Freesurfer

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30088 discussions

Cortical Parcellation: ROIs not covering gray matter in depth direction
by Yixin Ma 29 Oct '18

29 Oct '18

External Email - Use Caution Hi, I’m writing to ask about cortical parcellation (Desikan-Killiany and Destrieux), which do not work well on my recent anatomical scan (a new anatomical scan sequence that gives better grey and white matter contrast). I’m writing to ask if you know what is causing this artifact (ROIs are not covering all gray matter in depth direction) and from which step should I start to debug. Thank you for your help. Best regards, Yixin Ma [image: Screen Shot 2018-10-29 at 12.19.43 PM.png]

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resampling data onto cortical surface
by GREGORY R KIRK 29 Oct '18

29 Oct '18

External Email - Use Caution I have R1 values that I want to resample onto the cortical surface. The R1 values were computed from a multi echo T1 sequence that was also used to create the T1 weighted image that was used in recon-all to produce the cortical surface reconstructions and thus is inherently in registration to the 001.mgz that was used to start recon. There will be a difference in orientation in the volume in that orig.mgz is in coronal and in the .mgz format. I was thinking that if I run the first step of recon-all it should give me an volume named orig.mgz that is in registration to the freesurfer space for the subject ... or else some call to mri_convert reslice_as or whatever is used in the recon-all script to convert 001.mgz to orig.mgz then my problem is to get a file with the resampling of the R1 onto the cortical surface withR1 values at each vertex. when i work with fmri data I run bbregister and get the transformation from the epi volume to the freesurfer space and then use mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface --reg bb.register.dat \ --projfrac 0.5 --interp nearest \ --hemi lh --o lh.sig.mgh to resample the epi data onto the cortical surface. however in this case the R1 data is already in perfect registration to the T1 other than the reorientation and reslicing done to prepare the orig.mgz volume. so can someone tell me what is the proper way to cook this goose Greg

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Re: [Freesurfer] freeview libpng12.so.0 error
by fsbuild 29 Oct '18

29 Oct '18

External Email - Use Caution Hello Ashesh, You need to install the "gdebi" command on your Ubuntu machine. Then download and install the libpng12 package from, http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54… Then install that package with the gdebi command,   $ sudo gdebi libpng12-0_1.2.54-1ubuntu1_amd64.deb On Oct 29, 2018, at 14:43, Thaker, Ashesh A <ASHESH.THAKER(a)ucdenver.edu> wrote:        External Email - Use Caution        Dear FreeSurfer Team,I'm running FreeSurfer on a 64-bit Linux machine running Ubuntu 18.04 LTS. Here is my config:ashesh@ashesh-gpu:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurferFSFAST_HOME       /usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/subjectsMNI_DIR           /usr/local/freesurfer/mniFSL_DIR           /usr/local/fslI have this error running freeview:ashesh@ashesh-gpu:~$ freeviewfreeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directoryI have installed libjpeg62-dev but still get the same error.Any thoughts?Thanks,AsheshAshesh Thaker, MD | Assistant ProfessorSchool of Medicine, Department of RadiologyUniversity of Colorado Anschutz Medical Campus 720 848 6568 (office) | ashesh.thaker(a)ucdenver.edu

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freeview libpng12.so.0 error
by Thaker, Ashesh A 29 Oct '18

29 Oct '18

External Email - Use Caution Dear FreeSurfer Team, I'm running FreeSurfer on a 64-bit Linux machine running Ubuntu 18.04 LTS. Here is my config: ashesh@ashesh-gpu:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl I have this error running freeview: ashesh@ashesh-gpu:~$ freeview freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory I have installed libjpeg62-dev but still get the same error. Any thoughts? Thanks, Ashesh Ashesh Thaker, MD | Assistant Professor School of Medicine, Department of Radiology University of Colorado Anschutz Medical Campus  720 848 6568 (office) | ashesh.thaker(a)ucdenver.edu

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Freeview coordinates
by k3ops＠free.fr 29 Oct '18

29 Oct '18

External Email - Use Caution Hi Freesurfer team, Sorry to ask a new question about FreeSurfer coordinates (I know it has been debated multiple times reading old messages) but I am still confused with all these spaces. I have a very simple use case in Freeview, when I load the T1.mgz image I would need to get the "TkReg RAS" coordinate of points using the pixel positions (last line in Cursor/Mouse coordinates in Freeview). I know Freeview is providing the conversion but I would need to be able to extract the "TkReg RAS" coordinates for multiple pixel positions in the T1.mgz file. I've read the FreeSurfer documentation (https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) but it is still confused for me when I look at the coordinates in Freeview... Which transformation is used to convert pixel coordinate (T1.mgz) to Talairach, TKReg RAS and RAS systems? I also found this interesting link http://brainmap.org/icbm2tal/ and implemented the mni2tal / spm2tal / fsl2tal / other2tal transformations (in Python/Numpy) but unfortunately none of them gave me good results. Thanks for your help. Florent

