Re: [HCP-Users] spin echo phase encoding direction
Hi Gregory,
Actually, for an AP/PA phase encode axis, that will probably be incorrect. The PhaseEncodingDirectionPositive value in the Siemens DICOMs is useful because it summarizes the impact of both the Phase enc. dir setting and the
Invert RO/PE Polarity flag in the sequence, and we use that value to validate that the PA/AP/RL/LR labels that we assign to our Series Descriptions match what we would expect. However, that DICOM variable only tells you about Siemens internal coordinate
system, which is not actually what Positive in the input SpinEchoPhaseEncodePositive is based upon.
You'll notice that the comment inExamples/Scripts/GenericfMRIVolumeProcessingPipelineBatch.sh
says
SpinEchoPhaseEncodePositive is RL in HCP data, PA in 7T HCP data
So, our convention is to use PA as theSpinEchoPhaseEncodePositive input with scans acquired with an AP/PA phase encoding axis. But as you've seen, the DICOMs have PhaseEncodingDirectionPositive = 0 for PA scans. That's because the convention in the
HCP pipelines is to assign the positive SE Field Map direction as the one that will generate a topup-derived field map with the same polarity as what a standard gradient echo field map collected on a Siemens scanner (and created using 'fsl_prepare_fieldmap')
would look like, so that we can use the samePhaseEncodeList values either way for the EPI being corrected.
That hopefully explains the behavior of how this all comes together. However, let me stress again to you (and any future readers of this thread), that the accuracy of your settings as regards distortion correction should be confirmed empirically. i.e.,
switch EITHER your assignments for SpinEchoPhaseEncode{Positive,Negative}, OR the direction of PhaseEncodeList for the EPI scan being corrected (but not both). If your original settings are correct, then switching the polarity at one point in the chain in
that fashion will lead to more severe distortion. Similarly, if one is using gradient echo based field maps, I would switch the direction ofPhaseEncodeList and confirm the polarity that way.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Book, Gregory gregory.b...@hhchealth.org
Date: Wednesday, December 17, 2014 8:34 AM
To: Harms, Michael mha...@wustl.edu, Matt Glasser glass...@wusm.wustl.edu, hcp-users@humanconnectome.org
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] spin echo phase encoding direction
Thanks for the info. I ran all the possible combinations of phase encoding directions and the invert option, and their effects on the DICOM header. This was actually very useful for us to understand the data.
It seems that the CSA header field #20 (PhaseEncodingDirectionPositive) does take into account the prescribed direction and the invert option. So in this case, I assume I should use the SE image with the DICOM header of PhaseEncodingDirectionPositive=1 as
the SpinEchoPhaseEncodePositive image in the HCP setup script?
From: Harms, Michael [mailto:mha...@wustl.edu]
Sent: Monday, December 15, 2014 5:41 PM
To: Book, Gregory; Harms, Michael; Glasser, Matthew;
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] spin echo phase encoding direction
Hi Greg,
Ultimately, getting all the signs right is a complicated combination of (1) how the manufacturer implements its PE gradient blips, (2) the DICOM to NIFTI converter that you use (and whether you 'reorient' the data,
e.g., using 'fslreorient2std'), (3) your settings for Phase enc. dir. and Invert RO/PE Polarity and (4) the plane/oriention that the EPI is acquired in. It is very dangerous for us to provide you a rule, as it is very difficult to anticipate all usage
cases. That's why I stressed the importance of confirming that you have all the conventions correct in your own data (by explicitly inverting the value of the PhaseEncodeList parameter in the pipeline, and seeing if the result indeed gets worse).
