There was a reply from Christian Beckmann to this email on July 6.
In fact it was sent 32 minutes after the original message was posted!
I've included it below in case your email lost it.
All the best,
Mark
> Hi,
>
> Your voxel dimensions in Z seem to be wrong. Check with avwsize
> filename that the voxel size in Z (pixdim3) is what it should be.
> If not, you can use avwedithd to change this.
> cheers
> christian
On 8 Jul 2007, at 23:20, Naama Barnea-Goraly wrote:
>
> Haven't received any answers to my question. I hope it is not that
> difficult..
>
> Anyone? Any thoughts?
>
> Original question:
>
> I am trying to run TBSS on an older data set. Results of the
> transformation to the MNI template are attached below (mean_FA sand
> the MNI template separately). I have run a few other data sets
> before and never saw this problem before. All I can think of that
> is different in this data set is that two different (but similar)
> acquisition matrices were used, one is 128x128 19 slices and one
> was zerofilled to 256x256 x18, both scans did not cover the
> cerebellum. Any advice would be appreciated.
>
> Thanks much,
>
> Naama
>
> <MNImeanFA.tiff>
>
>
>> From: Naama Barnea-Goraly <[log in to unmask]>
>> Date: July 5, 2007 3:28:52 PM PDT
>> To: FSL - FMRIB's Software Library <[log in to unmask]>
>> Subject: [FSL] transformation problem (?)
>>
>>
>>
>> After some off-list clarifications (sorry, and thanks, Andreas!).
>> I would like to explain that the image I previously sent was an
>> artificial image created by me, not my mean_FA image. It was a
>> superimposed image of the mean_FA and and MNI template, I made the
>> template lighter so that the differences would be apparent, it is
>> not an intensity drop.
>>
>> To make things clearer I am attaching an image of my mean_FA and
>> (just for reference) the MNI template. Obviously they are not
>> registered.
>> I would appreciate any advice on why this happened.
>>
>> Thanks much!
>>
>> Naama
>>
>>
>>
>>
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>
>
> Naama Barnea-Goraly M.D.
> Research Associate
> Center for Interdisciplinary Brain Sciences Research
> Stanford University Division of Child and Adolescent Psychiatry
> 401 Quarry Rd. MC 5795
> Stanford University School of Medicine
> Stanford, CA 94305-5795
> fax: (650) 724-4794
> Phone: (650) 724-3779
>
>
> CONFIDENTIALITY NOTICE: This e-mail communication and any
> attachments may contain confidential information for the use of the
> designated recipients named above. If you are not the intended
> recipient, you are hereby notified that you have received this
> communication in error and that any review, disclosure,
> dissemination, distribution or copying of it or its contents is
> prohibited. If you have received this communication in error,
> please notify Stanford Medical Center immediately by telephone at
> (650) 725-5722 and destroy all copies of this communication and any
> attachments. Thank you.
>
>
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