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SPM  July 2008

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Subject:

Re: realign_and_unwarp.m

From:

Julie McEntee <[log in to unmask]>

Reply-To:

Julie McEntee <[log in to unmask]>

Date:

Tue, 8 Jul 2008 21:50:59 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (96 lines)

Thank-you for your reply.

The reason I inquired about realign & unwarp is that I am trying to
determine the optimal spatial preprocessing method for fMRI data acquired
from 2 groups: healthy controls and patients w/ Huntington's Disease.
T1-weighted images were also acquired.

My concern is that the patients' brains may be structurally different from
controls. After realign & unwarp, what would be the best way to estimate the
warp parameters to use to write normalize the functional images into MNI
space? If I use the parameters produced by segmentation of the T1 image,
would the functionals be in MNI space after write normalization? If I use
normalize: estimate to determine the warp parameters and use the
bias-corrected T1 from segmentation in addition to an MNI template, would I
use the mean functional image from realignment as the source image?

I may be making this more complicated than it needs to be. Your advice would
be greatly appreciated.

Regards,

Julie

-----Original Message-----
From: Dr. Karsten Mueller [mailto:[log in to unmask]] 
Sent: Tuesday, July 08, 2008 12:06 PM
To: JULIE E MCENTEE
Subject: Re: [SPM] pixdim4 in NIfTI header after realign_anbd_unwarp.m

Dear Julie,

thank you for your email. In SPM5, you can decide if you want "realign
and reslice" or "realign and unwarp". If you decide for unwarp, SPM is
calculating the EPI distortions from the images. Alternatively, you can
specify a "voxel displacement map (vdm)" that describes the EPI
distortions. Thus, you can do the EPI distortion correction while
applying the realign parameters to the data set.

Those things (realign and unwarp) are the first step in pre-processing
and have nothing to do with the normalization (into the MNI space). This
normalization can be done *after* the realignment.

With best wishes to Baltimore,
Karsten

JULIE E MCENTEE wrote:
> Dr. Mueller,
>
> I am interested in the SPM5 preprocessing option 'unwarp'. Could you
please tell me why you decided to use it? Did you normalize your images or
would that be redundant when you use unwarp?
>
> Thank-you,
>
> Julie
>
> Julie E. McEntee, M.A., C.C.R.P.
> Senior Research Program Coordinator
> Department of Psychiatry- Neuroimaging
> Johns Hopkins University School of Medicine
> 600 N. Wolfe St./ Phipps 300
> Baltimore, MD 21287
> Phone: 410-502-0468
> Fax: 410-614-3676
>
> ----- Original Message -----
> From: "Dr. Karsten Mueller" <[log in to unmask]>
> Date: Tuesday, July 8, 2008 5:08 am
> Subject: [SPM] pixdim4 in NIfTI header after realign_anbd_unwarp.m
> To: [log in to unmask]
>
>
>   
>> Dear Colleagues,
>>  
>>  we are using Realign and Unwarp (spm_realign.m,  spm_uw_estimate.m, and
>>  spm_uw_apply.m) with 4D-NIfTI data which gives very nice results.
>>  
>>  However, these m-routines seem to change the NIfTI-header. Before
>>  starting the realignment, our header shows
>>  
>>  time_units     ms
>>  pixdim4        2000.0000000000
>>  
>>  which is correct. After using realign and unwarp, the NIfTI header shows
>>  
>>  time_units     s
>>  pixdim4        1.0000000000
>>  
>>  This might be a problem when further programs are using the repetition
>>  time from the NIfTI header.
>>  
>>  With best wishes,
>>  Karsten 
>>     

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