That said, as a sanity check for you, on a Siemen's scanner, acquiring transverse slices, using 'dcm2nii' as your NIFTI converter, with transverse slices, I would expect that you find the following:
If phase encoding direction=COL, and directionPositive=1, then PEdir=-y
If phase encoding direction=COL, and directionPositive=0, then PEdir=y
As Matt noted, those PEdir (i.e.,PhaseEncodeList values)
themselves are dependent on a certain convention for the SpinEchoFieldMaps, which I believe is outlined in the comments of the HCP pipeline scripts.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department
Re: [HCP-Users] spin echo phase encoding direction
Thanks for the info. I ran all the possible combinations of phase encoding directions and the invert option, and their effects on the DICOM header. This was actually very useful for us to understand the data. It seems that the CSA header field #20 (PhaseEncodingDirectionPositive) does take into account the prescribed direction and the invert option. So in this case, I assume I should use the SE image with the DICOM header of PhaseEncodingDirectionPositive=1 as the SpinEchoPhaseEncodePositive image in the HCP setup script? From: Harms, Michael [mailto:mha...@wustl.edu] Sent: Monday, December 15, 2014 5:41 PM To: Book, Gregory; Harms, Michael; Glasser, Matthew; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction Hi Greg, Ultimately, getting all the signs right is a complicated combination of (1) how the manufacturer implements its PE gradient blips, (2) the DICOM to NIFTI converter that you use (and whether you 'reorient' the data, e.g., using 'fslreorient2std'), (3) your settings for Phase enc. dir. and Invert RO/PE Polarity and (4) the plane/oriention that the EPI is acquired in. It is very dangerous for us to provide you a rule, as it is very difficult to anticipate all usage cases. That's why I stressed the importance of confirming that you have all the conventions correct in your own data (by explicitly inverting the value of the PhaseEncodeList parameter in the pipeline, and seeing if the result indeed gets worse). That said, as a sanity check for you, on a Siemen's scanner, acquiring transverse slices, using 'dcm2nii' as your NIFTI converter, with transverse slices, I would expect that you find the following: If phase encoding direction=COL, and directionPositive=1, then PEdir=-y If phase encoding direction=COL, and directionPositive=0, then PEdir=+y As Matt noted, those PEdir (i.e., PhaseEncodeList values) themselves are dependent on a certain convention for the SpinEchoFieldMaps, which I believe is outlined in the comments of the HCP pipeline scripts. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edumailto:mha...@wustl.edu From: Book, Gregory gregory.b...@hhchealth.orgmailto:gregory.b...@hhchealth.org Date: Monday, December 15, 2014 4:17 PM To: Harms, Michael mha...@wustl.edumailto:mha...@wustl.edu, Matt Glasser glass...@wusm.wustl.edumailto:glass...@wusm.wustl.edu, hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction Ok, good to know what that means as to how the data is collected relative to the label. So with the original example of a console entered AP, what does that mean if the PhaseEncodingDirectionPositive is 1 or 0? -G From: Harms, Michael [mha...@wustl.edumailto:mha...@wustl.edu] Sent: Monday, December 15, 2014 4:10 PM To: Book, Gregory; Glasser, Matthew; Harms, Michael; hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction Hi, If you had AP with Invert RO/PE Polarity checked, then that would be the same as if you had set PA and Invert RO/PE Polarity was left unchecked. The *dInPlaneRot field does NOT include the impact of the Invert RO/PE Polarity flag. Sorry, I directed you to the wrong shadow field previously. PhaseEncodingDirectionPositive is (according to my notes) subfield #20 of (0029, 1010). If it doesn't have a value, that means it value was 0 for that scan. (Its value is either 0 or 1). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edumailto:mha...@wustl.edu From: Book, Gregory gregory.b...@hhchealth.orgmailto:gregory.b...@hhchealth.org Date: Monday, December 15, 2014 2:59 PM To: Matt Glasser glass...@wusm.wustl.edumailto:glass...@wusm.wustl.edu, Harms, Michael mha...@wustl.edumailto:mha...@wustl.edu, hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction I'm slightly more confused now. So, using the CMRR sequences, if I set the phase encoding direction on my spin echo to AP, and Invert RO/PE Polarity option is checked... a) what is the actual phase direction of the data b) what is recorded in the DICOM header in the *.dInPlaneRot field? From: Glasser, Matthew [mailto:glass
