Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

change the algorithm
by N Saf 20 Jun '16

20 Jun '16

Dear Freesurfer, I wonder if it is possible to segment just one sub-cortical structures like hippocampus by changing the algorithm (e.g. according to spatial prior knowledge divided the image to some sub-images and do analysis just on that sub-image which we sure the hippocampus located)and by that reducing the processing time ? and another general question I have is that in sub-cortical segmentation commands 1to12 commands of -all flag which parameters can I change to affect the outputs? Sincerely, Nazanin

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Using Freesurfer commands in matlab
by HARI GURAGAIN 18 Jun '16

18 Jun '16

Dear Freesurfer, I am using the new development version of freesurfer ( ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev) I am trying to call some of the freesurfer commands like: mri_coreg or some other. When I use the something like the following in Matlab: command='/Applications/freesurfer/bin/mri_coreg' and the below: [status,cmdout]=system(command) It is showing a weird error message like below: ########################################### dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib ########################################### I really don't understand why this error is coming. I have seen people have used the mri_*** commands a lot of times in matlab but unfortunately, it shows the above error in my case. Is it the error from Matlab, freesurfer, mac or something else? Any help in solving this issue will be greatly appreciated. Thank you.

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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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