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 fol
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 smoot
Hi Doug,
I just found the module.
All the best.
2013-12-19
Rujing Zha
发件人："Rujing Zha"
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 Greve"
抄送："freesurfer"
Hi Doug,
Doug, thanks for your attention.
When I type the com
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 nee
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
> contr
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. pic
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
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 wrote:
> Hi Doug,
>
> I am using the registration for subjects with ECoG electrodes. I have the
> electrode locations in
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 look
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, b
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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
Bri
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 a
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
wrote:
Hi Doug,
I am using the
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 conver
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UNIVERSITY OF WISCONSIN-MILWAUKEE. Sponsor: Krista Lisdahl, Ph.D.
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Psychology Department (http://www4.uwm.edu/letsci/psychology/) will be
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Hi All,
I would like to use "mri_vol2surf" to overlay a volume onto a surface. The
synopsis is mri_vol2surf [] --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!
Yue
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 [] --src inputfile --out outpufile
--srcreg registrationfile --hemi hemisphere.
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
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
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 subj
Hi Doug and others,
Thanks Doug.
All the best.
2013-12-20
Rujing Zha
发件人：Douglas N Greve
发送时间：2013-12-20 00:11
主题：Re: [Freesurfer] mri_glmfit error
收件人："Rujing Zha"
抄送："freesurfer"
On 12/18/2013 11:14 PM, Rujing Zha wrote:
> Hi Doug and others,
> Thanks Doug.
> For the 2nd problem: I u
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
发送时间：2013-12-20 00:14
主题：Re: [Freesurfer] tksurfer visualization and -as
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