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
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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
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. 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.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_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.edu> > https://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.edu> 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 Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> 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.
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>
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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
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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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_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.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://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.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> 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> <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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> 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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> 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>
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 greve@nmr.mgh.harvard.eduwrote:
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 < greve@nmr.mgh.harvard.edu> 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 < greve@nmr.mgh.harvard.edu mailto:greve@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_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.edu>https://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.edu
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 Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
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 greve@nmr.mgh.harvard.edu 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
Hi Zonglei, you should contact the FSL list as to exactly what there requirements are and how to get your data to that point. doug
Zhen Zonglei wrote:
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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> 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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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_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.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://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.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> 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> <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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> 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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> 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@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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ythomas -
Zhen Zonglei