Hi Wen,
My colleague told me that psd refers to a kind of GE sequence file
format, it is not a specific sequence name. You may refer to Dave's ASL code
for GE. To answer your question, I'd like to have more information about the
specific sequence involved, not just "psd".
Thanks.
---------------------------------------------
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: Wen-Ching Liu [mailto:[log in to unmask]]
Sent: Monday, December 10, 2007 3:45 PM
To: Ze Wang
Subject: Re: [SPM] ASL data processing toolbox, FW: ASLtbx RE: [SPM] turning
off HRF in SPM5
Hi Ze:
I thought you have special pulse sequences to run ASL.
In GE, they called it psd. Two years ago, I was told
that we can establish an research contract between
UPenn, UMDNJ and Siemens to run the ASL psd developed
by UPENN. Is it still the same case?
Wen
On Dec 10, 2007, at 2:02 PM, Ze Wang wrote:
> Hi Wen,
> What do u mean psd? The gradient echo sequence used for imaging?
> Ze
> Quoting Wen-Ching Liu <[log in to unmask]>:
>
>> Hi Ze:
>>
>>
>> Does the psd of ASL for scanner(s) need research contract
>> or it can be loaded from some website?
>>
>> Our site (using Siemens 3T) has some problems with the
>> research contract from Siemens and it never settled.
>> I wonder if there anyway we can still install the ASL here
>> either GE 1.5T or Siemens 3T?
>>
>> Thanks,
>>
>>
>> Wen
>>
>>
>>
>>
>> On Dec 10, 2007, at 12:04 PM, zewang wrote:
>>
>>> 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 SPM5
>>>
>>> Hi 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
>>>
>>> <ASLtbx.zip>
>>
>> Wen-Ching Liu, Ph.D.
>>
>> Assistant Professor
>> Functional Imaging Laboratory
>> Department of Radiology
>> University of Medicine and Dentistry
>> of New Jersey-New Jersey Medical School
>>
>> 973-972-2281/fax: 973-972-0836
>> http://njms.umdnj.edu/departments/radiology/fmri/index.cfm
>>
>>
>>
>
>
> --
> Center for functional neuroimaging,
> Medicine School,
> University of Pennsylvania,
> 3400 Spruce Street,
> 3W Gates Building,
> Philadelphia,
> PA 19104, USA
> tel:215-662-7341
Wen-Ching Liu, Ph.D.
Assistant Professor
Functional Imaging Laboratory
Department of Radiology
University of Medicine and Dentistry
of New Jersey-New Jersey Medical School
973-972-2281/fax: 973-972-0836
http://njms.umdnj.edu/departments/radiology/fmri/index.cfm
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