Re: [HCP-Users] spin echo phase encoding direction
The value of PhaseEncodingDirectionPositive in the shadow field (0029,1020) reflects the combination of both Phase enc. dir. on the Routine tab (e.g., AP vs. PA) AND the setting of Invert RO/PE Polarity on the Sequence/Special tab. As long as you have one of each polarity, you can use the spin echo field map correction. I highly recommend that you purposely try both possible assignments, and visually confirm which one is giving the correct results. That's because the correct setting for PhaseEncodeList (e.g., y- vs. y) can in theory even be dependent on which DICOM to NIFTI converter you use. (e.g., if one converter returns a LAS orientation, while another returns a LPS orientation, then the proper settings for PhaseEncodeList may be swapped). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Book, Gregory gregory.b...@hhchealth.org Date: Monday, December 15, 2014 8:38 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] spin echo phase encoding direction I have another question about the spin echo images, hopefully this will be my last question! It turns out that we’ve been collecting our spin echo images with the “Invert RO/PE Polarity” option selected, which apparently inverts the phase encoding direction 180deg, but does not record this to the DICOM header. We’ve been collecting the EPI images without this inversion. So, for our data: EPI is AP “AP” SE is actually PA “PA” SE is actually AP Would we be able to use the spin echo correction if we simply switched the positive and negative images? So, would this work for our data? TaskList=”task1” PhaseEncodeList=”y-“ … SpinEchoPositiveImage=”the PA labeled image (actually acquired AP)” SpinEchoNegativeImage=”the AP labeled image (actually acquired PA)” -G _ Gregory Book Senior Technology Manager Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital 200 Retreat Avenue Hartford, CT 06106 Tel: 860-545-7267 Fax: 860-545-7797 gregory.b...@hhchealth.org http://nidb.sourceforge.net This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message, including any attachments. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___HCP-Users mailing listHCP-Users@humanconnectome.orghttp://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] spin echo phase encoding direction
Would that be the *.dInPlaneRot value for each slice in the CSA header? From: Harms, Michael [mailto:mha...@wustl.edu] Sent: Monday, December 15, 2014 10:11 AM To: Book, Gregory; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction The value of PhaseEncodingDirectionPositive in the shadow field (0029,1020) reflects the combination of both Phase enc. dir. on the Routine tab (e.g., AP vs. PA) AND the setting of Invert RO/PE Polarity on the Sequence/Special tab. As long as you have one of each polarity, you can use the spin echo field map correction. I highly recommend that you purposely try both possible assignments, and visually confirm which one is giving the correct results. That's because the correct setting for PhaseEncodeList (e.g., y- vs. y+) can in theory even be dependent on which DICOM to NIFTI converter you use. (e.g., if one converter returns a +LAS orientation, while another returns a +LPS orientation, then the proper settings for PhaseEncodeList may be swapped). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edumailto:mha...@wustl.edu From: Book, Gregory gregory.b...@hhchealth.orgmailto:gregory.b...@hhchealth.org Date: Monday, December 15, 2014 8:38 AM To: hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: [HCP-Users] spin echo phase encoding direction I have another question about the spin echo images, hopefully this will be my last question! It turns out that we've been collecting our spin echo images with the Invert RO/PE Polarity option selected, which apparently inverts the phase encoding direction 180deg, but does not record this to the DICOM header. We've been collecting the EPI images without this inversion. So, for our data: EPI is AP AP SE is actually PA PA SE is actually AP Would we be able to use the spin echo correction if we simply switched the positive and negative images? So, would this work for our data? TaskList=task1 PhaseEncodeList=y- ... SpinEchoPositiveImage=the PA labeled image (actually acquired AP) SpinEchoNegativeImage=the AP labeled image (actually acquired PA) -G _ Gregory Book Senior Technology Manager Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital 200 Retreat Avenue Hartford, CT 06106 Tel: 860-545-7267 Fax: 860-545-7797 gregory.b...@hhchealth.orgmailto:gregory.b...@hhchealth.org http://nidb.sourceforge.net This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message, including any attachments. ___ HCP-Users mailing list HCP-Users@humanconnectome.orgmailto:HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] spin echo phase encoding direction
