[Freesurfer] can I apply freesurfer significant clusters as ROI in fMRI study?

Dear freesurfer experts, I searched on the wiki but can not figure out how to solve this problem: I found some significant clusters on graymatter thickness, how can I use it as a ROI in my functional MRI study? I have both structure and function data of the same subjects, so I can either do it

[Freesurfer] workflow of trouble shooting?

Dear Freesurfer experts, Sorry I am posting this again, I do not know I missed you reply or nobody replied yet. Can anybody help? I am learning to do trouble shooting on recon-all results. But after read materials on the wiki, I am confused about the workflow. According to the tutorial slices,

[Freesurfer] workflow of trouble shooting?

Dear Freesurfer experts, I am learning to do trouble shooting on recon-all results. But after read materials on the wiki, I am confused about the workflow. According to the tutorial slices, the work flow should be 1,recon-all �Cautorecon1 (Stages 1-5) 2,Check talairach transform, skull strip,

[Freesurfer] what is inflating to sphere rms error?

Dear Freesurfers, I am new to freesurfer and I am afraid of doing something wrong, so I am writing to ask is this error indicating something wrong with my data? Any help is appreciated. below are detials of my question. Thank you! I used freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 with th

[Freesurfer] ERROR: comparison in expression (FS with SGE)

Dear Matt and freesurfers, I am encounting this old problem, that is, using fsl_sub to launch FreeSurfer jobs in SGE and get this error message: (standard_in) 2: Error: comparison in expression and freesurfer stoped. But running freesurfer without fsl_sub is OK (using fsl_sub to launch other c

[Freesurfer] ask about demean in GLM model setup

Dear experts, I am confused by demean during GLM model setup and would like someone here can help me. Thanks! Suppose I have a continuous behavior data and I want to find out which brain region(s) correlated with it. The simple way is to calculate correltation between brain data and behavior d

Re: [Freesurfer] How to switch order of Talairach and nu-correctionstages in recon-all

Hi experts, A quick question: I installed FS 5.1 a month ago, should I replace with this recon-all file and run it with flag -clean-tal in the future? why the steps have to be switched? Thanks! 2012-04-19 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and

[Freesurfer] how to extract data from significant cluster?

Dears freesurfers, I have just finished a GLM analysis in freesurfer and found a cluster whose thickness significantlyassociated with some behavior index. I would like to extract data from this cluster for further analysis, i.e., mean thickness in this cluster for each subject. How could I ext

Re: [Freesurfer] about QAtools

Got it. Thanks Louis! 2012-03-27 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 发件人： Louis Nicholas Vinke 发送时间： 2012-03-26 23:27:09 收件人： chenchunhuichina 抄送： freesurfer 主题： Re: Re

Re: [Freesurfer] about QAtools

China 100875 发件人： Louis Nicholas Vinke 发送时间： 2012-03-06 23:50:05 收件人： chenchunhuichina 抄送： freesurfer 主题： Re: [Freesurfer] about QAtools Hi Chunhui, I believe this is a dependency issue, since the convert command is part of the ImageMagick Studio. You'll need to

Re: [Freesurfer] about QAtools

： chenchunhuichina 抄送： freesurfer 主题： Re: [Freesurfer] about QAtools Hi Chunhui, I believe this is a dependency issue, since the convert command is part of the ImageMagick Studio. You'll need to download and install the binaries (http://www.imagemagick.org/). I'll make of note of this on the

[Freesurfer] about QAtools

Dear Freesurfer experts, I installed the QAtools and tried a subject with this commond: $QA_TOOLS/recon_checker -s sub13 -snaps-detailed -gen-asegLUT aseglut.txt but I encountered the following Error message, can someone help me figure it out? Any help is appreciated, thanks! Error message 1: Re

[Freesurfer] Ask question about QAtools

Dear Freesurfer experts, I installed the QAtools and tried a subject with this commond: $QA_TOOLS/recon_checker -s sub13 -snaps-detailed -gen-asegLUT aseglut.txt but I encountered the following Error message, can someone help me figure it out? Any help is appriciated, thanks! Error message 1: Re

[Freesurfer] Ask question about QAtools

Dear Freesurfer experts, I installed the QAtools and tried a subject with this commond: $QA_TOOLS/recon_checker -s sub13 -snaps-detailed -gen-asegLUT aseglut.txt but I encountered the following Error message, can someone help me figure it out? Any help is appriciated, thanks! Error message 1: Re

[Freesurfer] (no subject)

Hello FreeSurfer users, I may be asking a stupid question but it really troubled me a while. I converted dicom files to nift using dcm2niigui (MRIcron). In fslview, it displayed in RAS coordinates, but template of FSL are in LAS coordinates. Should I filp L-R before doing any further analysis?

Re: [Freesurfer] Reorientation of raw images?

in some regions like left amygdata, the difference exceed 5% 2010-02-02 Chunhui Chen _ Institute of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 发件人： Bruce Fischl 发送时间： 2010-01-22 12:38:11 收件人： chenchunhuichina 抄送： 主题： Re: Re

[Freesurfer] Reorientation of raw images?

38:11 收件人： chenchunhuichina 抄送： 主题： Re: Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data no, that shouldn't matter On Fri, 22 Jan 2010, chenchunhuichina wrote: > May I ask a related question? > > My structural data are acquired in sagital view, do I have to re-o