You're right, it is best to use the command line rather than the GUI as it allows us to use the --rpts option. Also, your command is nearly there, it should be:
oxford_asl -i <asl_data> \
-o <output_filename> \
--casl --iaf=tc --ibf=tis \
--tis=1.7,2.3,2.8,3.3,3.8 \ # the TIs listed here are equal to the bolus_duration + PLD1, bolus_duration + PLD2, etc.
--rpts=4,5,6,8,10 \ # give the number of label-control
pairs at each TI i.e half the number of volumes at each TI
--bolus=1.5 --slicedt=0.0045 \
--sliceband=6 \
--fslanat=T1.anat \
--pvcorr \
-c <calibration_images> \ # i.e. the two calibration volumes you extracted from the original 70 volume file
--tr=8 \
--mc \
NOTE: the fieldmaps that I have from the HCP data are not AP and PA acquired calibration images, they are separately acquired AP and PA fieldmaps, so it isn't possible to use the --cblip option in oxford_asl. At the moment I am using topup with
the two fieldmaps before I call oxford_asl. I am taking the fieldmap generated by topup and correcting its units (from Hz to rad/s), and then putting that into oxford_asl using the options:
--fmap=<fieldmap_from_topup_rad_s> \ # the --fout output from topup, with units corrected to rad/s using fslmaths
--fmapmag=<averaged_of_corrected_fieldmaps_from_topup> \ # fslmaths -Tmean of the --out output from topup
--fmapmagbrain=<brain_extracted_fmapmag> \
--echospacing=<value> \
--pedir=y
This method of dealing with the fieldmaps isn't ideal. I think we will adapt the oxford_asl code at some point so that it can use blip reversed fieldmaps that are not calibration images.
Hope that helps. All the best,
Michael, Flora (so sorry for the back to back..)
I think I managed to find all the information I need to run an analysis of the multiband/multiPLD PCASL, the only issue I have is that I do not find how to specify the blocks for each PLD (i.e., the set-up, which is the one Flora mentioned, is that we acquire
8 tag-control pairs at 0.2 PLD, 10 at 0.8, 12 at 1.3, etc..). In asl_file there is the option --rpts to do that, is there something similar for oxford_asl?
Currently, then, what I am envisioning is something like (other than the -rpts option, which I cannot find how to set with oxford_asl):
oxford_asl -i mbpcaslAP_data.nii.gz \ # data in (A>>P)
-o mbpcaslAP_data_dir \ # folder out
--bolus 1.50 --ibf=tis --tis=0.2,0.8,1.3,1.8,2.3 # labeling duration (1.5 s), multi-PLDs (from *.INI file)
--rpts=8,10,12,16,20 \
# number of repeats per PLD block (from *.INI file)
--mc --casl --wp --iaf=tc --pvcorr \ # mot corr, pcasl, white paper, tag-control, partial volume correction
--echospacing=0.00049 --slicedt=0.0045 --sliceband 6\ # echo spacing (0.49 ms), time per bands (4.5 ms), 6 bands
-c mbpcaslAP_calib.nii.gz --tr=8 --tissref csf \ # calibration image, TR of calibration image, tissue reference CSF
--cblip=mbpcasl_fieldmapPA --pedir=y \ # fieldmap, reverse direction (P>>A)
--fslanat="T1.anat" # use the T1.anat file previously made
What is the right way to input the blocks (i.e., to obtain the same result as --rpts in asl_file)?
thank you for the patience and input
martin
Flora,
so under your set-up (i.e., your number of volumes and specific PLDs), in asl_gui you just put the total number of volumes, mark the PLDs, but how do you tell the software which PLD is in which volume?
M
Hi Martin,
My data were acquired with a labelling duration of 1.5s, and have 5 PLDs: 0.2s, 0.7s, 1.2s, 1.7s, and 2.2s. But, there are different numbers of repeats for each PLD:
6 tag-control pairs for the 0.2s, 0.7s and 1.2s PLDs, 10 tag-control pairs for the 1.7s PLD, and 15 tag-control pairs for the 2.2s PLD. This is what makes up the 86 volumes in my asl data file (12x3 + 20 + 30).
Is that all of the detail given in the 'Sequence - special' part of your scan PDF? I doubt that 184000us i.e. 0.18 seconds would be the
PLD used in a single PLD acqusition (1.8 seconds is more typical). I don't think it is possible to determine the PLDs from the data alone (particularly because there may be different numbers of repeats acquired for the different PLDs), and the PLDs don't tend
to be reported in the .json files. Are you able to give me any more information e.g. scan pdf or images of the scanner console pop-up you mentioned? It may be that you need to get in touch with whoever set up the sequence on your scanner to get the details.
