I believe that the DICOM field 0019,1018 (readout sample spacing) for Siemens is units of nanoseconds. A value of 6500 sounds about right if your T1 scan has a BW around 240 Hz/Px. For example, for the young adult HCP data, collected with a BW of 210 Hz/Px, that value is 7400. You just need to convert it to seconds. Hence the example in PreFreeSurferPipelineBatch.sh that
# DICOM field (0019,1018) in s or "NONE" if not used T1wSampleSpacing="0.0000074" I believe that formula contained in PreFreeSurferPipelineBatch.sh for GE scanners was supplied to us by an outside user, and unfortunately it appears that it might not be accurate. 0018,0095 is “ACQ Pixel Bandwidth” 0028,0010 is “IMG Rows”, which is reflective of the *reconstructed* image, not the parameters of the actual acquisition. (And in fact, for a sagittal MPRAGE acquisition, the readout direction is “COL”, not “ROW”, so the use of 0028,0010 is probably wrong in multiple ways). So, I’m skeptical as to whether that formula is a general purpose one that is accurate for GE scanners (and definitely doesn’t look accurate for Siemens scanners). Note that the readout distortion effect that is being corrected here is a very small effect — you have to look carefully in OFC or temporal cortex to see it. And as you’ve deduced, the “t1samplespacing” value is a completely different thing from the “echospacing” value of the SpinEchoFieldMaps. @Tim Brown: Barring a justification from a GE scanner user, we should probably remove those "1/((0018,0095)x(0028,0010))” comments from PreFreeSurferPipelineBatch.sh 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: [email protected] From: <[email protected]<mailto:[email protected]>> on behalf of "Stevens, Michael" <[email protected]<mailto:[email protected]>> Date: Tuesday, January 3, 2017 at 4:36 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] T1w and T2w sample spacing Hi folks, We’re altering some of our HCP scripts to use updated T1w and T2w in a new project and I want to make sure I’m entering the correct “Sample Spacing” values for TOPUP distortion correction in the PreFreeSurferPipelineBatch.sh step. Tim’s annotation of the PreFreeSurfer.sh code refers to DICOM field 0019,1018 for Siemens. In our Skyra T1w data, this field contains a rather unhelpful “6500” value, which is nothing like the sample values. There’s also annotation in the PreFreeSurferPipelineBatch.sh script for GE scanner users, which refers to 1/((0018,0095)x(0028,0010)). Although we don’t have a GE scanner, these fields give us information that creates a value comparable to the example given (e.g., for the T1 these fields refer to ACQ Pixel Bandwidth=240 and IMG rows=320… the resulting value is feasible = .00001302083333). The only other thing I have available is an “echo spacing” value from our T1w scan sequence card. This is originally what I thought was correct given how this is the term used when describing the unwarping of fMRI images and used for the fieldmaps themselves. However, that T1w echo spacing value of 7.6 msec is used (even when specified in sec, e.g., .0076), the resulting T1w_acpc_dc_brain.nii.gz image is wildly distorted (and I don’t think it’s because I’m using the wrong phase encoding value… It’s equally weird whatever phase encoding value I try). If anyone can clarify were exactly we can find the sample spacing info that should be used with the HCP scripts, I’d appreciate it. Best, Mike Michael C. Stevens, Ph.D. Director, Clinical Neuroscience & Development Laboratory, Olin Neuropsychiatry Research Center Director, Child & Adolescent Research, The Institute of Living / Hartford Hospital Adjunct Associate Professor of Psychiatry, Yale University School of Medicine 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 [email protected]<mailto:[email protected]> 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
