Re: [Freesurfer] freeview problem on Linux RHEL 7-4 libGLU.so.1
External Email - Use Caution Dear Avner and fellow freesurfer users, I've just came across the same issue testing QDEC after the installation of Freesurfer 6.0 using FEDORA 28 “qdec.bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory" I would like to report how I solved the problem in order to help future users of freesurfer using Fedora28 1. I installed a graphical package manager called dnfdragora 2. Inside the dnfdragora I searched "mesa-libglu" 3. Selected all packages found 4. Apply QDEC is running smoothly Hope this helps anyone Best regards, *Felipe Picon, MD, MSc* Child and Adolescent Psychiatrist == ADHD Neuroimaging Researcher at the Adult ADHD outpatient research program PRODAH-A <http://www6.ufrgs.br/prodah/prodah/e-equipe.html> - HCPA <http://www.hcpa.ufrgs.br/> - UFRGS <http://www.ufrgs.br/> Porto Alegre - RS - Brazil Vice-Coordinator of the Technology Addiction Study Group - GEAT <http://dependenciadetecnologia.org/quem-somos/> Founding Member and Former Secretary of the Early Career Psychiatrists Section - World Psychiatric Association (WPA) Member of the Neuroimaging in Psychiatry Section - World Psychiatric Association (WPA) Member of the ADHD Section - World Psychiatric Association (WPA) Member of the American Academy of Child and Adolescent Psychiatry (AACAP) Member of the Organization for Human Brain Mapping (OHBM) Member of the International Society for the Study of Behavioural Addictions (ISSBA) Member of the International Association for Child and Adolescent Psychiatry and Allied Professions (IACAPAP) == Web based CV <http://lattes.cnpq.br/3896757276389918> Google Scholar Profile <http://scholar.google.com/citations?user=TxI0ZYYJ=en> felipepi...@gmail.com Em ter, 15 de ago de 2017 às 12:59, Avner Meoded escreveu: > Hello all, > > > I installed the latest version for Linux > > > I get this message when trying to run an example: > > > > *"freeview.bin: error while loading shared libraries: libGLU.so.1: cannot > open shared object file: No such file or directory*" > > > I installed the missing library and now it is in > > > /usr/local/fsl/bin/FSLeyes/libGLU.so.1 > > any idea ho to solve this problem > > > > Thanks > > > avner > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Siemens SPECTRA 3T - Help with sequences
Dear colleagues, I’m a researcher psychiatrist who is currently testing image acquisitions with different sequences on a Siemens 3T SPECTRA scanner. I would like to learn from you if any of you had experience with this scanner in the collection of high-resolution structural images (MPRAGE), DTI, and Resting State Functional Connectivity images. We only have access to a 12-channel Head Coil, though. Luckily the scanner has the possibility of acquiring 128 direction of DTI. If any of you can share with me any good quality sequences that could fit this set of characteristics it would be highly appreciated Thank you very much Best regards, Felipe Picon -- *Felipe Picon, MD, MSc* Child and Adolescent Psychiatrist = ADHD Neuroimaging Researcher at the Adult ADHD outpatient research program PRODAH-A <http://www6.ufrgs.br/prodah/prodah/e-equipe.html> - HCPA <http://www.hcpa.ufrgs.br> - UFRGS <http://www.ufrgs.br> Porto Alegre - RS - Brazil Vice-Coordinator of the Technology Addiction Study Group - GEAT <http://dependenciadetecnologia.org/quem-somos/> Secretary of the Early Career Psychiatrists Section - World Psychiatric Association <http://www.wpanet.org/detail.php?section_id=11_id=1703> Corresponding Member of the American Academy of Child and Adolescent Psychiatry - AACAP = Web based CV <http://lattes.cnpq.br/3896757276389918> Google Scholar Profile <http://scholar.google.com/citations?user=TxI0ZYYJ=en> felipepi...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freeview.bin - error while loading shared libraries: libvtkverdict.so.5.6 cannot open sharted ...
