Yes, you might also want to re-mask:
avwmaths++ input-FA-image -sub mean -div std \
-mas input-FA-image output-Z-image
On Mon, 15 Jan 2007 09:37:05 +0800, xu haibo <[log in to unmask]> wrote:
>Hi Steve,
>
> How to use avwmaths++ to convert the FA to a Z image? The cmd line is
>"avwmaths++ input-FA-image -sub mean -div std output-Z-image, isn't it
>right? Thanks.
>
>haibo
>
>>From: Steve Smith <[log in to unmask]>
>>Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>To: [log in to unmask]
>>Subject: Re: [FSL] How to calculate CC on the FA map
>>Date: Sun, 14 Jan 2007 18:41:25 +0000
>>
>>Hi - yes, use avwstats++ to get the std and mean within the ROI, and
>> then avwmaths++ to convert the FA to a Z using this.
>>Steve
>>
>>
>>
>>On 12 Jan 2007, at 11:44, xu haibo wrote:
>>
>>>Hi, Steve,
>>>
>>> Right. I want to convert an FA image into a Z image on the
>>>basis of similarity of voxel FA values to that mean and to use the
>>> stddev inside the ROI. How to do that? BTW, what is different if
>>>using the stddev across the image? Thanks.
>>>
>>>haibo
>>>>From: Steve Smith <[log in to unmask]>
>>>>Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>>>To: [log in to unmask]
>>>>Subject: Re: [FSL] How to calculate CC on the FA map
>>>>Date: Thu, 11 Jan 2007 17:26:04 +0000
>>>>
>>>>Hi,
>>>>
>>>>I think you're saying that you want to define an ROI within which
>>>>to estimate a mean FA value. You then want to convert an FA image
>>>> into a Z image on the basis of similarity of voxel FA values to
>>>> that mean. However, in order to do that you will also need to
>>>>define what standard deviation you want to use to form the Z. Do
>>>>you want to use the stddev inside the ROI, or across the image,
>>>>or maybe some other measure?
>>>>
>>>>Cheers.
>>>>
>>>>
>>>>On 11 Jan 2007, at 11:56, xu haibo wrote:
>>>>
>>>>>Hi, Steve,
>>>>>
>>>>> Thanks for your time for answering my question. I try to get a
>>>>> Z map where I can adjust the threshold to see the FA value of
>>>>>which voxel is close that of ROI on the FA map. Sorry for my
>>>>>poor english. Do I make myself clear? Thanks.
>>>>>
>>>>>
>>>>>>From: Steve Smith <[log in to unmask]>
>>>>>>Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>>>>>To: [log in to unmask]
>>>>>>Subject: Re: [FSL] How to calculate CC on the FA map
>>>>>>Date: Wed, 10 Jan 2007 16:34:21 +0000
>>>>>>
>>>>>>Hi - I'm sorry, I can't understand what you're asking here.
>>>>>>Please could you clarify what you are wanting to do?
>>>>>>Thanks.
>>>>>>
>>>>>>
>>>>>>On 7 Jan 2007, at 14:13, Haibo Xu wrote:
>>>>>>
>>>>>>>Hi, FSL experts,
>>>>>>>
>>>>>>> I want to calculate the correlation coefficient of the FA
>>>>>>> value each
>>>>>>>voxel referred to the FA value of ROI based on the FA map. If
>>>>>>>I define the
>>>>>>>ROI as the mass on the FA map, for example, then compare the
>>>>>>>FA value each
>>>>>>>voxel in the same brain volume to the FA value of ROI and try
>>>>>>>to get a CC
>>>>>>>map. In addition, to adjust the threshold to see which voxel
>>>>>>>is highly
>>>>>>>related to the ROI on the CC map. But I do not know to how to
>>>>>>>use FSL
>>>>>>>tools to get the CC map based on the FA map. Please tell me
>>>>>>>how to do it.
>>>>>>>Any suggestion or advice will be greatly appreciated.
>>>>>>>
>>>>>>>Haibo
>>>>>>
>>>>>>
>>>>>>-------------------------------------------------------------------
>>>>>>-- --- ---
>>>>>>Stephen M. Smith, Professor of Biomedical Engineering
>>>>>>Associate Director, Oxford University FMRIB Centre
>>>>>>
>>>>>>FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>>>>>+44 (0) 1865 222726 (fax 222717)
>>>>>>[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>>>>>-------------------------------------------------------------------
>>>>>>-- --- ---
>>>>>
>>>>>_________________________________________________________________
>>>>>享�世界上最大的���
>>>>>邮件系统â€?MSN Hotmailã� http://
>>>>>www.hotmail.com
>>>>
>>>>
>>>>---------------------------------------------------------------------
>>>>--- ---
>>>>Stephen M. Smith, Professor of Biomedical Engineering
>>>>Associate Director, Oxford University FMRIB Centre
>>>>
>>>>FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>>>+44 (0) 1865 222726 (fax 222717)
>>>>[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>>>---------------------------------------------------------------------
>>>>--- ---
>>>
>>>_________________________________________________________________
>>>Ãâ·Ñ�ÂÔØ MSN Explorer: http://explorer.msn.com/lccn
>>
>>
>>------------------------------------------------------------------------
>>---
>>Stephen M. Smith, Professor of Biomedical Engineering
>>Associate Director, Oxford University FMRIB Centre
>>
>>FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>>+44 (0) 1865 222726 (fax 222717)
>>[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>>------------------------------------------------------------------------
>>---
>
>_________________________________________________________________
>ÓëÁª»úµÄÅóÓѽøÐн»Á÷£¬ÇëʹÓà MSN Messenger: http://messenger.msn.com/cn
>===========================================================
=============
|