Freesurfer September 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
131 discussions

errors
by Zhangyuanchao 15 Sep '09

15 Sep '09

Dear experts, I have some data of format .dc3, I would like to calculate the cortical thickenss of the data. I launched the command "recon-all -i subjectname/***.dc3 -s subjectname", In addition, I also tried "recon-all -i ****** -force", For some of the subjects, It runs without error, while for others it exited with errors. The error log is "file not find or unknown file type for file **/**/**/**.dc3". How can I fix this problem? 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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Help in Qdec
by Gergely Orsi 15 Sep '09

15 Sep '09

Hi All! Could anyone help me in 3 questions regarding Qdec and freesurfer? 1, I'd like to know what Curv does stand for? Because We have a highly significant difference in Curv among our groups unilaterally. 2. Is it possible to list the total brain volume for all my subjects? If so, how to do that. 3, And finally, could anyone cite an article where the processing steps of recon-all is described or mentioned. I need it for the methods, but i don't really know what happens to my data if i give the recon-all -autorecon-all command. Thank you very much for your help! Gergő

2 1

FS versions
by Jose Soares 14 Sep '09

14 Sep '09

Hi all, I am doing a study with FreeSurfer (80 subjetcs till now), and I have cases reconstructed with the versions 4.2 and 4.3. I want to continue the study, and install the 4.5 version. I saw that in this release the Destrieux Atlas was updated. Could i compare the cases from the versions 4.2, 4.3 and 4.5? Is it correct or I only should compare cases (volumes, thickness, ...) between the same version? Thanks for the help, Miguel. ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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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. ----------------------------------------------------------------------------

1 0

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

1 0

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

2 4

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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Freesurfer September 2009