Re: [HCP-Users] T1UnwarpDir
That note in the pipeline example code was put there because I don¹t know
how to tell what readout direction was used from the DICOMs and z seems to
be the Siemens default. If someone else does, I¹d be interested in what
field(s) they used.
Gordon, I¹d be a bit surprised here if the shim mattered given how small
the correction is already and the fact that the bulk of the correction is
likely to be the same from one shim to another. I don¹t think it¹s likely
to be made worse by reshiming, just won¹t be quite as precise of a
correction.
Peace,
Matt.
On 10/24/14, 10:33 PM, Xu, Junqian junqian...@mssm.edu wrote:
As for importance, it depends on your application but readout distortion
is typically quite small. Btw, we¹ve observed that the scanner
re-shimming often happens between the fieldmap and the structural scans
if the scanner operator is not well-educated for the importance of
preventing re-shimming. In such cases, I think it is better to disable
the readout distortion correction in the PreFreeSurferPipeline.
Gordon
On Oct 24, 2014, at 11:18 PM, Xu, Junqian junqian...@mssm.edu wrote:
'Unwarp Dir¹ should correspond to the Readout (frequency encoding)
direction for the ŒPreFreeSurferPipeline', in which case is the Z
direction (Head - Foot) for the sagittal T1w/T2w HCP structural
acquisitions. Not sure what you mean by The only comment is that z
appears best.² Below is what¹s in PreFreeSurfer/PreFreeSurferPipeline.sh
--unwarpdir={x, y, z} Readout direction of the T1w and T2w
images
(Used with either a regular
field map or a spin
echo field map)
On Oct 24, 2014, at 8:28 PM, Micah Chambers micahc...@gmail.com
wrote:
Could anyone provide a better explanation of the importance of Unwarp
Dir in the example file 'PreFreeSurferPipelineBatch.sh'? The only
comment is that z appears best. It seems like direction of warping
should be a known value, is that not the case.
I don't know if this is related, but I have been testing the scripts
with HCP subject 901038 and I am finding that the outputs do not match
up. There is a slight tilt to the head. While not a big issue (the
brain is still labeled correctly), it makes validation of scripts
harder. Has anyone else had such an issue? I have included screenshots
(ours.png is our local version, hcp.png is the downloaded version).
Note that this came from '901038_3T_Structural_preproc.zip' and was
downloaded about a month ago.
Thanks
-MIcah
--
Micah Chambers, M.S.
Ahmanson-Lovelace Brain Mapping Center
University of California Los Angeles
635 Charles E. Young Drive SW, Suite 225
Los Angeles, CA 90095-7334
310-206-2101 (Office)
310-206-5518 (Fax)
703-307-7692 (Cell)
email: mica...@ucla.edu
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Re: [HCP-Users] T1UnwarpDir
On Oct 26, 2014, at 9:21 AM, Glasser, Matthew
glass...@wusm.wustl.edumailto:glass...@wusm.wustl.edu wrote:
That note in the pipeline example code was put there because I donąt know
how to tell what readout direction was used from the DICOMs and z seems to
be the Siemens default. If someone else does, I’d be interested in what
field(s) they used.
It may take some deductive work. Mike Harms once figured out the phase encoding
direction from the DICOM header. We just need to find the corresponding code of
slice direction in the DICOM header. The one left is the readout direction.
However, to be completely sure about the sign would be tough or might be
impossible from the DICOM header alone.
Gordon, I’d be a bit surprised here if the shim mattered given how small
the correction is already and the fact that the bulk of the correction is
likely to be the same from one shim to another.
I agree that the bulk of the correction is not likely to change between
re-shims. However, I assume the main reason to do readout distortion correction
is for regions close to sinuses, where local fields could vary substantially
between re-shims with global (whole brain) optimization.
I don’t think it’s likely
to be made worse by reshiming, just won’t be quite as precise of a
correction.
I agree that no matter what it is a “small” effect. However I don’t completely
agree it can’t be made worse by a wrong fieldmap due to re-shimming. I think we
can do an experiment of: Fieldmap - Structural - re-shim - wrong Fieldmap, to
evaluate.
Gordon
Peace,
Matt.
On 10/24/14, 10:33 PM, Xu, Junqian
junqian...@mssm.edumailto:junqian...@mssm.edu wrote:
As for importance, it depends on your application but readout distortion
is typically quite small. Btw, weąve observed that the scanner
re-shimming often happens between the fieldmap and the structural scans
if the scanner operator is not well-educated for the importance of
preventing re-shimming. In such cases, I think it is better to disable
the readout distortion correction in the PreFreeSurferPipeline.
Gordon
On Oct 24, 2014, at 11:18 PM, Xu, Junqian
junqian...@mssm.edumailto:junqian...@mssm.edu wrote:
'Unwarp Dirą should correspond to the Readout (frequency encoding)
direction for the ŚPreFreeSurferPipeline', in which case is the Z
direction (Head - Foot) for the sagittal T1w/T2w HCP structural
acquisitions. Not sure what you mean by The only comment is that z
appears best.˛ Below is whatąs in PreFreeSurfer/PreFreeSurferPipeline.sh
--unwarpdir={x, y, z} Readout direction of the T1w and T2w
images
(Used with either a regular
field map or a spin
echo field map)
On Oct 24, 2014, at 8:28 PM, Micah Chambers
micahc...@gmail.commailto:micahc...@gmail.com
wrote:
Could anyone provide a better explanation of the importance of Unwarp
Dir in the example file 'PreFreeSurferPipelineBatch.sh'? The only
comment is that z appears best. It seems like direction of warping
should be a known value, is that not the case.
