Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Re: [Freesurfer] GLM_Fit Question
by Arkadiy Maksimovskiy 18 Jun '16

18 Jun '16

Hi Freesurfers, I am having a similar problem with the FSGD file as the user indicated at this thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html I am trying to access the script that Doug wrote in order to fix it, however, the link to download the script does not seem to be working. I was wondering if someone might be able to upload it again. Thank you in advance for your help, Arkadiy

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ERROR: mpr2mni305 failed
by Marita Partanen 17 Jun '16

17 Jun '16

Hi there I running freesurfer-Darwin-lion-stable-pub-v5.3.0 on a Mac 10.10.5. I have run recon-all successfully in the past, but now I am getting an error of mpr2mni305 failed, see transforms/talairach_avi.log This issue appears the same as a recent post http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg47393.html but I couldn't see a solution. Any ideas? Here's the full error log: /Users/ophthalmologylab/Studies/Dyslexia_MRI/Intervention/freesurfer/DEGDY001B/mri /Applications/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Darwin cfri2163m.bcricwh.lan 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 Fri Jun 17 13:29:22 PDT 2016 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=8.14, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.91038e-11, -3.72529e-09) j_ras = (-3.72529e-09, -5.82077e-11, -1) k_ras = (7.27596e-12, 1, -5.82077e-11) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 126.275; 0.000 -0.000 1.000 -112.522; -0.000 -1.000 -0.000 132.333; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Fri Jun 17 13:29:25 PDT 2016 /Applications/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 17 13:29:25 2016 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- dyld: Library not loaded: /usr/local/gfortran/lib/libgcc_s.1.dylib Referenced from: /Applications/freesurfer/bin/gauss_4dfp Reason: image not found Trace/BPT trap ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133 ERROR: mpr2mni305 execution aborted _________________________________ Marita Partanen, M.Sc., M.Ed. Ph.D. Candidate in School Psychology The University of British Columbia 2125 Main Mall Vancouver, BC V6T 1Z4 partanen(a)alumni.ubc.ca<mailto:partanen@alumni.ubc.ca>

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controlling for ICV in LME
by Clara Kühn 17 Jun '16

17 Jun '16

Dear FreeSurfer experts, I conducted a study with 3 groups of children (2 trainings, 1 control) and I want to analyze them longitudinally with LMEs. While preparing my data 2 topics came up that I would like to know more about. A. controlling for ICV/mean thickness/surface area 1) I want to look at changes in cortical thickness and surface area at the whole brain level. Would I then have to control for mean thickness/ area, respectively, per parcellation? Or rather ICV? 2) Is it the same for looking at changes in thickness and area in different ROIs? 3) Since I have (up to) 3 scans per kid, do I include mean thickness/area/ICV for each scan or should I use it from baseline or a mean of all scans? B. demeaning covariates 1) Is it necessary to demean the covariates? I have not seen any hints on the FS wiki pages about that yet. 2) Would I also have to demean the dependent variable (in my case whole brain cortical thickness/surface area)? Thank you! Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Postdoctoral Position in Infant MRI Analysis at UNC-Chapel Hill
by gangli 17 Jun '16

17 Jun '16

Postdoctoral research associate positions are available in the Department of Radiology and Biomedical Research Imaging Center (BRIC) at the University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current focuses are to better understand the dynamic and critical early brain development in both health and disease, via multimodal neuroimaging analysis. The successful candidate will support our efforts either in advancing neuroimaging analysis technologies or in neuroscience applications. We are seeking highly motivated individuals who have extensive research experience in neuroimaging analysis (e.g., structural, diffusion or functional MRI) and demonstrated academic excellence, including publications in first-class journals and conferences. The candidate should have a Ph.D. (or equivalent) in Neuroscience, Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or related fields. Good command of programming tools including Matlab, C++, Linux, and scripting are necessary to carry out the research work in this group. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis. If interested, please email resume to Dr. Gang Li (gang_li(a)med.unc.edu <https://outlook.unc.edu/owa/redir.aspx?SURL=r-ilRGXKGkv6jOyzGz3FjAPbDG9VNfM…> ). For more information, please visit: http://www.unc.edu/~gangl/contact.html <https://outlook.unc.edu/owa/redir.aspx?SURL=HcVZFV_dUot9RdWseT8XGNDO-UYKJHN…> .

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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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