Thank you very much, Doug.
In my case, the fMRI data is in LPS orientation, but the MNI152 in FSL are in LAS orientation. To overlay our fMRI results to MNI152 template, I wonder I should reorient the fMRI data to LAS orientation, am I right?
When I use mri_convert to do the task, it only convert the first volme and discard other volume. Why?
Thanks again
Zonglei Zhen
On Tue, Jan 10, 2012 at 6:44 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Zonglei, it should be fixed for version 5. Note that you should not use --out_orientation unless the orientation information is actually wrong. I think FSL has some tools to re-orient the
doug
Zhen Zonglei wrote:
Hi, Doug; Is the bug still in FS5.0.
When I used mri_convert to reorient a 4D BOLD volume. All frames except the first frame are discarded. My command: mri_convert --out_orientaiton LAS f.nii.gz flas.nii.gz Is there a convenient way to reorient the 4D volume to match the MNI template in FSL ?
fslswapdim in fsl can not adaptively swap to the assigned orientation based on the nii header.
Best
Zonglei Zhen
On Fri, Mar 12, 2010 at 6:40 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
This is a bug in the released version of FS. Our development version is fixed. I've put a version here
ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/mri_convertftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
ythomas wrote:
Hi,
I am trying to downsample a 4D volume using mri_convert. However, it seems to be killing the 4 dimension. For example, if I do
mri_convert -voxsize 4 4 4 tmp.mgz tmp444.mgz
The original volume which is 256 x 256 x 256 x 120 becomes 64 x
64 x 64.
Thanks, Thomas ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html