All the best,
Flora Kennedy McConnell
------------------------------
Postdoctoral Research Associate
Department of Engineering Science
University of Oxford
Old Road Campus Research Building
Oxford, UK
OX3 7DQ
Hi Flora,
thank you, this is tremendously helpful.
Re your point #2, great, that is similar to what I did (except for the fact I have fewer volumes). I will try to pull the info out of the JSON image (though, after emailing the list it occurred to me that I might be able to infer it from the dicom header values
too perhaps..).
At present, then, my uncertainty is about how many PLD there are. Just as you said, the PDF from the console when I look in Sequence - special reports:
PCASL Options: mdPCASL
Labeling Duration: 1500000 us.
Postlabeling delay: 184628 us.
LabelPlaneOffset: 95 mm.
However, when I set the first option (mdPCASL) at the console, the "pop up help text" says that this setting is for multi-PLD (the other two options I think were single PLD mdPCASL and a third one I cannot recall [I'll be at the scanner later today or
tomorrow, so will verify]); however, I cannot find any trace of the other PLDs.
I will report (and print a PDF) later today or tomorrow.
Thank you so much for the input already!
best
Martin
Hi Martin,
I have some experience of working with the multiband ASL data from the HCP Aging/Development studes. I should be able to help with the analysis.
- The data I have from HCP are multi PLD pcASL. I am not familiar with the scanner console setup, as I haven't been involved in the acquisition. However, it is very common for me to receive Siemens datasets with a scan parameter PDF that describes a single
PLD PASL sequence in the 'Contrast - ASL' field, and then includes a 'Sequence - special' field which describes the multi PLD pcASL sequence I am expecting. I wonder if the more specialised research-focused multi PLD squences are included on the scanners
as modifications to the existing single PLD product sequence.
- There are some differences between our datasets: the HCP ASL data have 90 volumes (86 label-control pairs + 2 noise images + 2 calibration images). My initial analysis steps have been to:
- use fslroi to separate off the label-control pairs (volumes 0 to 85 in my case).
- use fslroi to separate off the calibration images (volumes 88 and 89 in my case)
- so far, I've not come across a way to use the noise images.
- then feed the label-control pairs into oxford_asl as the input data (-i option), and the two calibration images into oxford_asl using the -c option.
- The HCP datasets that I am using are also multibands with 6 bands. I was able to calculate the time per slice from the .json file that I was given with the data. If that is something that you have access to, then it is the difference between the times in
the "SliceTiming" field.
I hope that helps. Get back in touch if you have more questions. I am happy to help.
All the best,
Flora Kennedy McConnell
------------------------------
Postdoctoral Research Associate
Department of Engineering Science
University of Oxford
Old Road Campus Research Building
Oxford, UK
OX3 7DQ
Hi All,
I'm "bumping" this post again in case, one year later, there is someone on the mailing list who can help.
The question is for anyone who has used the UMinn mb-PCASL sequence (part of the HCP project sequences I believe). Unfortunately there is just very little documentation which makes it hard (for me!) to "translate" the parameters from the scanner's console to
the FSL ASL tools.
Here are some questions for anyone who uses the sequence:
1. The sequence seems to me to be single PLD [but in the siemens sequence screen under the “Sequence>Special” tab it seems to say it is a multi PLD acquisition? I can only see one PLD specified however..]
2. The sequences has 70 (tag-control) measurements, but the last 4 are radically different. The v1.0 documentation says that "The implemented MB-EPI PCASL sequence acquires two M0 images after label/control images series. The mean image of these two
M0 images can be used for CBF quantification" but what are the 3rd-/4th-to-last scans (which I assume I have to remove?)
3. This is multiband with 6 bands, but how to find the acquisition time per slice?
Cheers
Martin
Hi everyone
Does anyone have experience with using the UMinn multiband pCASL sequence and processing in FSL? There isn't much documentation, but as far as I can gather, 4 additional images are acquired at the end of the sequence, the last two I think are the M0 calibration
images and the two preceding are maybe thermal noise? Is there a way to use these in FSL or should I just remove these from the asl nifti?
Also, I presume these are tag-control pairs, but not sure how to tell for certain.
I would appreciate any guidance on using this sequence in FSL if anyone has used this. Thanks in advance!
Erik
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