Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR

Hi Doug, Doug, it's very kind of you to help me all the time. Thanks. I didnot do anything except move all DICOM files into one folder which is the same as other subjects. According your prompt, I checked the DICOM and found that this subjects have two 3d imag. And I separated the data into 2

Re: [Freesurfer] New features in TRACULA

Hi Ruth - It's possible that your scans don't have any slices with excessive intensity drop-out. You can gauge that visually, by checking if there are any slices that are much darker than their neighbors. Any operation that performs interpolation on the image intensity values, and thus

Re: [Freesurfer] visualizing lh.gender_age.thickness.10.mgh after mris_preproc

Hi Doug, I just found the module. All the best. 2013-12-19 Rujing Zha 发件人：Rujing Zhacharujing...@163.com 发送时间：2013-12-19 15:02 主题：Re: [Freesurfer] visualizing lh.gender_age.thickness.10.mgh after mris_preproc 收件人：Douglas N Grevegr...@nmr.mgh.harvard.edu

Re: [Freesurfer] Does this registration need to be fixed?

Hi Bruce, Thanks! I looked at the other slices and they look similar to the screenshot I sent you; to my untrained eyes they look like they could use a slight rotation and shift. I am assuming that means it is a reasonable registration. However, I am not sure how much a talairach registration

Re: [Freesurfer] mri_glmfit error

On 12/18/2013 11:14 PM, Rujing Zha wrote: Hi Doug and others, Thanks Doug. For the 2nd problem: I understand orthogonalization between nuisance variables. I just want to test the difference between two group mean pial thickness controling the age and edu (if it is necessary to control

Re: [Freesurfer] tksurfer visualization and -aseg option in tkmedit

On 12/19/2013 07:22 AM, Rujing Zha wrote: Hi Doug, Bruce and others. Would you please help me deal with 2 problems? The 1st one is : There is a excellent segmentation in -surfs after editing the pial and running -autorecon-pial. Some voxels was removed from the brainmask.mgz(i.e. picture

Re: [Freesurfer] Does this registration need to be fixed?

It kind of depends on what is going to happen next. The talairach transform is only used in a couple of contexts: to compute the estimated intracranial volume and when doing volume-based analysis of subcortical structures in FS-FAST. It would also be used if you report tal coordinates for the

Re: [Freesurfer] Does this registration need to be fixed?

P.S. I am assuming there is no simple way to get the broadman area and sulcus/gyrus directly from the RAS coordinates. Sujith On Thu, Dec 19, 2013 at 11:41 AM, sujith vijayan svijay...@gmail.comwrote: Hi Doug, I am using the registration for subjects with ECoG electrodes. I have the

Re: [Freesurfer] Does this registration need to be fixed?

Hi Doug, I am using the registration for subjects with ECoG electrodes. I have the electrode locations in RAS coordinates. I convert the RAS coordinates to talairach coordinates using the mri.nii and talairach.xfm files. I realize that talairach coordinates has some limitations, but I am just

Re: [Freesurfer] analyzing fMRI data across runs with slightly different slice prescriptions

Thanks Doug, I have a registration file for each run (for both the undistorted and not) and am curious how to pass that reg file for each run when I call either mkanalysis-ess or selxavg3-sess. It would seem I need to indicate the appropriate registration file during at least one of those calls,

[Freesurfer] 2 post-docs in cognitive neuroscience of memory (fMRI and neuropsychology)

Two post-doc positions in cognitive neuroscience of episodic memory Sussex is sunny. Memory is interesting. 2014 is looming. Time for a new job? Two 3-year positions are available to work with Chris Bird on a European Research Council funded project (TRANSMEM) at the University of Sussex in

Re: [Freesurfer] Does this registration need to be fixed?

we don't use it for much, so I wouldn't worry about it (unless someone disagrees?) On Thu, 19 Dec 2013, sujith vijayan wrote: Hi Bruce, Thanks! I looked at the other slices and they look similar to the screenshot I sent you; to my untrained eyes they look like they could use a slight rotation

Re: [Freesurfer] Does this registration need to be fixed?

no, not with any degree of accuracy On Thu, 19 Dec 2013, sujith vijayan wrote: P.S. I am assuming there is no simple way to get the broadman area and sulcus/gyrus directly from the RAS coordinates. Sujith On Thu, Dec 19, 2013 at 11:41 AM, sujith vijayan svijay...@gmail.com wrote: Hi

[Freesurfer] convert FSL .mat matrix to TkReg-RAS space

Hi, I'm using FSL's mcflirt for motion correction with the -mats option to store a registration matrix for each time point. In my application, I would like to use a one-step interpolation process to sample points from the freesurfer surfaces (e.g. white) from the 4D fMRI data. I tried to convert

[Freesurfer] POST-DOCTORAL POSITION IN NEUROIMAGING, NEUROPSYCHOLOGY AND ADDICTION; UNIVERSITY OF WISCONSIN-MILWAUKEE

POST-DOCTORAL POSITION IN NEUROIMAGING, NEUROPSYCHOLOGY AND ADDICTION; UNIVERSITY OF WISCONSIN-MILWAUKEE. Sponsor: Krista Lisdahl, Ph.D. A Postdoctoral Fellow position at the University of Wisconsin-Milwaukee (UWM), Psychology Department (http://www4.uwm.edu/letsci/psychology/) will be

[Freesurfer] volume to surface

Hi All, I would like to use mri_vol2surf to overlay a volume onto a surface. The synopsis is mri_vol2surf [options] --src inputfile --out outpufile --srcreg registrationfile --hemi hemisphere.But I don't know how to generate the registrationfile. Could someone help me with that? Thanks a lot!

Re: [Freesurfer] volume to surface

Hi Yue you can use bbregister to generate the registration. cheers Bruce On Thu, 19 Dec 2013, 赵越 wrote: Hi All, I would like to use mri_vol2surf to overlay a volume onto a surface. The synopsis is mri_vol2surf [options] --src inputfile --out outpufile --srcreg registrationfile --hemi

[Freesurfer] 3 groups and one covariate

Hi experts, I'd like to find group difference (thickness) among 3 groups taking in account one covariate. I'd like to use DOSS. Is correct? I have read the guide and I have carried out fsgd file as suggest for Three Groups (One Factor/Three Levels), No Covariates. Now, my problem is which are

[Freesurfer] Surface ROIs

Dear FreeSurfer Experts, I have defined an ROI as a FreeSurfer label on the pial surface of a single subject. Could someone recommend the best way to determine the corresponding ROIs for other subjects in my study? Thanks in advance, Danielle -- Danielle Sliva, MA Boston Children's Hospital

Re: [Freesurfer] Surface ROIs

Hi Danielle, try mri_label2label cheers Bruce On Thu, 19 Dec 2013, Danielle Sliva wrote: Dear FreeSurfer Experts, I have defined an ROI as a FreeSurfer label on the pial surface of a single subject. Could someone recommend the best way to determine the corresponding ROIs for other subjects

Re: [Freesurfer] mri_glmfit error

Hi Doug and others, Thanks Doug. All the best. 2013-12-20 Rujing Zha 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-12-20 00:11 主题：Re: [Freesurfer] mri_glmfit error 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu On 12/18/2013 11:14 PM, Rujing Zha

Re: [Freesurfer] tksurfer visualization and -aseg option in tkmedit

Thanks Doug. All the best. 2013-12-20 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zh...@mail.ustc.edu.cn charuj...@gmail.com charujing...@163.com 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2013-12-20 00:14 主题：Re: [Freesurfer]