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I see the problem, it is to do with the slices - asl_file assumes that the data comes as a 4D volume with slices in the 3rd dimension and all the tag and controls in the 4th dimension. What you will need to do is stitch the data together so that you have volumes with all the slices at each TI tag and control paired together.
I think that something like this might work (although I have probably made a mistake in typing somewhere):
Assume you have 104 images in a stack that are 2D slices in the order in your email (if the data is not in this form then use fslsplit to get there) and are each called image_{n}
for ((i=1; i<=8; i++)); do
list=""
for ((j=$i; j<=13; j++)); do
k=`expr $j \* 8 + $i`
  l=`expr $k + 104`
list="$list image_$k image_$l"
done
fslmerge -z out_$i $list
done
This assumes you have 8TIs and 13 slices, which doesn't quite match the list you gave - but you can swap around if need be.
The result of this is that out_1 should be all the slices at TI1, tag then control, out_2 at TI2 etc
So now:
fslmerge -t Rpt_1 out_*
(note that if you had more than 9 TIs this would not be ideal since the TIs could end up in the wrong order because I have not been careful about numbering)
Then you need to run this again only any repeats you have to get Rpt_2 etc
Finally:
fslmerge -t Data Rpt_*

This should now be 4D with slices in dim 3 and in dim 4 the data as: TI1 (tag), TI1 (ctrl), TI2 (tag), TI2 (ctrl) …, TI1 (tag), TI1 (control) …
This is now in a format that asl_file can handle (--ibf=rpt)

Michael

On 9 Apr 2013, at 21:22, Inge Rasmussen <[log in to unmask]> wrote:

Dear dr. Chappel; 


Thanx for taking the time to help solve our problems concerning multi-TI-analysis! You wanted some more details on the readout order of our data; they are acquired on a Philips Achieva, using a STAR sequence with a Look-Locker readout. The data we are struggling with, has 8 TI-s and 13 slices, read in ascending order. A stack is thus 13x8=104 images. This means that we read out in the following manner:


Image 1: Slice 1, TI1, tagged.
Image 2: Slice 1, TI2, tagged.
Image 3: Slice 1, TI 3, tagged.
...
...
...
...
...
Image 14: Slice 2, TI1, tagged.
Image 15: Slice 2, TI2, tagged.
Image 16: Slice 2, TI 3, tagged.
...
...
...
...
...
Image 27: Slice 3, TI1, tagged.
Image 28: Slice 3, TI2, tagged.
Image 29: Slice 3, TI3, tagged.
...
...
...
...
..............
Image 105: Slice 1, TI1, control.
Image 106: Slice 1, TI2, control.
Image 107: Slice 1, TI 3, control.
...
...
...
...
...
Image 118: Slice 2, TI1, control.
Image 119 Slice 2, TI2, control.
Image 120: Slice 2, TI 3, control.
...
...
...
...
...
..............
Image 209 and forward: Second tagged volume. 

Etc.

What we need to do, is to have the asl_file provide the t-c differences and make the mean over all repeats before piping it into oxford_asl.  We are unable to get the asl_file to do this...



Would you have a good tip??


Kind regards from


Dr. Inge Groote
Oslo University Hospital
Norway

> Date: Wed, 3 Apr 2013 16:02:22 +0100
> From: [log in to unmask]
> Subject: Re: [FSL] asl_file
> To: [log in to unmask]
> 
> The simplest thing to do is provide oxford_asl with your data as the tag-control differences at your 8 TIs having taken the mean over all the repeats within each TI. The exact command you want will depend upon what order things are in your current data, perhaps you can provide more details on that?
> 
> Michael
> 
> On 31 Mar 2013, at 12:35, Inge R. Groote <[log in to unmask]> wrote:
> 
> > Hi, Experts!
> > 
> > Attempting to move all ASL analysis steps to FSL, I am currently struggling with sorting multi-TI ASL images before piping it into oxford_asl, but with remarkably little success. 
> > 
> > My data is Philips, 13 slices, 8 Tis, read out with 2D EPI. The format thus differs from the 3D-GRASE images in the BASIL tutorial concerning the exact asl_file commands. I am trying to generate the difference images, but can only generate numerous wrongful suggestions. I have tried most permutations of commands, but obviously not the correct one...
> > 
> > I have successfully sorted and subtracted the data using other softwares, thus the data itself is valid.
> > 
> > Any good tips on how to proceed?
> > 
> > Kind regards
> > 
> > Dr. I. Groote
> > Norway
> >