Print

Print
Davide,

What do you mean by ‘pre processing’ in this context? oxford_asl should provide all results, both relative and absolute perfusion in native_space, along with results in structural space if appropriate. 

Michael

On 17 Jan 2018, at 05:40, Davide Momi <[log in to unmask]> wrote:

Thanks Michael!! Now it works well. I was wondering whether is possibile run the pre processing in the subject space (without any normalization step)

Best

Davide

On Jan 15, 2018 16:16, "Michael Chappell" <[log in to unmask]> wrote:
This could well be a shell issue, you should be fine if you run it under a bash shell, but a few people have had issues when their terminal doesn’t support the use of arrays (something we have fixed in the pre-release of the BASIL tools).

Michael


On 12 Jan 2018, at 16:16, Davide Momi <[log in to unmask]> wrote:

Hello,

thanks for your reply. This is the script that I've run:

oxford_asl -i /home/max/Scrivania/sb1/FUNC/PASL.nii -o /home/max/Scrivania/pippo/  -s /home/max/Scrivania/sb1/STRUC/T1_brain.nii.gz  -c /home/max/Scrivania/sb1/FUNC/M0.nii --tr=3 --tis=1.8

But I still get the same error:

OXFORD_ASL - running
Saving results in natve (ASL aquisition) space to /home/max/Scrivania/pippo//native_space
Saving results in structural space to /home/max/Scrivania/pippo//struct_space
Pre-processing
Creating mask
Performing registration
ASL_REG
Input file is: /tmp/fsl_3gh19b_ox_asl/meanasl
Running FLIRT
Tidying up
ASL_REG - Done.
Calculating M0a - calling ASL_CALIB
ASL_CALIB
Tissue reference is: csf
M0:1410.13000000000000000000
ASL_calib - DONE.
/usr/local/fsl/bin/oxford_asl: 1176: /usr/local/fsl/bin/oxford_asl: alltis[0]=1.8: not found
Number of inversion times: 1
Number of timepoints in data: 88
Number of repeats in data: 88

Any tips?

Davide



Davide Momi
-----------
PhD Candidate
Unit of Behavioral Economics and Neuroeconomics
Department of Neuroscience, Imaging and Clinical Sciences
University "G. d'Annunzio" of Chieti
Via dei Vestini 31, 66013 Chieti, Italy

2018-01-12 16:49 GMT+01:00 Michael Chappell <[log in to unmask]>:
From your scan parameters you only have one TI (at least as far as oxford_asl understands the term). You are clearly using pASL and your TI is 1.8 (your TI2) seconds and your bolus duration is 0.7 seconds (your TI1).

Michael


On 12 Jan 2018, at 13:28, Davide Momi <[log in to unmask]> wrote:

Dear FSL experts,

From previous exchanges it wasn't clear to me what is the solution to this problem. The Oxford_ASL script produces an error:
SCRIPT LINE: oxford_asl -i data_pasl/diffdata --tis 0.7, 1.8 -o ex1_1 --bolus 1.1 --bat 0.7 --t1 1.3 --t1b 1.66 --artoff --spatial

/usr/local/fsl/bin/oxford_asl: 1176: /usr/local/fsl/bin/oxford_asl: alltis [0]= 0: not found
/usr/local/fsl/bin/oxford_asl: 1176: /usr/local/fsl/bin/oxford_asl: alltis [0]= 7: not found

Number of inversion time: 2
Number of timepoints in data: 88
Number of repeats in data: 44

I was wondering what shall I put as TIs. I mean my machine parameters are:

- Inversion Time 1: 0.7
- Saturation Stop Time: 1,6
- Inversion Time 2: 1,8

Could you please help me with that?

Thanks

---
Michael Chappell MEng DPhil
Associate Professor, Institute of Biomedical Engineering, University of Oxford.
Director of Training, EPSRC-MRC CDT in Biomedical Imaging
Governing Body Fellow, Wolfson College, Oxford.










---
Michael Chappell MEng DPhil
Associate Professor, Institute of Biomedical Engineering, University of Oxford.
Director of Training, EPSRC-MRC CDT in Biomedical Imaging
Governing Body Fellow, Wolfson College, Oxford.









---
Michael Chappell MEng DPhil
    T: +44 1865 617657
Associate Professor, Institute of Biomedical Engineering, University of Oxford.
Director of Training, EPSRC-MRC CDT in Biomedical Imaging
Governing Body Fellow, Wolfson College, Oxford.
    http://www.wolfson.ox.ac.uk