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Re: [Freesurfer] pial surface editing
by Harms, Michael 30 Aug '13

30 Aug '13

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Rejoindre mon réseau sur LinkedIn
by Leila Nasehy via LinkedIn 29 Aug '13

29 Aug '13

LinkedIn ------------ Leila Nasehy souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Leila Nasehy http://www.linkedin.com/e/-qq80um-hkysl7zy-4d/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Leila Nasehy http://www.linkedin.com/e/-qq80um-hkysl7zy-4d/rso/283777087/4DOv/name/66471… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hkysl7zy-4d/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Question about mni305 subcortical ROI mask
by Omar Singleton 29 Aug '13

29 Aug '13

Dear List, I have a couple questions I need help with. First, I am trying to constrain my subcortical (mni305) analysis with mri_glmfit to a certain ROI. Can I run mri_glmfit with the --mask flag and use a volume mask to constrain it to this space? Second, if so, then how do I create a mask from the subcortical activation map I have from my fsfast analysis. Is there a way like in tksurfer to add all voxels up to a certain threshold to a mask? Thanks! Best, Omar

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Error message of Ubuntu 13.04 and Centos4 & Centos6
by JoJo 29 Aug '13

29 Aug '13

Dear Freesurfer experts, I installed FS Centos4-64(and also tried Centos6) on Ubuntu 13.04. I followed the commands in tutorial and got error message, listed as follows. (Nevertheless, FS can read in volume and surface from GUI.) Another question is, which one of Centos4 or Centos6 is more suitable for Ubuntu 13.04? 1. tkmedit bert orig.mgz Couldn't create output file .xdebug_tkmeditReading /usr/local/freesurfer/tktools/tkm_common.tcl 2. tkmedit -segmentation mri/aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt bert norm.mgz Couldn't create output file .xdebug_tkmeditmghRead(/usr/local/freesurfer/subjects/bert/mri/mri/aseg.mgz, -1): could not open file a window pop up: Error: loading segmentation mri/aseg.mgz Couldn't import the segmentation volume. Tkmedit couldn't read the segmentation specified. This could be because the segmentation volume wasn't a valid COR volume directory. (Note: In fact, I can load segmentation volume from window.) 3. tksurfer bert rh pial Couldn't create output file .xdebug_tksurfersubject is bert Thanks for your help, JoJo

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Fwd: how to transform white or pial surface of one subject into corresponding surface of another subject
by David Romano 29 Aug '13

29 Aug '13

Hi everyone, I'm new to FreeSurfer (so sorry in advance for any failures to make sense!), and have read through Bruce Fischl's '99 papers on how FreeSurfer maps the yellow (white?) surface onto a template sphere (equipped with convexity information), and have tried to go through the introductory material on the wiki, but I can't seem to figure out an answer to my question. Ideally, given subjects A and B, I'd like to be able to find a one-to-one map between the white surface of A given in A's native volume space, and the white surface of B, given in B's native volume space. My (vague) understanding from the '99 HBM paper is that the transformation of the white surface proceeds in two steps: first the mesh in native space is "spherized" in a way that minimizes metric distortion, and then the resulting mesh is warped to optimize a match between the convexity at each mesh vertex and the convexity at the point of the spherical convexity template that the vertex is mapped to (by "spherizing" followed by warping). >From this, I assume that a vertex in native space may be mapped to a non-vertex in the spherical convexity template, which could make impossible to have a sensible one-to-one map from the white surface mesh of subject A to the white surface mesh of subject B (via maps back and forth to the template). But does the corresponding map between the full white surface of subject A to the full white surface of subject B exists? And if so, are there FreeSurfer commands could I use to extract this map explicitly, or might it only exists in form of calculations that aren't stored? I hope this makes some sense, or at least that if it doesn't, someone might be able to point me to the right resources that could clear up my confusion. Thanks in advance for your help and your patience! Best regards, David Romano P.S. I have the same question about the pial surface, but this seems like it would be an order of magnitude more complicated.

