Freesurfer December 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
175 discussions

Re: [Freesurfer] Freeview command not found {Disarmed}
by fsbuild 05 Dec '18

05 Dec '18

External Email - Use Caution It should be OK to use qt4 on Ubuntu 16, though I think qt5 would work as well. Please test to see if you can freeview from where it was installed.  Your output below says that FREESURFER_HOME is /usr/local/freesurfer, so you should have a /usr/local/freesurfer/bin/freeview.  Or I am assuming that if you built freesurfer, then after you did the “make” command to build it, you did “make install” with the install prefix set to to /usr/local/freesurfer After you are in the freesurfer shell with FREESURFER_HOME and the other environment variables set, the which command can verify the location of freeview,$ which freeview/usr/local/freesurfer/bin/freeview You can check what libraries freeview cannot find with the following,$ ldd `which freeview` | grep not If all the libraries are found, you will get no output from the ldd command, and you should be able to test just running freeview from the command line.  They GUI should come up with no volume loaded. $ freeview But if the ldd command reports some libraries are not found, then freeview will not run. Does the ldd command report that libvtkverdict.so.5.6 (or any other libraries) are not found ? - R. On Dec 5, 2018, at 18:24, Maeve Barrett <barretm2(a)tcd.ie> wrote:        External Email - Use Caution        Thanks so much!I installed the qt4 library but I received another error the 'freeview: command not found error'When I attempted it again, I received the following error:freeview.bin $argvfreeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directoryI then tried to install the libvtkverdict.so.5.6: package but received the following error:sudo apt install libvtkverdict.so.5.6Reading package lists... DoneBuilding dependency tree       Reading state information.... DoneE: Unable to locate package libvtkverdict.so.5.6E: Couldn't find any package by glob 'libvtkverdict.so.5.6'E: Couldn't find any package by regex 'libvtkverdict.so.5.6'I then installed the qt5 library and tried to start freeview again but I received this error:freeview: error while loading shared libraries: libQt5X11Extras.so.5: cannot open shared object file: No such file or directoryI tried to install this package but then I received this error:Reading package lists... DoneBuilding dependency tree       Reading state information... DoneE: Unable to locate package libQt5X11Extras.so.5E: Couldn't find any package by glob 'libQt5X11Extras.so.5'E: Couldn't find any package by regex 'libQt5X11Extras.so.5'Am I missing another library? Thanks in advance!Best,M.On Wed, 5 Dec 2018 at 15:32, fsbuild <fsbuild@contbay..com> wrote:        External Email - Use Caution        Hello Maeve,You can search for the package to install with apt-file, but you may need to install that first, so try,$ sudo apt install apt-file$ sudo apt update… now search for the package with that library name using apt-file$ sudo apt-file search libQtScriptTools.so.4I think it will come back with something like,libqt4-scripttools:  /usr/lib/x86_64-linux-gnu/libQtScriptTools.so.4…..- but the name of the package to the left hand side of the colon is what you want to install, so try$ sudo apt install libqt4-scripttoolsIf that does not fix the libqt references, then you could also try$ sudo apt install qt4-default- R.On Dec 5, 2018, at 13:32, Maeve Barrett <barretm2(a)tcd.ie> wrote:        External Email - Use Caution        Hello,I've been trying to resolve this issue but I haven't found a fix on the mailing lists. I downloaded and installed the most recent version of Freesurfer for Linux. I am running Ubuntu 16.04 LTS as guest on Virtualbox 5.2.22 on a windows 10 host. My tcsh version is 6.18.01 (Astron). When I type the commands $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.cshI get the following output: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurferFSFAST_HOME       /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /home/maevebarrett/Documents/AM8750_Structural/MNI_DIR           /usr/local/freesurfer/mniI have been able to run recon-all with no errors. However, when I try to open freeview, I receive the error message 'freeview: command not found.'I ensured I have permissions on the requisite folders. When I navigate to freesurfer/bin and type freeview.bin $argv I get the following error:/usr/local/freesurfer/bin> freeview.bin $argvfreeview..bin: error while loading shared libraries: libQtScriptTools.so.4: cannot open shared object file: No such file or directoryI tried downloading the libQtScriptTools.so.4 but when I attempt to install it I get the following error:sudo apt-get install libQtScriptTools.so.4Reading package lists... DoneBuilding dependency tree       Reading state information... DoneE: Unable to locate package libQtScriptTools.so.4E: Couldn't find any package by glob 'libQtScriptTools.so.4'E: Couldn't find any package by regex 'libQtScriptTools.so.4'I'm at a loss. Any help would be greatly appreciated.Best,M._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freeview command not found
by fsbuild 05 Dec '18