I don't know if this is related, but I have been testing the scripts
with HCP subject 901038 and I am finding that the outputs do not match
up. There is a slight tilt to the head. While not a big issue (the
brain is still labeled correctly), it makes validation of scripts
harder. Has anyone else had such an issue? I have included screenshots
(ours.png is our local version, hcp.png is the downloaded version).
Note that this came from '901038_3T_Structural_preproc.zip' and was
downloaded about a month ago.
Thanks
-MIcah
--
Micah Chambers, M.S.
Ahmanson-Lovelace Brain Mapping Center
University of California Los Angeles
635 Charles E. Young Drive SW, Suite 225
Los Angeles, CA 90095-7334
310-206-2101 (Office)
310-206-5518 (Fax)
703-307-7692 (Cell)
email: mica...@ucla.edumailto:mica...@ucla.edu
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Re: [HCP-Users] T1UnwarpDir
'Unwarp Dir’ should correspond to the Readout (frequency encoding) direction
for the ‘PreFreeSurferPipeline', in which case is the Z direction (Head - Foot)
for the sagittal T1w/T2w HCP structural acquisitions. Not sure what you mean by
The only comment is that z appears best.” Below is what’s in
PreFreeSurfer/PreFreeSurferPipeline.sh
--unwarpdir={x, y, z} Readout direction of the T1w and T2w images
(Used with either a regular field
map or a spin
echo field map)
On Oct 24, 2014, at 8:28 PM, Micah Chambers micahc...@gmail.com wrote:
Could anyone provide a better explanation of the importance of Unwarp Dir in
the example file 'PreFreeSurferPipelineBatch.sh'? The only comment is that z
appears best. It seems like direction of warping should be a known value, is
that not the case.
I don't know if this is related, but I have been testing the scripts with HCP
subject 901038 and I am finding that the outputs do not match up. There is a
slight tilt to the head. While not a big issue (the brain is still labeled
correctly), it makes validation of scripts harder. Has anyone else had such
an issue? I have included screenshots (ours.png is our local version, hcp.png
is the downloaded version). Note that this came from
'901038_3T_Structural_preproc.zip' and was downloaded about a month ago.
Thanks
-MIcah
--
Micah Chambers, M.S.
Ahmanson-Lovelace Brain Mapping Center
University of California Los Angeles
635 Charles E. Young Drive SW, Suite 225
Los Angeles, CA 90095-7334
310-206-2101 (Office)
310-206-5518 (Fax)
703-307-7692 (Cell)
email: mica...@ucla.edu
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Re: [HCP-Users] T1UnwarpDir
As for importance, it depends on your application but readout distortion is
typically quite small. Btw, we’ve observed that the scanner re-shimming often
happens between the fieldmap and the structural scans if the scanner operator
is not well-educated for the importance of preventing re-shimming. In such
cases, I think it is better to disable the readout distortion correction in the
PreFreeSurferPipeline.
Gordon
On Oct 24, 2014, at 11:18 PM, Xu, Junqian junqian...@mssm.edu wrote:
'Unwarp Dir’ should correspond to the Readout (frequency encoding) direction
for the ‘PreFreeSurferPipeline', in which case is the Z direction (Head -
Foot) for the sagittal T1w/T2w HCP structural acquisitions. Not sure what you
mean by The only comment is that z appears best.” Below is what’s in
PreFreeSurfer/PreFreeSurferPipeline.sh
--unwarpdir={x, y, z} Readout direction of the T1w and T2w images
(Used with either a regular field
map or a spin
echo field map)
On Oct 24, 2014, at 8:28 PM, Micah Chambers micahc...@gmail.com wrote:
Could anyone provide a better explanation of the importance of Unwarp Dir in
the example file 'PreFreeSurferPipelineBatch.sh'? The only comment is that z
appears best. It seems like direction of warping should be a known value, is
that not the case.
I don't know if this is related, but I have been testing the scripts with
HCP subject 901038 and I am finding that the outputs do not match up. There
is a slight tilt to the head. While not a big issue (the brain is still
labeled correctly), it makes validation of scripts harder. Has anyone else
had such an issue? I have included screenshots (ours.png is our local
version, hcp.png is the downloaded version). Note that this came from
'901038_3T_Structural_preproc.zip' and was downloaded about a month ago.
Thanks
-MIcah
--
Micah Chambers, M.S.
Ahmanson-Lovelace Brain Mapping Center
University of California Los Angeles
635 Charles E. Young Drive SW, Suite 225
Los Angeles, CA 90095-7334
310-206-2101 (Office)
310-206-5518 (Fax)
703-307-7692 (Cell)
email: mica...@ucla.edu
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