I use FEAT from FSL to do the fMRI analysis. But the data were unpacked with the Freesurfer unpacksdcmdir.
Zonglei Zhen On Tue, Jan 10, 2012 at 1:49 PM, Douglas Greve <[email protected]>wrote: > what software package are you using to do the fMRI analysis? > doug > > > On 1/9/12 9:19 PM, Zhen Zonglei wrote: > > 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 < > [email protected]> wrote: > >> 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 < >>> [email protected] <mailto:[email protected]>> 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_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 >>> > [email protected] >>> <mailto:[email protected]> >>> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> > >>> > >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> [email protected] <mailto:[email protected]> >>> >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] <mailto:[email protected]> >>> >>> >>> https://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/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 >> [email protected] >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >
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