If your phase encoding directions are inverted, I would recommend swapping the SpinEchoPositive and NegativeImage values. This would make the computed field map have the same sign as a typical field map and then the PhaseEncodeList would not have to change. Peace, Matt. From: Book, Gregory gregory.b...@hhchealth.org Date: Monday, December 15, 2014 at 12:16 PM To: Harms, Michael mha...@wustl.edu, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction Would that be the *.dInPlaneRot value for each slice in the CSA header? From: Harms, Michael [mailto:mha...@wustl.edu] Sent: Monday, December 15, 2014 10:11 AM To: Book, Gregory; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction The value of PhaseEncodingDirectionPositive in the shadow field (0029,1020) reflects the combination of both Phase enc. dir. on the Routine tab (e.g., AP vs. PA) AND the setting of Invert RO/PE Polarity on the Sequence/Special tab. As long as you have one of each polarity, you can use the spin echo field map correction. I highly recommend that you purposely try both possible assignments, and visually confirm which one is giving the correct results. That's because the correct setting for PhaseEncodeList (e.g., y- vs. y) can in theory even be dependent on which DICOM to NIFTI converter you use. (e.g., if one converter returns a LAS orientation, while another returns a LPS orientation, then the proper settings for PhaseEncodeList may be swapped). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu From: Book, Gregory gregory.b...@hhchealth.org Date: Monday, December 15, 2014 8:38 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] spin echo phase encoding direction I have another question about the spin echo images, hopefully this will be my last question! It turns out that we’ve been collecting our spin echo images with the “Invert RO/PE Polarity” option selected, which apparently inverts the phase encoding direction 180deg, but does not record this to the DICOM header. We’ve been collecting the EPI images without this inversion. So, for our data: EPI is AP “AP” SE is actually PA “PA” SE is actually AP Would we be able to use the spin echo correction if we simply switched the positive and negative images? So, would this work for our data? TaskList=”task1” PhaseEncodeList=”y-“ … SpinEchoPositiveImage=”the PA labeled image (actually acquired AP)” SpinEchoNegativeImage=”the AP labeled image (actually acquired PA)” -G _ Gregory Book Senior Technology Manager Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital 200 Retreat Avenue Hartford, CT 06106 Tel: 860-545-7267 Fax: 860-545-7797 gregory.b...@hhchealth.org http://nidb.sourceforge.net This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message, including any attachments. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___HCP-Users mailing listHCP-Users
Re: [HCP-Users] spin echo phase encoding direction
I'm slightly more confused now. So, using the CMRR sequences, if I set the phase encoding direction on my spin echo to AP, and Invert RO/PE Polarity option is checked... a) what is the actual phase direction of the data b) what is recorded in the DICOM header in the *.dInPlaneRot field? From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Monday, December 15, 2014 2:33 PM To: Book, Gregory; Harms, Michael; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction If your phase encoding directions are inverted, I would recommend swapping the SpinEchoPositive and NegativeImage values. This would make the computed field map have the same sign as a typical field map and then the PhaseEncodeList would not have to change. Peace, Matt. From: Book, Gregory gregory.b...@hhchealth.orgmailto:gregory.b...@hhchealth.org Date: Monday, December 15, 2014 at 12:16 PM To: Harms, Michael mha...@wustl.edumailto:mha...@wustl.edu, hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction Would that be the *.dInPlaneRot value for each slice in the CSA header? From: Harms, Michael [mailto:mha...@wustl.edu] Sent: Monday, December 15, 2014 10:11 AM To: Book, Gregory; hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction The value of PhaseEncodingDirectionPositive in the shadow field (0029,1020) reflects the combination of both Phase enc. dir. on the Routine tab (e.g., AP vs. PA) AND the setting of Invert RO/PE Polarity on the Sequence/Special tab. As long as you have one of each polarity, you can use the spin echo field map correction. I highly recommend that you purposely try both possible assignments, and visually confirm which one is giving the correct results. That's because the correct setting for PhaseEncodeList (e.g., y- vs. y+) can in theory even be dependent on which DICOM to NIFTI converter you use. (e.g., if one converter returns a +LAS orientation, while another returns a +LPS orientation, then the proper settings for PhaseEncodeList may be swapped). