • User Defined • SCC Defined • Hostname is always localhost

  29. Information Services & Technology Exercise 6: VirtualGL/OpenGL • Open a new command line interface (Terminal/MobaXterm) which will be a local session • Copy/Paste sshtuta0@scc-v01.bu.edu -L XXXX:localhost:5907 into command prompt of local session • Choose any 4-digit number greater than 6000: [Dustin@My_PC~]$ ssh tuta0@scc-v01.bu.edu-L7777:localhost:5907 • Open your VNC client • Windows/Linux: MobaXterm, RealVNC • macOS: Connect to Server, Real VNC

  30. Information Services & Technology Exercise 6: VirtualGL/OpenGL MobaXterm – Windows Connect to Server - macOS 7777

  31. Information Services & Technology Exercise 6: VirtualGL/OpenGL [tuta0@scc-v01 ~]$ module load freesurfer/6.0 -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /share/pkg/freesurfer/6.0/install FSFAST_HOME /share/pkg/freesurfer/6.0/install/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /share/pkg/freesurfer/6.0/install/subjects MNI_DIR /share/pkg/freesurfer/6.0/install/mni [tuta0@scc-v01 ~]$ tksurferfsaveragelh inflated GLUT: Fatal Error in tksurfer.bin: OpenGL GLX extension not supported by display: :7.0 [tuta0@scc-v01 ~]$ vglruntksurferfsaveragelh inflated ...

  32. Information Services & Technology Revisit – Using the SCC • There are 5 major Uses of the SCC: • Code development and debugging • Jobs < 15 minutes • Login Node • Non-Interactive Batch Procession • Automated processes that take more than 15 minutes • qsub • Interactive Batch Session • Processes with User Interaction running more than 15 minutes • qsh or qrsh • Interactive Batch Session with VNC • Processes with User Interaction running more than 15 minutes where Desktop Experience is preferred and intermittent access is required • vncstart • Interactive Batch Session with VirtualGL • Processes with User Interaction running more than 15 minutes where OpenGL is required • qvgl

  33. Information Services & Technology Neuroimaging File Formats • DICOM – Digital Imaging and Communications in Medicine • Subject_001.1107.00073708-7-1-iewoin780.dcm

  34. Information Services & Technology Neuroimaging File Formats • Metadata: information that describes the data (e.g. FOV, # of Frames, TR, TE, etc. [clarkdc@scc2:scans]$ mri_info7-T1_MEMPRAGE_1_0mm_p2_RMS/resources/DICOM/files/1.3.12.2.1107.5.2.43.166024.30000017112119401737100000001-7-1-1vy7g7l.dcm Getting Series No Scanning Directory INFO: Found 178 files in 7-T1_MEMPRAGE_1_0mm_p2_RMS/resources/DICOM/files ... PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Volume information for 7-T1_MEMPRAGE_1_0mm_p2_RMS/resources/DICOM/files/1.3.12.2.1107.5.2.43.166024.30000017112119401737100000001-7-1-1vy7g7l.dcm type: siemens_dicom dimensions: 256 x 256 x 176 voxel sizes: 1.000000, 1.000000, 1.000000 type: SHORT (4) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2530.00 msec, TE: 1.69 msec, TI: 1100.00 msec, flip angle: 7.00 degrees nframes: 1 PhEncDir: ROW FieldStrength: 3.000000

  35. Information Services & Technology Neuroimaging File Formats • NIfTI • Subject_001.nii, Subject_001.nii.gz • FreeSurfer, FSL, AFNI, SPM, CONN • MGH/MGZ • Subject_001.mgh, Subject_001.mgh.gz, Subject_001.mgz • FreeSurfer • BRIK & HEAD • Subject_001.BRIK & Subject_001.HEAD • AFNI • IMG & HDR (Analyze Format) • Subject_001.img & Subject_001.hdr • SPM, FreeSurfer, FSL, AFNI

  36. Information Services & Technology Unpacking: Converting DICOMs to Neuroimaging File Formats • Unpacking DICOMs • Reads through DICOM metadata to sort and stack slices/volumes into specified file format • dcmunpack • FreeSurfer • dcm2nii, dcm2niix • MRICron, MRICroGL • spm_dicom_convert • SPM • to3d • AFNI

