Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

Long seg for hippo subfields
by Thomas, Adam (NIH/NIMH) [E] 01 Aug '16

01 Aug '16

This look very cool: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields But the flag is not being recognized by recon-all using the most recent build: [adamt@felix scratch]$ cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos6_x86_64-dev-20160730-bda65ec [adamt@felix scratch]$ recon-all -long-hippocampal-subfields-T1 md105Templ -hsfTP md105-1.long.md105Templ -hsfTP md105-2.long.md105Templ -hsfTP md105-3.long.md105Templ -hsfTP md105-4.long.md105Temp1 -hsfTP md105-5.long.md105Templ ERROR: Flag -long-hippocampal-subfields-T1 unrecognized. -long-hippocampal-subfields-T1 md105Templ -hsfTP md105-1.long.md105Templ -hsfTP md105-2.long.md105Templ -hsfTP md105-3.long.md105Templ -hsfTP md105-4.long.md105Temp1 -hsfTP md105-5.long.md105Templ Linux felix.nimh.nih.gov 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Mon Aug 1 18:42:51 EDT 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [adamt@felix scratch]$ uname -a Linux felix.nimh.nih.gov 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux [adamt@felix scratch]$ which recon-all /data/adamt/Apps/fs6-2016-07-31/bin/recon-all [adamt@felix scratch]$ Is there a newer version of recon-all hiding somewhere? Thanks, -Adam

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mris_label2annot
by Caroline Beelen 01 Aug '16

01 Aug '16

Dear FS, Sorry to bother again, but I'm currently in need for some quick help. Today, I also ran into another problem. I tried to display only few ROI's in Freeview instead of the whole brain. Therefore, I tried to create a new annotation file consisting of only few labels (from regions of DK-atlas) and I used the mri_annotation2label on my own created fsaverage to get these labels. This worked fine. Then I used the command of mris_label2annot to create the annotation file, but part of the command, --ctab aparc.annotation.ctab, is not recognized. Replacing it by -ctab fsaverage/label/lh.aparc.annot (file exists in the label folder of fsaverage) gives me the following error: CTABreadASCII: badly formed file. ERROR: reading fsaverage/label/lh.aparc.annot. I couldn't find, or create, any other aparc.annot file. What would be the right command (for the part of ctab) to get mris_label2annot working? Or is there perhaps a better way to only display certain ROI's in Freeview? (the latter I could still explore but assistance is certainly appreciated) Thanks a lot! Caroline

2 1

freesurfer 6.0 release date
by Fengji Geng 01 Aug '16

01 Aug '16

Hi fs developers, I am wondering if you have any estimation when fs 6.0 will come out. The reason that I ask this is because we are running some analysis using fs 5.1 and planning to switch to a more recent version of fs. If fs 6.0 will come out soon, we will probably hold and wait for it. If not, we will just switch to fs 5.3. Thanks! -- Fengji Geng

2 1

Freesurfer dev version
by Liu, Daniel 01 Aug '16

01 Aug '16

Hi, I wanted to follow up on the error that came up in the freesurfer dev version this past week. Has it been fixed yet? If so, has the link to the download page been changed? The one I booked marked does not lead me to the page anymore and I would appreciate it if you could direct me to the correct location. Thanks, Daniel

3 3

Cannot launch freeview
by Da, Xiao 01 Aug '16

01 Aug '16

Hi Freesurfer Developers, I tried to run freeview but got this following error message. freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux version: NAME="Red Hat Enterprise Linux Workstation" VERSION="7.2 (Maipo)" ID="rhel" ID_LIKE="fedora" VERSION_ID="7.2" PRETTY_NAME="Red Hat Enterprise Linux" I tried "locate libXss.so.1", but returned nothing. Please let me know if you have the solution to fix this error. Thanks and best regards, Xiao Da Biomedical Engineer - Programmer Analyst II Functional Neuroimaging Laboratory Brigham and Women's Hospital 221 Longwood Avenue, Braunwald Building, Room LM116 Boston, MA 02115 xda(a)bwh.harvard.edu

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mri_label2label error
by Aquino Domenico 01 Aug '16

01 Aug '16

Dear Freesurfer team, I'm trying to segment a pre-processed 3D PSIR volume. Everything seems to work correctly, however at the end of recon-all something goes wrong. The command "mri_label2label" returns the ERROR "No such file or directory\ mri_label2label: could not open label file...". Actually the file has not been created but I don't understand why. I checked the path for special characters, I checked the permissions and so on and it seems all ok. Which could be the issue? In attachment you'll find the recon-all.log file. Thanks a lot, Domenico ___________________________________________ Eng. Domenico Aquino Department of Neuroradiology IRCCS Foundation Neurological Institute "Carlo Besta" Via Celoria,11-20133 Milano Phone: +39 02 23942472 Fax +39 02 23942543 [1463859753944_LogoWhite.jpg]

