Thanks Michael. My data is a little bit different so it goes like this tag,
control alternating, but each tag/control image has two TIs ( if that makes
sense). Basically, after two pulses (TI1=0.7,TI2=1.8), one image is
acquired. I used SIMENS PICORE Q2T sequence to collect pASL data in case
you need more details. So I am wondering whether I should treat my data as
a single TI data when I use asl_file to get differenced data. Thanks very
much.
On Tue, May 14, 2013 at 9:23 AM, Michael Chappell
<[log in to unmask]>wrote:
> If you are using oxford_asl then you need to have already performed the
> tag-control difference (usually using asl_file, but it could be done via
> FEAT).
>
> Michael
>
> On 13 May 2013, at 21:31, Shan(Hannah) Luo <[log in to unmask]> wrote:
>
> Thanks very much Michael. Is it ok if my input data is feat preprocessed
> pASL data ( perfusion subtraction turned on)? Or it requires just one
> volume differenced data ( tag vs. control)?
>
>
> On Mon, May 13, 2013 at 11:29 AM, Michael Chappell <
> [log in to unmask]> wrote:
>
>> If you M0 has only one volume (implying that the mean has been taken
>> already of any multiple volumes) then you just need to fool oxford_asl into
>> thinking that you have two volumes and it will discard the first one (I
>> will modify this behaviour in future to avoid confusion). This is easy with
>> fslmerge
>> fslmerge -t M0 M0 M0
>>
>> Michael
>>
>> On 13 May 2013, at 15:53, Shan(Hannah) Luo <[log in to unmask]> wrote:
>>
>> There's only one volume for M0.
>>
>> On Monday, May 13, 2013, Mark Jenkinson wrote:
>>
>>> Hi,
>>>
>>> The first problem can be fixed by doing the following in a terminal
>>> before running the GUI:
>>> export FSLDEVDIR=$FSLDIR
>>>
>>> The second problem sounds more serious. How many volumes are in your
>>> M0 image? You can find out by using fslsize and looking at dim4.
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>> On 10 May 2013, at 18:51, Shan(Hannah) Luo <[log in to unmask]> wrote:
>>>
>>> Hi Michael,
>>>
>>> Thanks for your detailed response. I am also currently analyzing
>>> resting state pASL data and when I typed Asl_gui in my terminal, it gave me
>>> an error message:
>>> Error in startup script: can't read "env(FSLDEVDIR)": no such variable
>>> while executing
>>> "set FSLDEVDIR $env(FSLDEVDIR) "
>>> (file "/usr/local/fsl/tcl/asl.tcl" line 72)
>>> invoked from within
>>> "source ${FSLDIR}/tcl/${origname}.tcl"
>>> (file "/usr/local/fsl/bin/Asl_gui" line 22)
>>>
>>> Any ideas what's wrong? I also tried using oxford_asl -i input -s
>>> struct -t high2standard.mat -c M0 --tis 0.7,1.8, it gave me this error
>>> message" *Error: Insufficient volumes in calibration image (to make a
>>> mask), please check M0.nii.gz*".
>>>
>>> Thanks ahead of time.
>>>
>>>
>>>
>>> On Fri, May 10, 2013 at 1:54 AM, Michael Chappell <
>>> [log in to unmask]> wrote:
>>>
>>>> If you are trying to quantify resting perfusion from pASL data then the
>>>> easiest thing to do is use oxford_asl (or the new user interface Asl_gui) -
>>>> I would recommend that you make sure you are using FSL 5.0.3 for this,
>>>> since it handles single TI data better.
>>>>
>>>> In essence what you need to do if you want absolute perfusion are three
>>>> steps (all carried out by the GUI now):
>>>> 1. Tag-control subtraction (asl_file).
>>>> 2. Kinetic model inversion (oxford_asl does this)
>>>> 3. Calibration (estimation of M0a) (oxford_asl or asl_calib)
>>>> If you can live with relative perfusion then the first step might be
>>>> all you want to start with. I think that correction for partial volume
>>>> effects is a good idea, but this is not widely used as of yet in the
>>>> community so it can currently be harder to interpret the results since
>>>> there is less literature to refer to.
>>>> Motion correction is generally a good idea and mcflirt can be used as a
>>>> first step. Motion correction can be problematic with ASL data though.
>>>>
>>>> Michael
>>>>
>>>> On 9 May 2013, at 14:00, Dídac Vidal <[log in to unmask]> wrote:
>>>>
>>>> > Hi everybody!.
>>>> >
>>>> > I am trying to preprocess fMRI perfusion data with BASIL toolset
>>>> scripts for first time in a pASL with single TI data and I am getting a
>>>> little confused.
>>>> >
>>>> > I think I would use
>>>> > a) asl_reg for registration,
>>>> > b) asl_file in order to get a CBF quantification,
>>>> > and then I woul use c) asl_calib in order to get an absolute
>>>> quantification of CBF.
>>>> >
>>>> > My questions are:
>>>> > 1) is that correct?
>>>> > 2) I am missing something?
>>>> > Is PVE recommended /necessary?
>>>> > I guess some motion correction should be carried out before asl_file?
>>>> Probably mcflirt should work fine.
>>>> >
>>>> > Thanks in advance
>>>> >
>>>>
>>>
>>>
>>>
>>
>
>