  37. Information Services & Technology XNAT • Software platform that will store CNC neuroimaging data • Live Upload from MRI Scanner to XNAT • Inspect/Download raw data for artifacts before processing in Web API (Demo) Image sources on Image Sources Slide

  38. Information Services & Technology Exercise 7: Downloading from XNAT [tuta0@scc-v01 ~]$ cd neuroimaging [tuta0@scc-v01 neuroimaging]$ module load dcm2scc/beta ------------------------------------------------------------------------------ ERROR: dcm2scc/beta requires several additional modules. Run the following commands to load all of the dependencies (including this module): module load python/3.6.2 module load dcm2scc/beta Download XNATpy locally before using dcm2scc: pip install xnat --user -------------------------------------------------------------------------------- [tuta0@scc-v01 neuroimaging]$ module load python/3.6.2 [tuta0@scc-v01 neuroimaging]$ pip install xnat --user Collecting xnat Using cached xnat-0.3.5.tar.gz ... [tuta0@scc-v01 neuroimaging]$ module load dcm2scc/beta

  39. Information Services & Technology Exercise 7: Downloading from XNAT • dcm2scc • In-house script for moving data from your CNC project to your SCC project • Username: tuta1, tuta2, tuta3, tuta4, tuta5 • Pick one of the five options • Password: tutorial18 • -u <user> -p <cnc_project> -s <subject> -d <output_directory> [tuta0@scc-v01 neuroimaging]$ dcm2scc –u tuta? –p speech_systems –s xnatTest –d . Please enter the password for user 'tuta?': 378.9 MiB | # | 54.6 MiB/s Elapsed Time: 0:00:06 xnatTest [tuta0@scc-v01 neuroimaging]$ ls AnnArbor_sub00306_2_1_2018_10_??_??.zip AnnArbor_sub00306_2_1_2018_10_??_?? xnatTest Troubleshooting [tuta0@scc-v01 neuroimaging]$ cp /project/scv/examples/tutorials/neuroimaging_scc/xnatTest.tar.gz [tuta0@scc-v01 neuroimaging]$ tar xf xnatTest.tar.gz

  40. Information Services & Technology Exercise 8: Unpacking [tuta0@scc-v01 neuroimaging]$ dcmunpack -srcxnatTest/xnatTest/scans/7-T1_MEMPRAGE_1_0mm_p2_RMS/resources/DICOM/files/ -targ $PWD -run 7 T1 mgz 007 ... [tuta0@scc-v01 neuroimaging]$ mri_infoT1/007/007.mgz Volume information for T1/007/007.mgz type: MGH dimensions: 256 x 256 x 176 voxel sizes: 1.000000, 1.000000, 1.000000 type: SHORT (4) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2530.00 msec, TE: 1.69 msec, TI: 1100.00 msec, flip angle: 7.00 degrees nframes: 1 PhEncDir: ROW FieldStrength: 3.000000 ...

  41. Information Services & Technology Exercise 8: Unpacking [tuta0@scc-v01 neuroimaging]$ dcmunpack -srcxnatTest/xnatTest/scans/7-T1_MEMPRAGE_1_0mm_p2_RMS/resources/DICOM/files/ -targ $PWD -run 7 T1 nii.gz 007 ... [tuta0@scc-v01 neuroimaging]$ mri_infoT1/007/007.nii.gz Volume information for T1/007/007.nii.gz type: nii dimensions: 256 x 256 x 176 voxel sizes: 1.000000, 1.000000, 1.000000 type: SHORT (4) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2530.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ... [tuta0@scc-v01 neuroimaging]$ freeview -v T1/007/007.nii.gz

  42. Information Services & Technology Check-In • Loading Software on the SCC • Modules • Working with Virtual Networks and 3D Hardware Acceleration • VNC, VirtualGL/OpenGL • Hostname, Ports • Neuroimaging File Formats • DICOM, NIfTI, etc. • Metadata (Header) vs Image data • Unpacking DICOMs • Networking with the CNC • XNAT • dcm2scc, python • Linux CLI • grep, tar, “environment variables” • ‘$’ ‘|’ ‘.’ Image sources onImage Sources Slide • Next: Visualizing Brain Scans on SCC

