Dear All,
I encounter some problems with mri_motion_correct2. I scanned 10 structurals of a monkey that was not moved or moving during the whole scan time. Now I expect mri_motion_correct2 to produce nice averages of my ten runs, but it insists upon displacing/rotating some of my scans. That is in one "beautiful" example a single run's volume was turned by 90 degrees. Are there any expert options for mri_motion_correct2 to clue it in on the expected scan quality? A before I forget centos4_x86_64-dev20060224 is the version I am trying.
Ahoi Sebastian
have you looked at all the images to assure that none have any artifacts? Have you tried a subset to see if that will work? All the images have the same geometry, I presume?
doug
Sebastian Moeller wrote:
Dear All,
I encounter some problems with mri_motion_correct2. I scanned 10 structurals of a monkey that was not moved or moving during the whole scan time. Now I expect mri_motion_correct2 to produce nice averages of my ten runs, but it insists upon displacing/rotating some of my scans. That is in one "beautiful" example a single run's volume was turned by 90 degrees. Are there any expert options for mri_motion_correct2 to clue it in on the expected scan quality? A before I forget centos4_x86_64-dev20060224 is the version I am trying.
Ahoi Sebastian
Hi Doug,
On 28. Feb 2006, at 16:27 Uhr, Doug Greve wrote:
have you looked at all the images to assure that none have any artifacts?
I had a relative quick look, without scrutinizing them, they look okay and very similar, but I will redo this.
Have you tried a subset to see if that will work? All the images have the same geometry, I presume?
Well yeah I can exclude the offending volume, even though it was scanned with the same parameters and no giant artifacts.
Ahoi Sebastian
doug
Sebastian Moeller wrote:
Dear All,
I encounter some problems with mri_motion_correct2. I scanned 10 structurals of a monkey that was not moved or moving during the whole scan time. Now I expect mri_motion_correct2 to produce nice averages of my ten runs, but it insists upon displacing/rotating some of my scans. That is in one "beautiful" example a single run's volume was turned by 90 degrees. Are there any expert options for mri_motion_correct2 to clue it in on the expected scan quality? A before I forget centos4_x86_64-dev20060224 is the version I am trying.
Ahoi Sebastian
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
So if you exclude that one image, the average of the rest of the 9 look ok?
Sebastian Moeller wrote:
Hi Doug,
On 28. Feb 2006, at 16:27 Uhr, Doug Greve wrote:
have you looked at all the images to assure that none have any artifacts?
I had a relative quick look, without scrutinizing them, they lookokay and very similar, but I will redo this.
Have you tried a subset to see if that will work? All the images have the same geometry, I presume?
Well yeah I can exclude the offending volume, even though it wasscanned with the same parameters and no giant artifacts.
Ahoi Sebastian
doug
Sebastian Moeller wrote:
Dear All,
I encounter some problems with mri_motion_correct2. I scanned 10 structurals of a monkey that was not moved or moving during the whole scan time. Now I expect mri_motion_correct2 to produce nice averages of my ten runs, but it insists upon displacing/rotating some of my scans. That is in one "beautiful" example a single run's volume was turned by 90 degrees. Are there any expert options for mri_motion_correct2 to clue it in on the expected scan quality? A before I forget centos4_x86_64-dev20060224 is the version I am trying.
Ahoi Sebastian
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Hi Doug,
On 28. Feb 2006, at 17:04 Uhr, Doug Greve wrote:
So if you exclude that one image, the average of the rest of the 9 look ok?
Yes, the average of the remaining scans does look ok. And the offender does not look different even at closer inspection... strange
Ahoi Sebastian
Sebastian Moeller wrote:
Hi Doug,
On 28. Feb 2006, at 16:27 Uhr, Doug Greve wrote:
have you looked at all the images to assure that none have any artifacts?
I had a relative quick look, without scrutinizing them, they lookokay and very similar, but I will redo this.
Have you tried a subset to see if that will work? All the images have the same geometry, I presume?
Well yeah I can exclude the offending volume, even though it wasscanned with the same parameters and no giant artifacts.
Ahoi Sebastian
doug
Sebastian Moeller wrote:
Dear All,
I encounter some problems with mri_motion_correct2. I scanned 10 structurals of a monkey that was not moved or moving during the whole scan time. Now I expect mri_motion_correct2 to produce nice averages of my ten runs, but it insists upon displacing/rotating some of my scans. That is in one "beautiful" example a single run's volume was turned by 90 degrees. Are there any expert options for mri_motion_correct2 to clue it in on the expected scan quality? A before I forget centos4_x86_64-dev20060224 is the version I am trying.
Ahoi Sebastian
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Hmmm, not sure what to tell you about the 10th volume. What tool do you use to inspect the volumes? You can check the geometry ("vox2ras" matrix and voxel size) with mri_info to make sure that the parameters are the same (though that should not have made much of a difference). mri_motion_correct2 uses minctracc, so I'm not sure what's really going on inside.
doug
Sebastian Moeller wrote:
Hi Doug,
On 28. Feb 2006, at 17:04 Uhr, Doug Greve wrote:
So if you exclude that one image, the average of the rest of the 9 look ok?
Yes, the average of the remaining scans does look ok. And theoffender does not look different even at closer inspection... strange
Ahoi Sebastian
Sebastian Moeller wrote:
Hi Doug,
On 28. Feb 2006, at 16:27 Uhr, Doug Greve wrote:
have you looked at all the images to assure that none have any artifacts?
I had a relative quick look, without scrutinizing them, theylook okay and very similar, but I will redo this.
Have you tried a subset to see if that will work? All the images have the same geometry, I presume?
Well yeah I can exclude the offending volume, even though it wasscanned with the same parameters and no giant artifacts.
Ahoi Sebastian
doug
Sebastian Moeller wrote:
Dear All,
I encounter some problems with mri_motion_correct2. I scanned 10 structurals of a monkey that was not moved or moving during the whole scan time. Now I expect mri_motion_correct2 to produce nice averages of my ten runs, but it insists upon displacing/rotating some of my scans. That is in one "beautiful" example a single run's volume was turned by 90 degrees. Are there any expert options for mri_motion_correct2 to clue it in on the expected scan quality? A before I forget centos4_x86_64-dev20060224 is the version I am trying.
Ahoi Sebastian
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Sebastian Moeller