I got many troubles for sending a mediate size package here, but see the following message.
-----Original Message-----
From: zewang [mailto:[log in to unmask]]
Sent: Monday,
December 10, 2007 11:18 AM
To: [log in to unmask]
Cc: [log in to unmask]
Subject: ASLtbx RE: [SPM] turning
off HRF in SPM5
Dear all,
Attached is the latest version of ASLtbx, consisting of a series of batch scripts. The one for calculating CBF is: asl_perf_subtract.m, all others beginning with “batch” are for preprocessing or statistical analysis. The scripts should work for both SPM2 and SPM5. A rough instruction is included in the readme file. We will put the scripts and an example data set online, though our website has not been updated for couple years since the web administrator left.
For turning off HRF modeling in SPM, you can do it manually like what Janniko said in his email, or activate line 74 “% SPM.xBF.name='Fourier set';” in batch_model.m by deleting the “%” sign, and comment out line 75 “ SPM.xBF.name='hrf';”. I would suggest using the HRF convolving since there is a delay between the onset of the stimuli and the acquisition time due to the labeling time and post label delay. Or you can adjust the reference function to incorporate this delay. I didn’t modify the reference function in the attached package.
Another note for manually running GLM on ASL data in SPM is that you need to change the default threshold for removing the background or unsafe regions. That is, you should load spm_defaults, and then set “defaults.mask.thresh=-inf;” or another value you want. As you can see from the time course, ASL data has a very low temporal SNR, regular threshold works for BOLD will remove most of the ASL signals.
Please let me know if you have any questions.
---------------------------------------------
Ze Wang, Ph. D
Center for functional neuroimaging,
Dept of Neurology,
Medicine school,
University of Pennsylvania
3400 Spruce Stree,
3W Gates building,
Philadelphia, PA 19104
Tel: 215-662-7341
-----Original Message-----
From: SPM (Statistical Parametric
Mapping) [mailto:[log in to unmask]] On
Behalf Of [log in to unmask]
Sent: Monday,
December 10, 2007 3:51 AM
To: [log in to unmask]
Subject: Re: [SPM] turning off HRF
in SPM5
Hi Callum,
There is a number of things that you could do:
1) Define your condition blocks as regressors: this eliminates the HRF as no basis functions are carried out over regressors.
2) Under basis functions, choose Finite Impulse Response. For "window length" fill in your TR (after subtraction of the tagged and untagged images) divided by 16 (TR/16). For "order" fill in 1. This procedure essentially deactivates the basis functions.
3) Use the factorial design specification, and treat your ASL data as if they were PET-data. No basis functions are carried out in the factorial design specification.
4) Use the ASLtbx, a toolbox that was recently developed for SPM2 and SPM5 ASL-analyses. It is not yet available as SPM-plug in, but it was recently presented in Wang et al. (Magn. Res. Imaging 2007). You might try to contact the authors and ask them to make the tool available for you.
Good luck
Janniko
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Callum Thorpe
Sent: maandag 10 december 2007 1:17
To: [log in to unmask]
Subject: [SPM] turning off HRF in SPM5Hi All
Sorry if this is a basic question. We are currently using functional perfusion imaging and have started the analysis in spm5. We need to specify the design matrix without the hemodynamic response function, after a good look we cannot find a way of producing a design matrix withouth this step. Any help would be greatly appreciated.
Callum Thorpe
University of Auckalnd, NZ