  43. pial_edits_before/mri/T1.mgz Information Services & Technology Exercise 9: FreeSurfer [tuta0@scc-v01 neuroimaging]$ moduleavail | grepfreesurfer ... [tuta0@scc-v01 neuroimaging]$ module load freesurfer/6.0 ... [tuta0@scc-v01 neuroimaging]$ export SUBJECTS_DIR=/projectnb/scv/clarkdc/tutorials/neuroimaging_scc/buckner_data/tutorial_subjs [tuta0@scc-v01 neuroimaging]$ cd $SUBJECTS_DIR [tuta0@scc-v01 neuroimaging_scc]$ vglrun freeview -v pial_edits_before/mri/T1.mgz pial_edits_before/mri/brainmask.mgz -f pial_edits_before/surf/lh.white:edgecolor=yellow pial_edits_before/surf/lh.pial:edgecolor=red pial_edits_before/surf/rh.white:edgecolor=yellow pial_edits_before/surf/rh.pial:edgecolor=red &

  44. pial_edits_before/mri/T1.mgz Information Services & Technology Exercise 9: FreeSurfer • File > Load Surface > lh.inflated • Set Overlay to lh.thickness • File > Load Volume > /usr4/tutorial/tuta?/AnnArbor_sub00306_func_rest.nii.gz/NIfTI/scan_rest.nii.gz • View > Show Time Course

  45. pial_edits_before/mri/T1.mgz Information Services & Technology FSL [tuta0@scc-v01 neuroimaging]$ moduleavail | grepfsl fsl/5.0(default) fsl/5.0.10 ... [tuta0@scc-v01 neuroimaging]$ module load fsl/5.0 [tuta0@scc-v01 neuroimaging]$ fsl & BET FLIRT MELODIC FEAT FSLView

  46. pial_edits_before/mri/T1.mgz Information Services & Technology AFNI [tuta0@scc-v01 neuroimaging_scc]$ cd [tuta0@scc-v01 neuroimaging]$ moduleavail | grepafni afni/2017.01.29.1818_openmp afni/AFNI_2011_12_21_1014 ... [tuta0@scc-v01 neuroimaging]$ module load afni/2017.01.29.1818_openmp [tuta0@scc-v01 neuroimaging]$ vglrun afni AnnArbor_sub00306/SCANS/AnnArbor_sub00306_func_rest.nii.gz/NIfTI/scan_rest.nii.gz & [tuta0@scc-v01 neuroimaging]$ afni -help ...

  47. pial_edits_before/mri/T1.mgz Information Services & Technology SPM [tuta0@scc-v01 neuroimaging]$ moduleavail | grepmatlab ... matlab/2017a matlab/2017b(default) [tuta0@scc-v01 neuroimaging]$ module load matlab/2017b [tuta0@scc-v01 neuroimaging]$ moduleavail | grepspm spm/12 spm/12b spm/8 [tuta0@scc-v01 neuroimaging]$ module load spm/12b [tuta0@scc-v01 neuroimaging]$ vglrun matlab & >> spmfmri

  48. Information Services & Technology SPM • DICOM Import -- utilizes spm_dicom_convert() for unpacking • Display -- opens NIfTI files for processing (*.nii - NOT *.nii.gz) • Navigate to ~/AnnArbor_sub00306/SCANS/AnnArbor_sub00306_func_rest.nii.gz/NIfTI/scan_rest.nii.gz [tuta0@scc-v01 neuroimaging]$ mri_convertAnnArbor_sub00306/SCANS/AnnArbor_sub00306_func_rest.nii.gz/NIfTI/scan_rest.nii.gz AnnArbor_sub00306/SCANS/AnnArbor_sub00306_func_rest.nii.gz/NIfTI/scan_rest.nii ---Close Matlab---

  49. Information Services & Technology CONN [tuta0@scc-v01 neuroimaging]$ moduleavail | grepconn conn/17.f ... [tuta0@scc-v01 neuroimaging]$ module load conn/17.f [tuta0@scc-v01 neuroimaging]$ matlab & >> conn

  50. Information Services & Technology Nipype [tuta0@scc-v01 neuroimaging]$ moduleavail | grep python ... python/2.7.13(default) python/2.7.14 python/3.6.1 python/3.6.2 ... [tuta0@scc-v01 neuroimaging]$ module load python/3.6.2 [tuta0@scc-v01 neuroimaging]$ pip install nipype --user [tuta0@scc-v01 neuroimaging]$ python ... >>> import nipype >>> help(nipype)

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