Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

cortical thickess of brains from a 7T scaner with resolution 0.6*0.6*0.6
by Zhangyuanchao 14 Sep '09

14 Sep '09

Dear expert, Our group have some data scaned from 7T scaner. I would like to calculate the cortical thickness of the data, however, when I processed them as I do for data from 3T scaner, I can not run recon-all command successfull to the end. Could you give me some suggestions on how to obtain the cortical thickness measure for the 7T data? Are there any parameters that I should chang when processing 7T data? Thanks a lot! Yuanchao ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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(no subject)
by Kim, Miyoung 11 Sep '09

11 Sep '09

Hi. Just a quick question - is cortical parcellation performed based on the pial line (red line) or the cortical segmentation (brown shade)? The reason for this question is that after recon2 we have an area in the lower occipital cortical region that is shaded as "cerebellum" (see attached) although the pial line seems to have correctly outlined it. Is this a potential problem that we need to fix and if so what should we do? Thanks for your help in advance! Miyoung ________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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Coordinates of center of gravity of FS parcellations
by Jürgen Hänggi 11 Sep '09

11 Sep '09

Dear FS experts I am looking for the MNI or Tal-coordinates of the center of gravity (COG) of the aparc.a2005s parcellations of the FS average brain. Do these coordinates exist or how can I compute them easily? Thanks Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Longitudinal analysis with old version
by l.gutierrez＠ion.ucl.ac.uk 11 Sep '09

11 Sep '09

Hi, We have installed the 4.0.1 version and we are starting the longitudinal analysis. I have some problems with -base flag( recon-all -base <baseid> -base-insubj <tp1subjid> -base-insubj <tp2subjid> ... -all). Should 4.0.1 version be one problem in order to do that? Many thanks Leticia >

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Calculating ROI size from label, min ROI size
by Agnieszka Burzynska 11 Sep '09

11 Sep '09

Dear all, I have 2 questions: 1) I created labels for some ROIs on fsavgerage (qdec analysis). I got statistics from these rois for each individual subject (by map-to-subjects, etc.), but what I am now interested in is to know the size of the ROI on the group level (so on the fsaverage surface). Following up on the recent post, I tried 'mris_curvature_stats' but it gives error if I dont specify the subject. I am not to familiar with different commands, perhaps there is another one that would work? 2) Is there any "golden standard" for the minimum p-value or minimum size of an ROI to be considered a significant finding? I expect this may differ quite a lot, depending on how strong the effects of a variable on cortical thickness can be expected. Still, if you could comment on this or refer me to some literature, I would be very grateful. Thank you a lot, Best regards, Aga

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qdec permission denied
by Ahmed, F, Me <fahmed＠sun.ac.za> 11 Sep '09

11 Sep '09

Hello, I have managed to get FS installed onto my Centos virtual machine and I'm currently trying to carry out the testing of my installation. I got to the qdec part and got the following: [fsl@localhost freesurfer]$ qdec qdec.bin: error while loading shared libraries: /usr/local/freesurfer/lib/vtk/lib/vtk-5.2/libvtkRendering.so.5.2: cannot restore segment prot after reloc: Permission denied [fsl@localhost freesurfer]$ Can someone please explain why this is happening? Thank you

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Converting single voxel to surface space
by benjamin.deen＠yale.edu 10 Sep '09

10 Sep '09

Hi, I'm wondering how to convert a single voxel coordinate in 2mm MNI152 space to a location on a cortical surface representation of MNI space generated by Freesurfer. My broader goal is to present a set of coordinates collected for a meta-analysis on surface space. Thanks, Ben Deen Department of Psychology, Yale University

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multimodel wm hypointensity labeling?
by Victoria Williams 10 Sep '09

10 Sep '09

Hello, Are there any freesurfer tools that allow labeling of wm hypointensities using imput from both T1 and T2 or lowb images? Also, I was wondering if there was further documentation for the use of the mri_relabel_hypointensities command? I got the impression this script dealt somehow with cortical surface hypointensities and not wm hypointensities... is that correct? (PS: the -a <annotation> flag is returned as being unrecognized when running this script) Thanks a bunch! Tori

2 1

Correlating two surfaces
by Nicolas Cherbuin 10 Sep '09

10 Sep '09

Dear All, I would like to correlate two surfaces with glmfit e.g. thickness and curvature but I don't seem to be able to find any document explaining how to do that. Could you please point me in the right direction? Thanks Nic

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Fwd: About the workflow of cortical thickness measurement.
by QQ Liu 10 Sep '09

10 Sep '09

---------- Forwarded message ---------- From: QQ Liu <qqliu16(a)gmail.com> Date: 2009/9/10 Subject: About the workflow of cortical thickness measurement. To: fischl(a)nmr.mgh.harvard.edu Hi Bruce, I want to do the cortical thickness measurement and I'm not sure the workflow in FreeSurfer commands in detail, because I'm a new hand to do fMRI processing and don't know anything about brain images before. Now for example, I have some subjects in two groups and there are 10 subjects in each group. I want to do the cortical thickness comparison between them. Do the workflow as follows? First, I run the "recon-all -s subjid -all" for every subject(then that needs 20times). Second, do group analysis with the thickness files? Can I run the group analysis automatically? There are something I want to clearly know: What functions should I use to get the average thickness of each group? Is there a simple function to do the work automatically? Is there a function to plot the subjects as a dot in a image and a curve to separate them? I'm looking forward to your response. I much appreciate your help. Thanks a lot. ------------------------ Best wishes. Q.Q Liu +8613426232824 qqliu16(a)gmail.com -- Best wishes. Q.Q Liu +8613426232824 qqliu16(a)gmail.com

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