05 Dec '18

External Email - Use Caution Hello Maeve, You can search for the package to install with apt-file, but you may need to install that first, so try, $ sudo apt install apt-file $ sudo apt update … now search for the package with that library name using apt-file $ sudo apt-file search libQtScriptTools.so.4 I think it will come back with something like, libqt4-scripttools:  /usr/lib/x86_64-linux-gnu/libQtScriptTools.so.4….. - but the name of the package to the left hand side of the colon is what you want to install, so try $ sudo apt install libqt4-scripttools If that does not fix the libqt references, then you could also try $ sudo apt install qt4-default - R. On Dec 5, 2018, at 13:32, Maeve Barrett <barretm2(a)tcd.ie> wrote:        External Email - Use Caution        Hello,I've been trying to resolve this issue but I haven't found a fix on the mailing lists. I downloaded and installed the most recent version of Freesurfer for Linux.. I am running Ubuntu 16.04 LTS as guest on Virtualbox 5.2.22 on a windows 10 host. My tcsh version is 6.18.01 (Astron). When I type the commands $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.cshI get the following output: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurferFSFAST_HOME       /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /home/maevebarrett/Documents/AM8750_Structural/MNI_DIR           /usr/local/freesurfer/mniI have been able to run recon-all with no errors. However, when I try to open freeview, I receive the error message 'freeview: command not found.'I ensured I have permissions on the requisite folders. When I navigate to freesurfer/bin and type freeview..bin $argv I get the following error:/usr/local/freesurfer/bin> freeview.bin $argvfreeview.bin: error while loading shared libraries: libQtScriptTools.so.4: cannot open shared object file: No such file or directoryI tried downloading the libQtScriptTools.so.4 but when I attempt to install it I get the following error:sudo apt-get install libQtScriptTools.so.4Reading package lists... DoneBuilding dependency tree       Reading state information... DoneE: Unable to locate package libQtScriptTools.so.4E: Couldn't find any package by glob 'libQtScriptTools.so.4'E: Couldn't find any package by regex 'libQtScriptTools.so.4'I'm at a loss. Any help would be greatly appreciated.Best,M._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview command not found
by Maeve Barrett 05 Dec '18

05 Dec '18

External Email - Use Caution *Hello,* *I've been trying to resolve this issue but I haven't found a fix on the mailing lists. I downloaded and installed the most recent version of Freesurfer for Linux. I am running Ubuntu 16.04 LTS as guest on Virtualbox 5.2.22 on a windows 10 host. My tcsh version is 6.18.01 (Astron). When I type the commands * $> setenv FREESURFER_HOME /usr/local/freesurfer $> source $FREESURFER_HOME/SetUpFreeSurfer.csh *I get the following output: * -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/maevebarrett/Documents/AM8750_Structural/ MNI_DIR /usr/local/freesurfer/mni *I have been able to run recon-all with no errors. However, when I try to open freeview, I receive the error message* 'freeview: command not found.' *I ensured I have permissions on the requisite folders. * *When I navigate to freesurfer/bin and type freeview.bin $argv I get the following error:* /usr/local/freesurfer/bin> freeview.bin $argv freeview.bin: error while loading shared libraries: libQtScriptTools.so.4: cannot open shared object file: No such file or directory *I tried downloading the libQtScriptTools.so.4 but when I attempt to install it I get the following error:* sudo apt-get install libQtScriptTools.so.4 Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package libQtScriptTools.so.4 E: Couldn't find any package by glob 'libQtScriptTools.so.4' E: Couldn't find any package by regex 'libQtScriptTools.so.4' *I'm at a loss. Any help would be greatly appreciated.* *Best,* *M.*