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edumailto:mha...@wustl.edu From: Book, Gregory gregory.b...@hhchealth.orgmailto:gregory.b...@hhchealth.org Date: Monday, December 15, 2014 8:38 AM To: hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: [HCP-Users] spin echo phase encoding direction I have another question about the spin echo images, hopefully this will be my last question! It turns out that we've been collecting our spin echo images with the Invert RO/PE Polarity option selected, which apparently inverts the phase encoding direction 180deg, but does not record this to the DICOM header. We've been collecting the EPI images without this inversion. So, for our data: EPI is AP AP SE is actually PA PA SE is actually AP Would we be able to use the spin echo correction if we simply switched the positive and negative images? So, would this work for our data? TaskList=task1 PhaseEncodeList=y- ... SpinEchoPositiveImage=the PA labeled image (actually acquired AP) SpinEchoNegativeImage=the AP labeled image (actually acquired PA) -G _ Gregory Book Senior Technology Manager Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital 200 Retreat Avenue Hartford, CT 06106 Tel: 860-545-7267 Fax: 860-545-7797 gregory.b...@hhchealth.orgmailto:gregory.b...@hhchealth.org http://nidb.sourceforge.net This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, or an employee or agent responsible for delivering the message to the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message, including any attachments. ___ HCP-Users mailing list HCP-Users@humanconnectome.orgmailto:HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance
Re: [HCP-Users] spin echo phase encoding direction
Hi, If you had AP with Invert RO/PE Polarity checked, then that would be the same as if you had set PA andInvert RO/PE Polarity was left unchecked. The *dInPlaneRot field does NOT include the impact of theInvert RO/PE Polarity flag. Sorry, I directed you to the wrong shadow field previously. PhaseEncodingDirectionPositive is (according to my notes) subfield #20 of (0029, 1010). If it doesn't have a value, that means it value was 0 for that scan. (Its value is either 0 or 1). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Book, Gregory gregory.b...@hhchealth.org Date: Monday, December 15, 2014 2:59 PM To: Matt Glasser glass...@wusm.wustl.edu, Harms, Michael mha...@wustl.edu, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction I’m slightly more confused now. So, using the CMRR sequences, if I set the phase encoding direction on my spin echo to AP, and “Invert RO/PE Polarity” option is checked… a) what is the actual phase direction of the data b) what is recorded in the DICOM header in the *.dInPlaneRot field? From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Monday, December 15, 2014 2:33 PM To: Book, Gregory; Harms, Michael; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction If your phase encoding directions are inverted, I would recommend swapping the SpinEchoPositive and NegativeImage values. This would make the computed field map have the same sign as a typical field map and then the PhaseEncodeList would not have to change. Peace, Matt. From: Book, Gregory gregory.b...@hhchealth.org Date: Monday, December 15, 2014 at 12:16 PM To: Harms, Michael mha...@wustl.edu, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction Would that be the *.dInPlaneRot value for each slice in the CSA header? From: Harms, Michael [mailto:mha...@wustl.edu] Sent: Monday, December 15, 2014 10:11 AM To: Book, Gregory; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction The value of PhaseEncodingDirectionPositive in the shadow field (0029,1020) reflects the combination of both Phase enc. dir. on the Routine tab (e.g., AP vs. PA) AND the setting of Invert RO/PE Polarity on the Sequence/Special tab. As long as you have one of each polarity, you can use the spin echo field map correction. I highly recommend that you purposely try both possible assignments, and visually confirm which one is giving the correct results. That's because the correct setting for PhaseEncodeList (e.g., y- vs. y) can in theory even be dependent on which DICOM to NIFTI converter you use. (e.g., if one converter returns a LAS orientation, while another returns a LPS orientation, then the proper settings for PhaseEncodeList may be swapped). