Freesurfer

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30063 discussions

Generating Mean thickness surface file for volume ROI mask
by Dev vasu 16 Oct '17

16 Oct '17

Dear all, I have a ROI mask volume file and i would like to generate Mean cortical thickness surface file (i.e lh.ROI.thickness.fsaverage.mgh and rh.ROI.thickness.fsaverage.mgh) , could some one guide me how i could obtain such file. I have 120 subjects and I have done recon-all for all subjects. Thanks Vasudev

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How to obtain a label for Custom ROI mask
by Dev vasu 16 Oct '17

16 Oct '17

Dear all, I have custom ROI mask ( MNI Space ) that i have prepared from Jülich atlas , I would be like to obtain corresponding surface label file, Could you please guide me necessary the steps that i have to follow inorder to obtain corresponding label for my mask. Thanks Vasudev

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Questions about the transformation of DKatlas from surface to volume
by Zhiqiang Sha 16 Oct '17

16 Oct '17

Hi, I have three questions about the transformation. (1) Is Desikan-Killiany Atlas in Talairach space? The volume was transposed onto the "inflated" cortical surface based on the image in freesurfer/average/mni305.cor.mgz ? (2) DK_atlas seems to be obtained from the inflation of interface of gray and white matter. Did you release the inflated surfaces based on the inner and outer surfaces ? (3) I have transformed this atlas from surface to volume using mri_aparc2aseg with default parameters (e.g. mri_aparc2aseg --s bert). Is this transformed volume in Talariach space ? Do I need transform it to MNI space again ? I am looking forward to your reply. Thank you very much ! Best Wishes, Zhiqiang Sha

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New Openings for Postdoctoral Fellows
by Thomas Yeo 16 Oct '17

16 Oct '17

Dear Everyone, My lab has new openings for postdoctoral fellows. Please see job descriptions here: https://yeolab.weebly.com/jobs.html Thanks, Thomas

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freesurfer output
by Z Hessam 14 Oct '17

14 Oct '17

Hello FreeSurfer Developers, I can't access numerical value of each volume after segmentation of MRI images. how can i access that? does "freesurfer" produce such value for each segment? Best, Hessam

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Errors on compiling FreeSurfer
by Aziz Nanthaamornphong 13 Oct '17

13 Oct '17

Hi Experts, I tried to compile FreeSurfer on Ubuntu 16. When I ran a command 'make check', I got these error messages: */usr/bin/ld: warning: libtk8.4.so <http://libtk8.4.so>, needed by /home/aziz/centos6-x86_64-packages/KWWidgets/current/lib/KWWidgets/libKWWidgets.so, not found (try using -rpath or -rpath-link)/usr/bin/ld: IconLoaderTest.o: undefined reference to symbol 'Tcl_GetStringResult'//usr/lib/x86_64-linux-gnu/libtcl8.4.so <http://libtcl8.4.so>: error adding symbols: DSO missing from command linecollect2: error: ld returned 1 exit statusMakefile:947: recipe for target 'IconLoaderTest' failedmake[2]: *** [IconLoaderTest] Error 1* Best Wishes, Aziz.

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mris_anatomical_stats: segmentation fault core dumped
by Keiko McCreary 13 Oct '17

13 Oct '17

Hello Freesurfer developers, After succesfully running two recon-all's (error free), the third failed during mri_anatomical_stats. Any help would be appreciated (I am new to freesurfer). I found this error reported but not when recon-all has already successfully ran. Linux xubuntu-virtual box Freesurfer v5.3 recon-all.log is attached Thank you, Keiko -- J. Keiko McCreary, PhD Postdoctoral Fellow SARTAN-AD Clinical Research Coordinator (Lethbridge Site) Canadian Centre for Behavioural Neuroscience University of Lethbridge Office: EP 1218 Phone: 403-394-3985 Cell: 403-393-0181 keiko.mccreary2(a)uleth.ca or @gmail.com

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cortical surface area
by Alexopoulos, Dimitrios 13 Oct '17

13 Oct '17

What measure is for the cortical surface area? The measure in the aparc.stats file states 'WhiteSurfArea' Jim ________________________________ 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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Qdec image considering multiple variables
by 박경일 13 Oct '17

13 Oct '17

Dear FS developer, I am a FS beginner and trying to make QDEC images of cortical thickness difference (color-coded inflated brain) between groups. No problem when fsid, diagnosis, age, and sex were only included in qdec.table.dat file. However, adding any other factors such as hypertension, diabetes... etc. made error messages in a terminal window. I guess this error came from the some blank data, because some subjects do not have any information regarding hypertension or diabetes. Is there a way to make a figure showing a results of multivariate analysis? Thanks a lot in advance. Kyung Il Park, MD

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Re: [Freesurfer] volume vs surface-based and surface smoothing
by Matt Glasser 12 Oct '17

12 Oct '17

Volume-based registration is fine with subject as you have the same brain that you are registering (ideally such registrations are 6 DOF rigid registrations and any image distortions are corrected for). Surface-based registration is better when comparing across subjects due to the variability in cortical folding patterns and locations of areas relative to folds across subjects. Smoothing is best done on the surface if it is done at all. Smoothing in the volume harms one¹s spatial localization precision much more than smoothing on the surface for an equivalent FWMH in mm. It is worth keeping in mind that smoothing on the surface does still blur across cortical areal boundaries, however, so for many analyses it may be better to average within cortical areas rather than to smooth a lot. Peace, Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Alissa Stafford <alissa.stafford(a)jhu.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, October 12, 2017 at 12:29 PM To: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] volume vs surface-based and surface smoothing Hello, I am trying to understand the preprocessing functions to successfully complete surface-based analysis. I am confused about what is happening on the volume level and when exactly the surface is being created. My questions revolve around register-sess and rawfunc2surf-sess. Registration has 2 parts: 1: the native anatomical space is registered with the fsaverage space. This is happening during recon-all. 2: native functional data is registered with the native anatomical data. This is happening during register-sess in preprocess-sess. Aren¹t these both volume-based registrations? If not when are the surfaces created? My concern is that it is volume-based and I was under the impression from this article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/ , that all registrations should be done on the surface. I am also confused about rawfunc2surf-sess. I believe up until this function in preprocess-sess, everything has been done in the volume so this is the first step that is done in the surface, is that correct? And then does this do smoothing? I realized it has a fwhm input option so it must smooth. So is this where the functional data is now expressed in the surface and it also smooths? Or does surfsmooth-sess need to be run in addition to rawfunc2surf-sess? I basically just want to be making sure I understand when registration is volume-based or surface-based and when it¹s appropriate to use volume-based. And I was using the rawfunc2surf function assuming it was for smoothing, but I am not so sure if this only creates the surface or also smooths. Thanks, Alissa _______________________________________________ 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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