2 1

significance overlay Freeview
by Caroline Beelen 01 Aug '16

01 Aug '16

Dear FS, Yes, I'm running FS 5.3. :) How can I visualize the significance overlay (correctly)? Which command should I use to view a significance overlay in freeview in FS 5.3? See also my email below. Thank you very much in advance! Best, Caroline Hi Caroline, Are you running FS 5.3? The command on the webpage is based on the upcoming 6.0, I believe. So some of the command line options are not available in 5.3. Best, Ruopeng > On Jul 29, 2016, at 9:11 AM, Caroline Beelen <caroline.beelen(a)kuleuven.be<mailto:caroline.beelen@kuleuven.be>> wrote: > > Dear FS team, > > Apologies in advance for perhaps again a rather basic question. I attempted to load the aparc overlay in freeview by using the written command from the group analysis page, however it failed to load correctly. > > I used the following command: > freeview -f fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5 -viewport 3d > ? roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis and dyslect is the contrast folder within this file (main effect of dyslexia), containing a sig.mgh file (all seems fine) > > Unfortunately, I got an error that it does not recognize overlay_treshold=4,5. I used freeview ?h and tried certain commands alike, but they didnt work. When leaving out this part, I got another error that it failed to recognize annot_outline=1. Again, leaving this out too, freeview loads itself and the DK-regions become visible. However, nothing else seems to get activated, and even not when putting configure overlay (which is set to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens. > When looking at the command line it says that it implemented the colortable of DK-atlas (even twice), but it tells me nothing else. Also, after closing and reloading Freeview by using the similar command and then clicking on configure overlay the screen sometimes gets stuck, giving me the impression that something must be wrong with the command. > > Could you please help me out and provide me the right command-line for loading the overlay of the significance map of roi.lh.area.dyslect_basic.glmdir/dyslect? > > Thanks in advance! > > Kind regards, Caroline

1 0

postdoc position
by Bruce Fischl 31 Jul '16

31 Jul '16

FYI --- The Neuroradiology Section at the University of California, San Francisco (UCSF) is seeking an exceptional postdoctoral candidate in multimodal imaging of neuropsychiatric and neurodegenerative disorders. Combining neuroimaging, genetics, and computational methods, our group is interested in elucidating mechanisms underlying neuropsychiatric and neurodegenerative conditions ranging from obsessive compulsive disorder to dementia. Our emphasis is on using multimodal imaging (including structural and functional MRI, MR spectroscopy, EEG/MEG) and imaging genetics to develop genetic and imaging biomarkers that can be leveraged to both diagnose neuropsychiatric disease and to provide a rational framework for targeting and monitoring therapy - including emerging neuro-modulatory technologies - in individual patients. We seek a postdoctoral candidate with advanced training in neurosciences or biomedical engineering, a strong background in human imaging, and a desire to pursue translational research using a multi-disciplinary approach. The ideal candidate should have considerable experience with data analysis, simulation, and visualization using packages such as Matlab, R, or Python, as well as facility with MRI image analysis tools such as Freesurfer, FSL, and SPM. Applicants should have a Ph.D. or M.D. degree with less than five years of postdoctoral experience. Highly motivated individuals with a record of productive research are encouraged to apply. The position is available starting August 1, 2016. UC San Francisco seeks candidates whose experience, teaching, research, or community service has prepared them to contribute to our commitment to diversity and excellence. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status. Salary is commensurate with qualifications and experience. Interested applicants should send curriculum vitae/NIH biosketch, Cover Letter, and three references to: Dr. Leo Sugrue (leo.sugrue(a)ucsf.edu) and Dr. Rahul Desikan (rahuldesikan(a)gmail.com)

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Siemens SPECTRA 3T - Help with sequences
by Felipe Picon 30 Jul '16

30 Jul '16

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&content_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=TxI0ZYYAAAAJ&hl=en> felipepicon(a)gmail.com

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Longitudinal single time point cross sectional comparison
by Emmanuel Nwosu 30 Jul '16

30 Jul '16

Dear Freesurfer users, I have longitudinal data with three time points but want to run a cross sectional comparison on the first instance between group on just one time point (using QDEC). Any Idea on how I could do that on longitudinal data. Thanks for your help. Emmanuel Nwosu

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