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu From: Book, Gregory gregory.b...@hhchealth.org Date: Monday, December 15, 2014 8:38 AM To: hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: [HCP-Users] spin echo phase encoding direction I have another question about the spin echo images, hopefully this will be my last question! It turns out that we’ve been collecting our spin echo images with the “Invert RO/PE Polarity” option selected, which apparently inverts the phase encoding direction 180deg, but does not record this to the DICOM header. We’ve been collecting the EPI images without this inversion. So, for our data: EPI is AP “AP” SE is actually PA “PA” SE is actually AP Would we be able to use the spin echo correction if we simply switched the positive and negative images? So, would this work for our data? TaskList=”task1” PhaseEncodeList=”y-“ … SpinEchoPositiveImage=”the PA labeled image (actually acquired AP)” SpinEchoNegativeImage=”the AP labeled image (actually acquired PA)” -G _ Gregory Book Senior Technology Manager Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital 200 Retreat Avenue Hartford, CT 06106 Tel: 860-545-7267 Fax: 860-545-7797 gregory.b...@hhchealth.org http://nidb.sourceforge.net This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any
Re: [HCP-Users] spin echo phase encoding direction
Ok, good to know what that means as to how the data is collected relative to the label. So with the original example of a console entered AP, what does that mean if the PhaseEncodingDirectionPositive is 1 or 0? -G From: Harms, Michael [mha...@wustl.edu] Sent: Monday, December 15, 2014 4:10 PM To: Book, Gregory; Glasser, Matthew; Harms, Michael; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction Hi, If you had AP with Invert RO/PE Polarity checked, then that would be the same as if you had set PA and Invert RO/PE Polarity was left unchecked. The *dInPlaneRot field does NOT include the impact of the Invert RO/PE Polarity flag. Sorry, I directed you to the wrong shadow field previously. PhaseEncodingDirectionPositive is (according to my notes) subfield #20 of (0029, 1010). If it doesn't have a value, that means it value was 0 for that scan. (Its value is either 0 or 1). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Book, Gregory gregory.b...@hhchealth.orgmailto:gregory.b...@hhchealth.org Date: Monday, December 15, 2014 2:59 PM To: Matt Glasser glass...@wusm.wustl.edumailto:glass...@wusm.wustl.edu, Harms, Michael mha...@wustl.edumailto:mha...@wustl.edu, hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction I’m slightly more confused now. So, using the CMRR sequences, if I set the phase encoding direction on my spin echo to AP, and “Invert RO/PE Polarity” option is checked… a) what is the actual phase direction of the data b) what is recorded in the DICOM header in the *.dInPlaneRot field? From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Monday, December 15, 2014 2:33 PM To: Book, Gregory; Harms, Michael; hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction If your phase encoding directions are inverted, I would recommend swapping the SpinEchoPositive and NegativeImage values. This would make the computed field map have the same sign as a typical field map and then the PhaseEncodeList would not have to change. Peace, Matt. From: Book, Gregory gregory.b...@hhchealth.orgmailto:gregory.b...@hhchealth.org Date: Monday, December 15, 2014 at 12:16 PM To: Harms, Michael mha...@wustl.edumailto:mha...@wustl.edu, hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction Would that be the *.dInPlaneRot value for each slice in the CSA header? From: Harms, Michael [mailto:mha...@wustl.edu] Sent: Monday, December 15, 2014 10:11 AM To: Book, Gregory; hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction The value of PhaseEncodingDirectionPositive in the shadow field (0029,1020) reflects the combination of both Phase enc. dir. on the Routine tab (e.g., AP vs. PA) AND the setting of Invert RO/PE Polarity on the Sequence/Special tab. As long as you have one of each polarity, you can use the spin echo field map correction. I highly recommend that you purposely try both possible assignments, and visually confirm which one is giving the correct results. That's because the correct setting for PhaseEncodeList (e.g., y- vs. y+) can in theory even be dependent on which DICOM to NIFTI converter you use. (e.g., if one converter returns a +LAS orientation, while another returns a +LPS orientation, then the proper settings for PhaseEncodeList may be swapped). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edumailto:mha...@wustl.edu From: Book, Gregory gregory.b...@hhchealth.orgmailto:gregory.b...@hhchealth.org Date: Monday, December 15, 2014 8:38 AM To: hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org Subject: [HCP-Users] spin echo phase encoding direction I have another question about the spin echo images, hopefully this will be my last question! It turns out that we’ve been collecting our spin echo images with the “Invert RO/PE Polarity” option selected, which apparently inverts the phase encoding direction 180deg, but does not record this to the DICOM header. We’ve been