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Lab manager position in Perception & Brain Dynamics Laboratory at NYU Medical Center
by Max Levinson 05 Dec '18

05 Dec '18

External Email - Use Caution The Perception & Brain Dynamics Laboratory (http://www.med.nyu.edu/helab/) at Langone Medical Center, New York University is looking for a lab manager to start in summer 2019. The Laboratory is within the Neuroscience Institute at NYU Langone Health (http://www.med.nyu.edu/neuroscience) affiliated with Departments of Neurology, Neuroscience and Physiology, and Radiology. Our research focus is on understanding the neural bases of perceptual awareness using multimodal imaging (fMRI, MEG, EEG, ECoG) and stimulation (tDCS, TMS) techniques in humans, combined with computational neuroscience approaches. We are looking for a bright and driven candidate with a Bachelor’s or Master’s degree who is dedicated to neuroscience research. A variety of backgrounds, including neuroscience, biology, psychology, and computer science is possible, and experience with programming is highly desirable. In addition, the ideal candidate has high responsibility and dependability, as well as excellent critical thinking, organizational and leadership skills. Performing independent research is an important aspect of the position, in addition to lab management duties. A minimal commitment of 2 years is required. Interested candidates please send a cover letter, a CV, undergraduate and/or graduate transcript, and names and contacts of two to three referees, to Prof. Biyu J. He at biyu.jade.he(a)gmail.com, with the subject line “Lab manager application 2019”.

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Re: [Freesurfer] Registering Anatomical Parcellation to DWI
by Yendiki, Anastasia 05 Dec '18

05 Dec '18

Yes, you can register other modalities to the T1 using bbregister. Then you can use that registration to transform any volume from T1 space to the space of the other modality. Check out the multimodal integration tutorials on the freesurfer wiki. On Dec 5, 2018 2:36 AM, Maedeh Khalilian <M.Khalilian(a)sutech.ac.ir> wrote: External Email - Use Caution Dear FreeSurfer experts, I have a parcellation and a whole brain white matter files which are the outputs of FreeSurfer. I want to register them to my DWI. I mean I want my parcellation and white matter to be in the physical space of my DWI. Can FreeSurfer do it for me? If not , can you suggest me a toolbox that can do it fast? I would be grateful if u could help me. Cheers, Maedeh,

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Map image in MNI onto fsaverage
by john Anderson 05 Dec '18

05 Dec '18

External Email - Use Caution Dear Freesurfer experts, I have the mean PET images for a number of subjects in MNI152 space. For visualization purposes, I would like to map this mean image onto brain surface. How can I do it. I appreciate any suggestion you may provide. Thanks! John

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Outer smoothed surface (lh.pial-outer-smoothed) only partly 'real' outer surface
by M. Jordan 05 Dec '18

05 Dec '18

External Email - Use Caution Hi!, i am using recon-all -s <subj> -localGI to get the outer smoothed surface of the pial files. This works, but when loading the original pial and the smoothed one, some parts of the original pial stand out. Is there any possibility / parameter to avoid this? I need an outer surface which completely covers the brain. Thank you!

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create ctab from annot
by Winkelbeiner, Stephanie A 04 Dec '18

04 Dec '18

External Email - Use Caution Hi freesurfer-experts, I used a customized script that produces a more fine-grained parcellation resulting in an .annot file. I don't seem to have a look-up-table (LUT), however. I tried the following: - mri_annotation2label --> allows me to extract the single labels. But I rather need a .ctab file when I want to read out my values. - mris_anatomical_stats with the -c flag --> to output the colortable as a text file I first need the .ctab file. Is there a way to get the LUT in a text file or the .ctab file just from the annotation file? Thanks a lot in advance! Cheers, Stephanie Stephanie Winkelbeiner, MSc Research Coordinator Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: swinkelbei(a)northwell.edu<mailto:swinkelbei@northwell.edu> Northwell Health Visit us at Northwell.edu<http://northwell.edu/> The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Voxel dimensions and final recon
by Michael ONeill 04 Dec '18

