John,
It is possible that you are loosing the geometry information after asl_file, something that we have been fixing in the pre-release of the new version of BASIL. Using fslcpgeom is sensible to overcome this, although clearly you only want the 45 volumes post-subtraction and not all the zero volumes.
I agree that you perfusion values sound rather high. That most probably comes down to the parameters you are entering about your data or the calibration image. You, however, wont be able to learn a great deal from the absolute values of your diffdata. These values are arbitrary and set by the scanner hardware - there is no ‘right’ range for these and this is why calibration is necessary. You could attempt to filter out outliers from the diffdata, but the best thing to start with is motion correction and then allow the averaging/model fitting to deal with the noise.
Michael
On 17 Nov 2017, at 12:00, John anderson <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear Dr Michael, thank you so much. This is very helpful! Kindly, I have follow-up questions and I highly appreciate your feedback:
1. After doing substraction using the command "asl_file". The output images in my data are "datadiff.nii.gz = 45 volume and datadiff_mean.nii.gz =1 volume" are missing orientation. For instance, when I run the command "mri_info" on these images, I see Orientation = "???". For so, I applied the command "fslcpgeom" on these images to copy orientation from the original "pcasl" images to these images. As a result:
-When the flag "-d" is not included in the command "fslcpgeom" then the output images are "datadiff.nii.gz = 90 volumes" (where the last 45 volume are empty)-this image has orientation.
-when I include the flag "-d" in the command "fslcpgeom", then the output images are "datadiff.nii.gz = 45 volumes" and has orientation.
The problem is when I feed these images to oxford_asl:
-In the first case (datadiff.nii.gz = 90 volumes (where the last 45 volume are empty). The values in the final "perfusion_calib.nii.gz" images are 30-120 mg/100/ml. Which make sense.
-In the second case, (datadiff.nii.gz = 45 volumes). The values in the final "perfusion_calib.nii.gz" images are 150 -250 mg/100/ml which doesn't make any sense.
I can't understand why this happens and how to deal with this issue.
2. What is the normal range of values for the relative CBF after doing subtraction (i.e. the output of asl_file)? I see that the values of some images in my data are consistent with the range of values in the "data_singleti" example in FSL wiki. Where some voxels have negative values and others positive values with maximum values ~15. On the other side, the voxels in some of the relative CBF images have values close to 40. Is this normal? Is this driven by motion? Can the maximum and minimum intensity values within each voxel of the relative CBF images be used to check the outliers in the data and excluded it. Is this procedure correct?
My apologies for the long email and I highly appreciate any feedback!
John
This is a reference to whether the subtraction of pairs of labeled (tag) and control images has been done before submitting to oxford_asl. This is something ideally you would determine from your acquisition, but a quick way to check is to look at the data. If the images look like (noisy) perfusion images as they are (even better take the mean over all the volumes) then it has already been differenced. Otherwise it is most likely to be ‘tag-control’ ordering - as that is the most common.
You can play with the data using asl_file, or alternatively load it into the (new) GUI and that allows you to preview the data and what happens once you have done the label control subtraction.
Michael
On 15 Nov 2017, at 01:22, John anderson <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear ASL experts,
My question is very basic, I highly appreciate any input!! I would like to learn from your experience to enrich my knowledge!
The flag --iaf in the command "asl_file" represent the ASL data form, and there are three options: difference data, tag-control and control-tag.
I highly appreciate if you can define in few words what each form means. If the data is PCASL, then how can I check its form?
Thanks
John
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Michael Chappell MEng DPhil
W: http://www.ibme.ox.ac.uk/qubic
T: +44 1865 617657
Associate Professor, Institute of Biomedical Engineering, University of Oxford.
http://www.ibme.ox.ac.uk
Director of Training, EPSRC-MRC CDT in Biomedical Imaging
http://www.onbicdt.ox.ac.uk
Governing Body Fellow, Wolfson College, Oxford.
http://www.wolfson.ox.ac.uk
PhysiologyforEngineers.org<http://PhysiologyforEngineers.org>
NeuroimagingPrimers.org<http://NeuroimagingPrimers.org>