Re: [HCP-Users] spin echo phase encoding direction
Hi Greg, Ultimately, getting all the signs right is a complicated combination of (1) how the manufacturer implements its PE gradient blips, (2) the DICOM to NIFTI converter that you use (and whether you 'reorient' the data, e.g., using 'fslreorient2std'), (3) your settings for Phase enc. dir. and Invert RO/PE Polarity and (4) the plane/oriention that the EPI is acquired in. It is very dangerous for us to provide you a rule, as it is very difficult to anticipate all usage cases. That's why I stressed the importance of confirming that you have all the conventions correct in your own data (by explicitly inverting the value of the PhaseEncodeList parameter in the pipeline, and seeing if the result indeed gets worse). That said, as a sanity check for you, on a Siemen's scanner, acquiring transverse slices, using 'dcm2nii' as your NIFTI converter, with transverse slices, I would expect that you find the following: If phase encoding direction=COL, and directionPositive=1, then PEdir=-y If phase encoding direction=COL, and directionPositive=0, then PEdir=y As Matt noted, those PEdir (i.e.,PhaseEncodeList values) themselves are dependent on a certain convention for the SpinEchoFieldMaps, which I believe is outlined in the comments of the HCP pipeline scripts. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Book, Gregory gregory.b...@hhchealth.org Date: Monday, December 15, 2014 4:17 PM To: Harms, Michael mha...@wustl.edu, Matt Glasser glass...@wusm.wustl.edu, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction Ok, good to know what that means as to how the data is collected relative to the label. So with the original example of a console entered AP, what does that mean if the PhaseEncodingDirectionPositive is 1 or 0? -G From: Harms, Michael [mha...@wustl.edu] Sent: Monday, December 15, 2014 4:10 PM To: Book, Gregory; Glasser, Matthew; Harms, Michael; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction Hi, If you had AP with Invert RO/PE Polarity checked, then that would be the same as if you had set PA andInvert RO/PE Polarity was left unchecked. The *dInPlaneRot field does NOT include the impact of theInvert RO/PE Polarity flag. Sorry, I directed you to the wrong shadow field previously. PhaseEncodingDirectionPositive is (according to my notes) subfield #20 of (0029, 1010). If it doesn't have a value, that means it value was 0 for that scan. (Its value is either 0 or 1). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Book, Gregory gregory.b...@hhchealth.org Date: Monday, December 15, 2014 2:59 PM To: Matt Glasser glass...@wusm.wustl.edu, Harms, Michael mha...@wustl.edu, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction I’m slightly more confused now. So, using the CMRR sequences, if I set the phase encoding direction on my spin echo to AP, and “Invert RO/PE Polarity” option is checked… a) what is the actual phase direction of the data b) what is recorded in the DICOM header in the *.dInPlaneRot field? From: Glasser, Matthew [mailto:glass...@wusm.wustl.edu] Sent: Monday, December 15, 2014 2:33 PM To: Book, Gregory; Harms, Michael; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction If your phase encoding directions are inverted, I would recommend swapping the SpinEchoPositive and NegativeImage values. This would make the computed field map have the same sign as a typical field map and then the PhaseEncodeList would not have to change. Peace, Matt. From: Book, Gregory gregory.b...@hhchealth.org Date: Monday, December 15, 2014 at 12:16 PM To: Harms, Michael mha...@wustl.edu, hcp-users@humanconnectome.org hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction Would that be the *.dInPlaneRot value for each slice in the CSA header? From: Harms, Michael [mailto:mha...@wustl.edu] Sent: Monday, December 15, 2014 10:11 AM To: Book, Gregory; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction The value of PhaseEncodingDirectionPositive in the shadow field (0029,1020) reflects the combination of both Phase enc. dir. on the Routine tab (e.g., AP vs. PA) AND the setting of Invert RO/PE Polarity