04 Dec '18

External Email - Use Caution Dear Freesurfer, I'm enquiring about the known effect that pixel spacing has on the reconstructions and final volume estimates produces by Freesurfer. Specifically, is there a range of pixel spacing values that are necessary for accuracy? Secondly, if the pixel spacing and slice thickness are different values (i.e non-isometric voxels) does this have much of an effect on the final recon and volume estimates? All the best, Michael The opinions, conclusions and other information expressed in the above message, or contained within attachments to the above message, are not given or endorsed by Beaumont Hospital unless otherwise indicated by an authorised representative independent of this message. This e-mail message and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. This e-mail has been scanned for viruses. This e-mail and all attachments are confidential and may be privileged. If you have received this e-mail in error, notify the sender immediately. Do not use, disseminate, store or copy it in any way.

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Postdoc openings on the Connectome 2.0 project
by Yendiki, Anastasia 04 Dec '18

04 Dec '18

https://www.ismrm.org/jobs/j06670.pdf The Connectome 2.0 Project is a new BRAIN initiative-funded effort at the Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School. Building on our experience designing the first Connectome scanner, we aim to engineer the next-generation MRI scanner for imaging the circuitry and microstructure of the human brain; and to use the unique data produced by this scanner to develop novel software tools for improving the analysis of more widely available neuroimaging data. We are seeking talented and driven postdoctoral fellows to contribute to this exciting effort. The fellows would join the Martinos Center’s team of leading experts in MRI instrumentation, analysis, and applications, as well as the vibrant neuroimaging community of Boston. We have multiple openings in the following areas: 1. Gradient characterization. The post-doctoral fellow will simulate and design gradient hardware optimized for high-slew rate, ultra-high gradient strength diffusion MRI. The research fellow will develop approaches to characterize and correct for eddy currents. Responsibilities will include mapping the gradient fields, developing gradient nonlinearity correction software, and incorporating information on the gradient coils and eddy currents into the diffusion preprocessing and analysis pipeline. Strong expertise in C/C++ and/or Matlab is highly desirable. 2. Diffusion microstructural modeling and analysis. The post-doctoral fellow will design, acquire, and analyze diffusion microstructural imaging experiments to showcase the capabilities of the next-generation ultra-high gradient 3T MRI scanner. Responsibilities will include acquiring, analyzing and interpreting diffusion microstructural imaging data for in vivo and ex vivo human brain imaging in the next-generation ultra-high gradient MRI system. A strong background in NMR and MRI physics with specific expertise in diffusion MRI and mathematical and computational modeling is essential. 3. Algorithms for connectional anatomy. The post-doctoral fellow will develop software tools that take advantage of the unprecedented diffusion MRI data collected by the Connectome 2.0 to produce the next-generation mapping of the connectional anatomy of the human brain. The fellow will use unique optical and histological ground truth data to validate these methods ex vivo, and will develop algorithms that can be trained on the unprecedented data of the Connectome 2.0 to improve the accuracy of diffusion MRI tractography in routine-quality, widely available in vivo data. Candidates with a strong background in image analysis/computer vision/machine learning are encouraged to apply. Experience in diffusion tractography and/or diffusion microstructural modeling is an asset. For all positions, a Ph.D. in electrical engineering, biomedical engineering, computer science, physics, applied physics, or related field is required. Creativity, initiative, proven ability to publish, and excellent oral and written communication skills are key. The position is full-time with benefits and available immediately. A two-year time commitment is required with a possible extension of another two years. Salary will be based on qualifications and experience. The Massachusetts General Hospital is an Equal Opportunity/Affirmative Action Employer. Applicants should submit a curriculum vitae, the contact information of two references, and a cover letter describing their research background, interests, and professional goals by email to Drs. Susie Huang (syhuang(a)nmr.mgh.harvard.edu) and Anastasia Yendiki (ayendiki(a)mgh.harvard.edu) Please include “Connectome 2.0 postdoctoral position” in the title of your email.

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Freesurfer December 2018