Freesurfer

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Research engineer in Neuroimaging wanted
by Olivier Coulon 13 Dec '17

13 Dec '17

Dear Freesurfer list, the 'Institut de Neuroscience de la Timone <http://int.univ-amu.fr>' (INT), Marseille, France, is looking for a research engineer for a duration of one year. The candidate will bring a scientific support to MR neuroimaging research. If satisfactory, the contract will lead to a permanent position as an Aix-Marseille University research engineer at INT. Do not hesitate to pass this annoucement to anybody interested. Full details are available following this link <https://amubox.univ-amu.fr:443/index.php/s/pUDtyMjJEI2VoxP>. contact: olivier.coulon(a)univ-amu.fr -- Olivier Coulon, CNRS Research Director Aix-Marseille University, Institut de Neurosciences de la Timone Faculté de Médecine, 27 Bd Jean Moulin 13005 Marseille - France MeCA Research Group http://www.meca-brain.org https://sites.google.com/site/oliviercoulon olivier.coulon(a)univ-amu.fr <mailto:olivier.coulon@univ-amu.fr> Tel: +33 (0)4 91 32 40 59

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Cortical thickness clarification
by Rockers, Elijah D. 12 Dec '17

12 Dec '17

Hello, I was hoping to get some clarification on how exactly the cortical thickness number is calculated. In the videos, Doug says it's "the distance between the vertex on the white to the vertex on the pial, and you go backwards and forwards to compute the average thickness", and the 2000 paper says "the thickness is computed as the average of this distance measured from each surface to the other". From what I understand, You find the closest vertex on the pial surface from a given white matter surface vertex, then calculate the distance both ways and take the average. Why is the value not the same both ways, i.e., from white to pial, and from pial to white? Thanks very much, Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Qdec Table Loading Error
by Arsenije Subotic 12 Dec '17

12 Dec '17

Dear experts, I'm currently trying to import some of my data into Qdec in order to perform a group analysis on cortical thickness. All of my data was originally in an excel sheet and it had the following variables (fsid, gender, age, and thickness). I tried converting it into a file that would be opened with Qdec. I use a mac and I originally tried to export the file into text editor and I tried saving it as "qdec.table.dat", which had no problems being opened in text edit. However, when I tried loading it into qdec it gives me an error:"error loading the data table". I'm quite new to Qdec (this is my first week trying it). Is there some code that I can use to convert my file into a .dat file so that it can be compatible with qdec? I tried looking through the previous questions and trying some commands (for instance dos2unix -c mac qdec.table.dat, which supposedly replaces LF chars with CR chars). Thanks for your help. Arsenije

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?h.pial_avg in make_average_subject in FS6.0
by Duran, Tugce 12 Dec '17

12 Dec '17

Dear Doug Greve, Where can I find the rh/lh.pial_avg file in fsaverage/surf/ created in freesurfer 6.0? Is this file named differently in FS 6.0 or do I need to process this step (where it makes rh or lh.pial_avg) separetely? Thanks, Tugce Duran

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Thalamus and Thalamus-Proper
by 郑凤莲 12 Dec '17

12 Dec '17

Hi FS professors, I am using FS 6.0 for subcortical structures. I have a doubt about thalamus and thalamus-Proper. I added thalamus to brainmask.mgz in Freeview, it shows nothing. However, choose thalamus-Proper, it's ok. I just want to ensure whether the thalamus-Proper in Freesurfer is the same as the thalamus (one of the deep gray matter nuclei) mentioned in other papers. Thank you very much in advance. Sincerely, Zheng

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--
by Dijkshoorn, A.B.C. (Aicha) 12 Dec '17

12 Dec '17

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Create surface Label from MNI152 Coordinate
by Bastian Cheng 12 Dec '17

12 Dec '17

Dear Freesurfer Experts. Is there a way to create a freesurfer surface label from entering a MNI152 coordinate? I would like to extract cortical thickness data from fMRI peak activation coordinates. I am aware that I can use tcl with tksurfer: mar_vertex X 1 labl_new_from_marked_vertices labl_dilate However as far as I know I can only input vertex numbers, not coordinates. Any helpt would be greatly appreciated!

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Re: [Freesurfer] freesurfer version update issue in MacOS
by 강준영 12 Dec '17

12 Dec '17

Thank you for your answer, Bruce and Eugenio. Then the way to do that might be,, 1. Install new version of freesurfer to a new location. 2. Move previous data from old version freesurfer path to the new location. 3. Do what I want (hippo subfield) Right..? Thanks. Sincerely, Joonyoung. 2017. 12. 12. 오후 5:56에 "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk>님이 작성: The answer is yes, indeed. Just be careful when you report your results, specifying which version you used for what. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 12/12/2017, 02:06, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote: Hi Joonyoung. I'll leave this for Eugenio, but I think the answer is yes cheers Bruce On Tue, 12 Dec 2017, 강준영 wrote: > Hi Bruce! > Thank you for your fast and kind answer. > > I have one more detailed question that I forgot to ask.. > > The main reason I want to update freesurfer is to use better hippocampal subfield and I want to make > the subfield based on my previous data (in the older version freesurfer path) > > I expected to do recon-all without -all option (but only with hippocampal subfield option) in the > new version because I've already done "recon-all -subjid ${subject} -all -hippo-subfields" in the > older version. > > Can I do it with new version installed in a new location? > > Thanks again! > > Sincerely, > > Joonyoung. > > > 2017-12-12 10:44 GMT+09:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > Hi Joonyoung > > you can just install the new version in a new location and point your path at it instead > of the older version. > > cheers > Bruce > On Tue, 12 Dec 2017, 강준영 wrote: > > Hello! > > I'm Joonyoung Kang, a graduate student in neuroscience. > > I've been using freesurfer over an year and I realized that I've used an old > version of it. > > So I decided to update freesurfer and I couldn't find a way to do that. > > Do I just have to re-install the new version of freesurfer? > > If so, do I have to make a backup for my previous data in freesurfer > folders? > > Thank you! > > > > p.s. > I'm currently using MacOS X (10.11.6), > freesurfer-Darwin-lion-stable-pub-v5.3.0, and > Xquartz 2.7.11 > > > Sincerely, > > Joonyoung Kang. > > > _______________________________________________ > 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. > > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freesurfer version update issue in MacOS
by 강준영 12 Dec '17

12 Dec '17

Hello! I'm Joonyoung Kang, a graduate student in neuroscience. I've been using freesurfer over an year and I realized that I've used an old version of it. So I decided to update freesurfer and I couldn't find a way to do that. Do I just have to re-install the new version of freesurfer? If so, do I have to make a backup for my previous data in freesurfer folders? Thank you! p.s. I'm currently using MacOS X (10.11.6), freesurfer-Darwin-lion-stable-pub-v5.3.0, and Xquartz 2.7.11 Sincerely, Joonyoung Kang.

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Global Signal Scaling in FSFAST Pipeline
by Taylor, Johnmark 11 Dec '17

11 Dec '17

Hello, When using preproc-sess and selxavg3-sess, how is global mean scaling handled? Is the session-wide (4D) mean subtracted, is each volume's mean subtracted, or neither? Thank you very much, JohnMark

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