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Peirhinal cortex thickness
by Gomar, Jesus 29 Aug '13

29 Aug '13

Dear all, I am interested on getting thickness measures of the perirhinal cortex. I am using version 5.3 and I am aware that a label for the perirhinal cortex has been created in version 5.2. However, when I run recon-all I don't get thickness measures of the perirhinal cortex (just as I do for instance for entorhinal cortex of middle temporal cortex) In summary, my questions are: 1. Is the calculation of perirhinal cortex thickness automated in version 5.3? 2. If not, Can I get some info on how to proceed to obtain this measure? Thanks in advance for any advice! Jesus J. Gomar The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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generating new surface
by Ian Charest 29 Aug '13

29 Aug '13

Dear Freesurfers, I need to generate a surface which lies halfway between the wm/gm border and the pial surface so that I can then import it in matlab using read_surf.m to get the vertex coordinates and faces for the surface that, as I said, would not be the pial surface, but defined at half cortical thickness. I looked at mri_vol2surf --help, and its option --projfrac 0.5 seemed to be what I wanted, but I don't know how to call mri_vol2surf for the specific needs I have. Also, mri_vol2surf produces an overlay mappable onto a surface and not a surface per se, so maybe what I am looking for lies elsewhere. Any help would be highly appreciated!! ian

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Re: [Freesurfer] Thickness vertex by vertex
by Giusy Chinnici 28 Aug '13

28 Aug '13

Thanks all, I did it :) Cheers Giusy Inviato da iPhone Il giorno 28/ago/2013, alle ore 18:40, Avram Holmes <holmes(a)wjh.harvard.edu> ha scritto: > check the .vol values I think they should match those from read_curv. > > Avram > > > On Wed, Aug 28, 2013 at 11:37 AM, Giusy Chinnici <giusy.chinnici(a)gmail.com> wrote: >> Thanks all, >> >> I opened the file subj/surf/?h.thickness with MATLAB using the function read_curv(subj/surf/lh.thickness). I obtained a vector with dimensions nverticesX1, but I need also the vertex IDs. Are vertex IDs in the thickness file ordered from 0 to n? Is there some other way to obtain a table with vertex IDs and the corresponding thickness values? >> >> @avram:as you suggested, I tryed to use MRIread('subj/surf/lh.thickness.mgh'), it doesn't return the desired values. You can find the result in the attachment . >> >> thanks >> Giusy >> >> >> 2013/8/28 Avram Holmes <holmes(a)wjh.harvard.edu> >>> Giusy, >>> >>> You can access vertex level info in Matlab with MRIread('SUBJECT.FILENAME'). >>> >>> Avram >>> >>> >>> On Wed, Aug 28, 2013 at 8:42 AM, Giusy Chinnici <giusy.chinnici(a)gmail.com> wrote: >>>> Dear all, >>>> >>>> Is there available a function that, given a certain ROI, returns per vertex thickness (not the average thickness)? >>>> >>>> Thanks >>>> Cheers >>>> >>>> Giusy Chinnici >>>> _______________________________________________ >>>> 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. >>> >>> >>> >>> -- >>> Avram Holmes PhD >>> Instructor in Psychiatry, Harvard Medical School >>> Assistant in Research, Massachusetts General Hospital >> >> >> >> -- >> Giusy Chinnici > > > > -- > Avram Holmes PhD > Instructor in Psychiatry, Harvard Medical School > Assistant in Research, Massachusetts General Hospital

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Brainhack 2013 Invitation and Registration Link
by MCLAREN, Donald 28 Aug '13

28 Aug '13

Dear colleagues, I wanted to draw your attention on the upcoming Brainhack 2013, which is being held from October 23-26 at the Centre International d'Études Pédagogiques, Sèvres, France (just outside of Paris). Brainhack 2013 is a unique workshop with the goals of fostering interdisciplinary collaboration and open neuroscience. The structure builds from the concepts of an unconference and hackathon: The term “unconference” refers to the fact that most of the content will be dynamically created by the participants — a "hackathon" is an event where participants collaborate intensively on projects. Participants interested in neuroimaging from any discipline are welcome. Ideal participants span in range from graduate students to professors across any disciplines willing to contribute (e.g., mathematics, computer science, engineering, neuroscience, psychology, psychiatry, neurology, medicine, art, etc…). The primary requirement is a desire to work in close collaborations with people outside of your specialization in order to address neuroscience questions that are beyond the expertise of a single discipline. One should come to brainhack ready to engage into collaborative projects, and with some material (slides, ideas, data, tools) ready to start a project or a discussion panel. Brainhack will build on the successful techniques used in other unconferences to keep the meeting focused and productive. It is possible to start a project and build a team as early as today. Please have a look at the website for information on the conference and a sample of projects (from Brainhack 2012): http://www.brainhack.org The Preliminary Schedule for Brainhack 2013 is available online: http://www.brainhack.org/?page_id=27753 ***NEW*** We will be accepting and publishing Brainhack 2013 abstracts. Abstracts should be submitted when you register. Registration is now open: http://www.brainhack.org/?page_id=27743 Please share this with your friends and colleagues. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Thickness vertex by vertex
by Giusy Chinnici 28 Aug '13

28 Aug '13

Dear all, Is there available a function that, given a certain ROI, returns per vertex thickness (not the average thickness)? Thanks Cheers Giusy Chinnici

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