Thanks, I'll look into that.
For now though, it seems like SPM shows a projection of the region onto the center slice--this helps so you can see all the slices. The nifti file produced is in the right location when opened in a 3D viewer and the timeseries in the .mat file is the same as one obtained through other methods, so even if the display looks a little off, the data produced is correct so I'm not worried.
thanks!
-qf
________________________________________
From: Guillaume Flandin <[log in to unmask]>
Sent: Friday, January 5, 2018 5:53 AM
To: Funk, Quentin
Cc: Funk, Quentin; [log in to unmask]
Subject: Re: [SPM] Images for time series extraction wrong?
Dear Quentin,
Could you try modifying the spm_dcm_display.m file by commenting out
line 68: %M1(j,4) = 0;
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_spm_spm12_blob_r7219_spm-5Fdcm-5Fdisplay.m-23L68&d=DwICAw&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=7C10W14ZIX10JExkk0acnrbfHuJ1ig7U_bS8JV8ELAw&m=r8Ujpur3D67o1ruQGu5-6mY4KVYMvWqINMgpAjosczk&s=hjKWkDJ05tOolRo5EKv7goYJUEajHdFv73phYjI7G1w&e=
You can ask to display again an extracted VOI file using the command:
>> spm_regions('Display','VOI_CSF_1.mat');
Best regards,
Guillaume.
On 04/01/18 16:36, Funk, Quentin wrote:
> SPM experts,
>
>
> I'm trying to use VOI's to extract time series for DCM in SPM. I'm using
> coordinates that came from a voxelwise analysis in SPM of some PET data,
> but when I plug those coordinates in, it shows the region in a different
> place than expected (e.g. if I open an MNI brain in a viewer and place
> the cursor at the same point, see attached images)
>
>
> Similarly, if I follow the example in the SPM 12 Manual (page 354)
> to get a voi for the CSF, the image in the graphics window shows a
> seed that intersects the cerebellum (see attached image). I had thought
> that these coordinates (0,-40,-5) must be incorrect--since they're
> supposed to be in the ventricle but they're at 0 on the X-axis, which is
> the midline in MNI space--and was unsurprised when I got the wrong
> image, but after getting a strange image with my own data I'm extra
> confused.
>
>
> Any help would be great!
>
>
> Quentin Funk, PhD
> Houston Methodist Research Institute
> 713-363-9003 <tel:713-363-9003>
>
> Houston Methodist. Leading Medicine.
>
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--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
Houston Methodist. Leading Medicine.
U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
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