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cavum septum pellucidum
by Keedy, Sarah [PSY] 29 Oct '18

29 Oct '18

External Email - Use Caution HI, wondering if there are thoughts on this question I posted a week ago? Repeated here: I'm comparing output of Freesurfer5.2 to 6 on the same set of brains. The "5th ventricle" (Cavum septum pellucidum) is not being detected by 6. I had eyeballed the output from 5.2 and convinced myself it was reasonably well detecting this developmentally abnormal finding pretty well. I am wondering what changed in version 6, if anything, that could explain this? Sarah K. Keedy, Ph.D. Assistant Professor, Psychiatry and Behavioral Neuroscience Director, Cognition Emotion Neuroscience Lab (CENSL) Grossman Institute for Neuroscience, Quantitative Biology, and Human Behavior University of Chicago ph (773) 834-7178 External Email - Use Caution

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Research Opportunity
by Nillo, Ryan Michael R 29 Oct '18

29 Oct '18

External Email - Use Caution UCSF, Dept. of Radiology & Biomedical Imaging is seeking a Postdoctoral Scholar for The Laboratory for Precision Neuroimaging We are seeking a postdoctoral candidate with a strong background in genetics human imaging and a desire to use a multi-disciplinary approach to pursue neurodegenerative and neurodevelopment research. The candidate should have a strong statistical/computational background with experience with data analytic tools such as Matlab, R, and PLINK and potentially, 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 immediately. Salary is commensurate with qualifications and experience. Job Requirements: 1.CV/NIH biosketch (must contain previous research experience) 2.Cover Letter - Short statement on why you are interested in this position and how this position will help you achieve your career goals 3.Three references If interested please contact Dr. Leo Sugrue at leo.sugrue(a)ucsf.edu<mailto:leo.sugrue@ucsf.edu> Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging

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Re: [Freesurfer] cluster failing on HCP freesurfer script
by Glasser, Matthew 29 Oct '18

29 Oct '18

External Email - Use Caution What version of FreeSurfer are you using? Is the FreeSurfer environment set up correctly? Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Sanchez, Juan (NYSPI)" <Juan.Sanchez(a)nyspi.columbia.edu<mailto:Juan.Sanchez@nyspi.columbia.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, October 26, 2018 at 3:12 PM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] cluster failing on HCP freesurfer script External Email - Use Caution Dear community, My group is using the latest version of condor clustering to process our data on OS X. We have a bash script that calls freesurfer to run our HCP pipelines. I can run the script to completion when running it locally on each of the clustered machines, however when submitting the job I get the following error Can’t locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup module) (@INC contains: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Applications/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. (standard_in) 2: comparison in expression Can anyone suggest a solution? Thanks J ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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subfield normalization vs. covarying for whole hippocampal volume
by Lauren Salminen 29 Oct '18

29 Oct '18

External Email - Use Caution Hello, I’m working on a multi-site hippocampal subfields project (FSv. 6) and am wondering if it is “better” to normalize subfield volumes by dividing each subfield by whole hippocampal volume, or covary for hippocampal volume as an independent predictor variable in the regression models. Ultimately the goal is to determine the degree that each subfield may be uniquely associated with my target predictor variable, and we would like to know if this effect can be observed independent of potential differences in the whole hippocampus. Traditionally we have covaried for whole hippocampal volume, but I’ve found more interesting effects by normalizing each subfield to their hippocampal volume. Any guidance is appreciated. Thank you! ____________________ Lauren E. Salminen, Ph.D. Imaging Genetics Center Stevens Neuroimaging and Informatics Institute Keck School of Medicine University of Southern California http://igc.ini.usc.edu/ <http://igc.ini.usc.edu/>

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Re: [Freesurfer] cluster failing on HCP freesurfer script
by fsbuild 29 Oct '18

29 Oct '18

External Email - Use Caution Mac OS comes with perl 5.18.  The module MNI/Startup.pm is not part of standard perl, and so it is provided in the freesurfer distribution.  When you source either the FreeSurferEnv.csh or FreeSurferEnv.sh script the environment variable MNI_PERL5LIB should get set to $FREESURFER_HOME/mni/lib/../Library/Perl/Updates/5.12.3   You should be able to ls that path and see an MNI Perl module there, i.e., the file MNI.pm. Subsrquently, the FreeSruferEnv scripts add MNI_PERL5LIB into the environment variable PERL5LIB.   But if something in the cluster environment is unsetting/setting PERL5LIB after FreeSurferEnv runs, then freesurfer will not be able to find the module.  You need to check the (final) values of MNI_PERL5LIB  and  PERL5LIB in the cluster environment.

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