Dear colleagues, I'm installing Freesurfer-Linux-CentOS4-stable-pub-v5.3.0 on Ubuntu 14.04 LTS (updated) and I managed to make tkmedit run correctly, but when I try QDEC and Freeview I'm getting this message: "qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such fie or directory and "freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory" Any ideas or suggestions of what I might have done wrong? Thank you very much Best, Felipe Picon 2015-04-06 19:04 GMT-03:00 Johannes Kaufhold <johannes.kaufh...@outlook.com> : > Hi Zeke, > > I managed to solve this issue. > > I have changed the ownership of all folders and files in > /usr/local/freesurfer to my Ubuntu user name and now Freeview is working > with the sample data. > > ..Just seeing your email coming in. > > Best, > jk > > On 06/04/15 22:34, Johannes Kaufhold wrote: > > Hi Zeke, > > > > Yes, I'm attempting to open freeview in the same terminal window in > > which I have sourced SetUpFreeSurfer.csh. > > > > Here's the output from ls -l > > $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict* > > > > lrwxrwxrwx 1 root root 22 May 13 2013 > > /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so -> > > libvtkverdict.so.5.6.0 > > lrwxrwxrwx 1 root root 22 May 13 2013 > > /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 -> > > libvtkverdict.so.5.6.0 > > -rwsrwsr-t 1 root root 189017 Aug 17 2010 > > /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0 > > > > Best, > > Johannes > > > > On 06/04/15 21:48, Z K wrote: > >> Hello Johannes, > >> > >> You are attempting to open freeview *in the same window* that you > >> sourced SetUpFreeSurfer.csh(sh), correct? Also, can you tell me what the > >> output of the terminal is when you type the following command: > >> > >> ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict* > >> > >> -Zeke > >> > >> On 04/06/2015 04:32 PM, Johannes Kaufhold wrote: > >>> Hi all, > >>> > >>> I'm super new to Freesurfer. I just set it up on my computer earlier > >>> today, following the official wiki on harvard.edu/fswiki... > >>> > >>> My system: > >>> - Ubuntu 14.04 LTS (up to date) > >>> - Tcsh installed > >>> - Freesurfer version: > >>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz > >>> < > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz > > > >>> - Mathlab not installed > >>> > >>> Sourcing the SetUpFreeSurfer.csh(sh) script worked fine and license.txt > >>> is in $FREESURFER_HOME. > >>> > >>> When trying to pull and view the sample data by entering the below in > >>> the terminal (tcsh) > >>> > >>> freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v > >>> $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f > >>> $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f > >>> $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f > >>> $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f > >>> $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red > >>> > >>> I'm getting the following error message* > >>> ** > >>> **freeview.bin: error while loading shared libraries: > >>> libvtkverdict.so.5.6: cannot open shared object file: No such file or > >>> directory* > >>> > >>> I was searching for the missing file in Aptitude and on the internet, > >>> but couldn't manage to find it. > >>> > >>> Any suggestions how to proceed from here? > >>> > >>> Thanks and best wishes! > >>> Johannes > >>> > >>> > >>> ___ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >> ___ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> The information in this e-mail is intended only for the person to whom > it is > >> ad
Re: [Freesurfer] Poor Cortical Reconstructions in Pediatrics
Hi Lilla, Is it possible to use our own sample to build an atlas and than start group comparisons based on that, even though the backengine is still based on an adult atlas? I ask this question, because my sample is of kids from 6-16 years Any suggestions? Thank you Best regards, Felipe Picon, MD 2012/5/10 Lilla Zollei lzol...