I would like to follow up on my previous question about our perfusion values which seemed very high (re-pasting these below) after using our separated control image from the ASL sequence as the calibration input along
with its TR value using this command: oxford_asl -i PREV_053_S1_ASL_real.nii.gz -c SingleSplitVol_even.nii.gz --tr=4.854 --mc --iaf=tc --wp --casl --tis 3.475 --bolus 1.45 --fslanat=PREV_053_S1_T1_sag.anat --sbrain PREV_053_S1_T1_sag_brain.nii.gz --senscorr
–pvcorr.
I would be extremely appreciative for any feedback on this, thank you so much!
Mean perfusion in gm is 1706.541063
Mean perfusion in cortical gm is 1782.053283
Mean arrival in gm is 0.001143
Mean arrival in cortical gm is 0.001067
Mean perfusion_wm in wm is 3384.354213
Mean perfusion_wm in cerebral wm is 3410.658000
Mean arrival_wm in wm is 0.343629
Mean arrival_wm in cerebral wm is 0.347908
Mean perfusion_calib in gm is 8169.734142
Mean perfusion_calib in cortical gm is 8619.137136
Mean perfusion_wm_calib in wm is 15115.901513
Mean perfusion_wm_calib in cerebral wm is 15187.194326
Thank you so much for getting back to me with the helpful walkthrough for separating the control volume and then using that for calibration. Our ASL data only contains 2 volumes (one label and one control) so I do not think taking the mean or motion correcting
applies in our case, please let me know if this is correct and if using a single control volume is still valid for calibration.
I used the following command to first separate out the control image: asl_file --data=PREV_053_S1_ASL_real.nii.gz
--ntis=1 --iaf=tc --spairs --out=SingleSplitVol, and then used the even output file (because our data is in label-control pairs) as the calibration input file to oxford asl along with the TR value using the following
command: oxford_asl -i PREV_053_S1_ASL_real.nii.gz -c SingleSplitVol_even.nii.gz --tr=4.854 --mc --iaf=tc --wp --casl --tis 3.475 --bolus 1.45 --fslanat=PREV_053_S1_T1_sag.anat
--sbrain PREV_053_S1_T1_sag_brain.nii.gz --senscorr –pvcorr.
However, the perfusion values that were produced seem extremely high, so I am wondering if anything stands out to you that may be offsetting the values?
I am pasting the values below:
Mean perfusion in gm is 1706.541063
Mean perfusion in cortical gm is 1782.053283
Mean arrival in gm is 0.001143
Mean arrival in cortical gm is 0.001067
Mean perfusion_wm in wm is 3384.354213
Mean perfusion_wm in cerebral wm is 3410.658000
Mean arrival_wm in wm is 0.343629
Mean arrival_wm in cerebral wm is 0.347908
Mean perfusion_calib in gm is 8169.734142
Mean perfusion_calib in cortical gm is 8619.137136
Mean perfusion_wm_calib in wm is 15115.901513
Mean perfusion_wm_calib in cerebral wm is 15187.194326
Thank you so much for your help with this!
Given that you did not acquire your label-control data with background suppression it should be possible to use the control images in place of an M0 image in oxford_asl.
As a first attempt, I would separate out just one control image from the label-control time series and just use that as the input to the “-c <M0_image>” option. Normally M0 images are acquired with a longer
TR than the label-control data, so it is worth inputting the TR for the label-control images into oxford_asl with the “--tr=<TR value>” option.
If that looks like it is producing sensible perfusion values, then I think I would try again but this time use the mean of all of the control images. So, separate all of the control images out from the label-control
time series, motion correct them so that they are aligned, then take the mean. Then use the mean control image as the input to “-c <M0_image>” option (and still use the “--tr=<TR value>” option to let it know the control images TR value).
Let us know if you have any problems with this.
My team is currently trying to run a single PLD/TI pcASL analysis with oxford_asl; however, we did not acquire a separate M0 image and none of our structural images have the same readout parameters as the ASL data. Do
you know if our ASL control images (they are in control-label pairs) can be used by any of the BASIL tools to estimate the M0 of arterial blood? I was looking into using asl_calib to compute this value, but I did not feel confident that this was supported.
We did not use presaturation or background suppression if this is helpful.
Thank you so much for your help.
This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please contact the sender and delete the email and
attachment.
Any views or opinions expressed by the author of this email do not
necessarily reflect the views of the University of Nottingham. Email
communications with the University of Nottingham may be monitored
where permitted by law.
