Freesurfer

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30081 discussions

All coordinates of volume of interest
by Aziz Nanthaamornphong 16 Jun '16

16 Jun '16

Hi, Is there a way to get all coordinates (x,y,z) of the particular volume of interest (e.g., left-insula, left-thalamus)? Best, Aziz. -- Aziz Nanthaamornphong, Ph.D., Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz

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modifying files on older versions of FS
by Alexopoulos, Dimitrios 16 Jun '16

16 Jun '16

I have successfully processed data with FS v5.3 (linux/CentOS) using recon-all -all. Is it possible to make modifications to the 5.3-generated brainmask.mgz (primarily dura removal) and wm.mgz files using a much older 4.4 version of FS and then re-run recon-all on 5.3 with these modified files. I'd also be generating control points (control.dat file) on 4.4 as well. In other works are there file formatting differences between these FS versions for just these 3 files that could pose a problem when re-running the dataset. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email.

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Brodmann annotation on fsaverage
by Reza Rajimehr 16 Jun '16

16 Jun '16

Hi, Freesurfer has an annotation file for Brodmann areas, which is ?h.PALS_B12_Brodmann.annot. This Brodmann parcellation doesn't seem to be accurate in certain regions (e.g. in retrosplenial and perirhinal cortex). Does anyone have an alternative Brodmann atlas that can be visualized in Freesurfer (i.e. on fsaverage)? We are particularly interested in medial structures in occipital, parietal, and temporal lobe. Best, Reza

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Re: [Freesurfer] modifying files on older versions of FS
by Matt Glasser 16 Jun '16

16 Jun '16

Why would you want to do that? Peace, Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios" <Alexopoulos_D(a)kids.wustl.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, June 16, 2016 at 4:06 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] modifying files on older versions of FS I have successfully processed data with FS v5.3 (linux/CentOS) using recon-all -all. Is it possible to make modifications to the 5.3-generated brainmask.mgz (primarily dura removal) and wm.mgz files using a much older 4.4 version of FS and then re-run recon-all on 5.3 with these modified files. I¹d also be generating control points (control.dat file) on 4.4 as well. In other works are there file formatting differences between these FS versions for just these 3 files that could pose a problem when re-running the dataset. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email. _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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FSFAST- Cerebellum
by sabin khadka 16 Jun '16

16 Jun '16

Hi all, I am trying to extract mean time series BOLD data using FSFAST from Cortical ROIs + sub cortical ROIs and cerebellum. preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd mri_segstats --annot fsaverage lh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt mri_segstats --annot fsaverage rh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt and for cortical time series mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf subCorticalTimeSeries.txt But I am not sure on how exactly to extract time series from cerebellar regions. So if I want to extract time series from regions as described in Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in FreeSurferCololLUT.txt? If not could you please direct me to processes that I can use. Cheers, Sabin Khadka

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Hippocampal subfields error
by Greenberg, Jonathan 16 Jun '16

16 Jun '16

Hi all I ran recon-all on data from about 60 participants pre and post an intervention, with the hippocampal subfields flag (e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). The recon-all.log file states that the process finished without errors. However, the hippocampal-subfieldsT1.log indicated the following: "Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf" (see below for the full content of hippocampal-subfieldsT1.log). I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all -s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and received the same error message. I tried to look in the indicated folder ("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not know if this is the source of the problem. My FREESURFER_HOME directory is /autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is /autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/. Any suggestions? (full hippocampal-subfieldsT1.log below) Thank you! Jonathan hippocampal-subfieldsT1.log content: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 2016 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf

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Job opening: Computational Neuroscience Faculty
by Kendrick Kay 16 Jun '16

16 Jun '16

Computational Neuroscience Faculty University of Minnesota, Minneapolis, MN, USA The University of Minnesota seeks 2 scientists with documented backgrounds and interests in using brain imaging and computational neuroscience to understand brain function in health and disease. The University of Minnesota seeks to fill two newly-created positions at the level of Assistant Professor, Associate Professor and/or Professor. For each position, rank and tenure status will be commensurate with experience. The research emphasis can be basic, translational or disease-focused neuroscience using innovative modeling and data analysis techniques. Appropriate tenure home departments would depend on the expertise, background and interest and could include: Neuroscience, Radiology, Psychiatry, Neurology, Psychology, Computer Science and Engineering, Biomedical Engineering, or Electrical and Computer Engineering. Irrespective of tenure home department, the successful candidate will be housed at the CMRR, which is an interdepartmental and interdisciplinary research laboratory that provides state-of-the-art instrumentation, expertise, and infrastructure for high field MRI research. CMRR plays a key role in the NIH’s Human Connectome Project and is equipped with magnets ranging in field strength from 3 to 10.5 Tesla for human imaging and up to 16.4 T for small animal model studies. To apply, please see http://neurojobs.sfn.org/jobs/8170600 The University of Minnesota is an Affirmative Action/Equal Opportunity Employer Candidates will have a Ph.D., M.D./Ph.D. or similar degree in neuroscience, biophysics, psychology, biomedical engineering or a related discipline. Background and training should include research experience in a combination of the following domains: cognitive neurosciences, computational neuroscience, and brain imaging technology, in particular Magnetic Resonance Imaging (MRI). The demonstrated ability to work in a collaborative, transdisciplinary and interactive environment is a requirement. The successful candidate will be expected to complement and exploit the unique capabilities that exist in the Center for Magnetic Resonance Research (CMRR, www.cmrr.umn.edu) in high field MRI. -- Kendrick Kay, PhD Assistant Professor Center for Magnetic Resonance Research, Room 2-116 University of Minnesota, Twin Cities Web: http://cvnlab.net E-mail: kay(a)umn.edu

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unit for hippocampus segmentation results
by Fengji Geng 16 Jun '16

16 Jun '16

Hi freesurfer experts, We used the development version of freesurfer 6.0 to segment hippocampus. We are wondering what the unit is for the segmentation results. Thanks, -- Fengji Geng

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Found 0 unique series
by Raney, Talia L. 15 Jun '16

15 Jun '16

Hi FreeSurfer users, I've been running dcmunpack and I get an error that said Found 0 unique series, even though it has dicom files. What does this mean and what could I do to fix the problem? Best, Talia

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wm.mgz edits
by marco mcsweeney 15 Jun '16

15 Jun '16

Dear all, I have a few questions regarding wm.mgz edits. I am very new to this area and have only recently started using Freesurfer so please excuse me if my questions appear naive or misinformed. I have managed to make most of the necessary edits needed to fix skullstrip errors, intensity normalization errors and pial errors, but I am a bit stuck when it comes to fixing topological defects. My question relates to what should or should not be included in the wm.mgz. Apart from the optic chiasm, which I have removed, is it normal to have, what appear to be, multiple specs included in the wm.mgz which when the aseg is loaded turn out to be parts of the amygdala and hippocampus. When I view the smoothwm.nofix these appear as jagged shard like shapes protruding out from the surface. In one publication I saw recently it was suggested that these should be removed but should this be done if they are parts of the amygdala and hippocampus. I am worried about this as these are the 2 main subcortical areas I will be focusing on. Also, is it normal for the wm.mgz to include parts of the cerebral cortex (labelled as such in the aseg). Also, most of the scans I am working with have numerous holes and handles and this is taking a very long time to fix. I have tried to run the automatic topology fixer again. This has helped a bit but the scans still require a lot of edits. Could this be down to the quality of the scans or could it be that I have edited too much - control points for example. I have followed the advice given and have tried not to make too many edits, but having said that it has taken me a very long time. Any advice in relation to any of these questions would be very very very much appreciated. Best wishes Marco

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