@nmr.mgh.harvard.edu Hi Xin, In general, we do not recommend the processing of MRI datasets of subjects younger than 4 with the FS recon pipeline. The backengine of recon-all is an atlas that is built from adult data sets, so the prior information about the intensities / structures do not represent the younger population. With the older ones, we had more success, but even then the outcome is going to heavily depend on the quality of your input images, so I would very carefully check each one of them. At the moment we do not have a pediatric atlas, but we are working on it. Lilla On Wed, 9 May 2012, Xin Zhang wrote: Hello FreeSurfers, Please ignore the previous email. This one includes an example picture. We are processing about 100 pediatric subjects ages 3-9 using FreeSurfer 5.1.0. For some reason, in about 25 of the subject, the right supramarginal, right middletemporal, and superiortemporal regions have poor cortical reconstructions. After reviewing the raw scans, we do not see any reason why these regions would be poorly segmentated. Can anyone give us any feedback for why these regions are reconstructing poorly? Our only ideas are that our subject ages might be causing issues, or normalizing the minor brightness gradient could be causing issues (although the poor segmentations occur even on subjects that have no brightness gradient on their raw scans). Thank you very much, Xin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- *Felipe Picon, MD* Child and Adolescent Psychiatrist = ADHD Neuroimaging Research Adult ADHD outpatient research program (PRODAH-A)http://www6.ufrgs.br/prodah/prodah/e-equipe.html Hospital de Clinicas de Porto Alegre (HCPA) http://www.hcpa.ufrgs.br Federal University of Rio Grande do Sul (UFRGS) http://www.ufrgs.br Porto Alegre - RS - Brazil Area Coordinator for the Americas http://www.wpanet.org/detail.php?section_id=22content_id=120 of the Early Career Psychiatrists Council (World Psychiatric Association)http://www.wpanet.org/detail.php?section_id=22content_id=120 = Web based CV http://lattes.cnpq.br/3896757276389918 Google Scholar Profile http://scholar.google.com/citations?user=TxI0ZYYJhl=en felipepi...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Using FreeSurfer with 6-14 year olds
Thank you Sita. So I can run recon-all for every subject and only after make a average subject? Thank you Best, Felipe Picon 2011/8/8 Sita Kakunoori s...@nmr.mgh.harvard.edu You might want to create a template from these datasets for any group analysis you might be doing but just for running recon-all, you don't need to. It's not necessary to separate them in age ranges to create an average. Sita. On Fri, 5 Aug 2011, Felipe Picon wrote: Dear FreeSurfer experts, I'm starting to recon-all the MPRAGE volumes of a large sample of 6-14 year olds So far I haven't had any errors (only 15 subjects runned so far) My questions are: - Should I make a template from the subjects of my whole sample, considering their age range? - Or FreeSurfer template would work just fine with this sample? If I should make a average from my whole sample, should I make it separating the sample in age ranges? Any suggestions are welcome Thank you!! The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- *Felipe Picon, MD* Child and Adolescent Psychiatrist Master's Degree Student - Department of Psychiatry of Federal University of Rio Grande do Sul - UFRGS - www.ufrgs.br Adult ADHD outpatient research program - PRODAH-A - http://www6.ufrgs.br/prodah/prodah/equipe.html Hospital de Clinicas de Porto Alegre - HCPA - www.hcpa.ufrgs.br Member of the World Psychiatric Association (WPA) Early Career Psychiatrists Council Area Coordinator for the Americas - http://www.wpanet.org/detail.php?section_id=22content_id=120 Web based CV: http://lattes.cnpq.br/3896757276389918 felipepi...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Using FreeSurfer with 6-14 year olds
Dear FreeSurfer experts, I'm starting to recon-all the MPRAGE volumes of a large sample of 6-14 year olds So far I haven't had any errors (only 15 subjects runned so far) My questions are: - Should I make a template from the subjects of my whole sample, considering their age range? - Or FreeSurfer template would work just fine with this sample? If I should make a average from my whole sample, should I make it separating the sample in age ranges? Any suggestions are welcome Thank you!! -- *Felipe Picon, MD* Child and Adolescent Psychiatrist Master's Degree Student - Department of Psychiatry of Federal University of Rio Grande do Sul - UFRGS - www.ufrgs.br Adult ADHD outpatient research program - PRODAH-A - http://www6.ufrgs.br/prodah/prodah/equipe.html Hospital de Clinicas de Porto Alegre - HCPA - www.hcpa.ufrgs.br Member of the World Psychiatric Association (WPA) Early Career Psychiatrists Council Area Coordinator for the Americas - http://www.wpanet.org/detail.php?section_id=22content_id=120 Web based CV: http://lattes.cnpq.br/3896757276389918 felipepi...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
