Hi Barbara,
Thank you very much, I will try it. (Currently I am also thinking of using programming language to manipulate the data/images. Will see.)
Regards,
Suhuai
From: SPM (Statistical Parametric
Mapping) [mailto:[log in to unmask]] On Behalf Of Barbara Kreilkamp
Sent: Wednesday, 21 March 2018 8:00 PM
To: [log in to unmask]
Subject: Re: [SPM] How to make SPM12 Segment work to get Grey Matter etc. - Re-posted
Hi Suhuai,
You could try out clinical_setorigin.m written by Chris Rorden, within his SPM clinical toolbox
https://github.com/neurolabusc/Clinical
Cheers,
Barbara
On 21/03/2018 04:51, Suhuai Luo wrote:
Hi John,
It worked – after setting the origin to right position as you suggested, SPM12 can segment GM for my images. Really thank you very much! So I can stay in SPM group, no need to seeking solution from other packages.
If you (or anyone seeing this message pls) know a further step, pls help:
I want to work on multiple images, so hope a batch job can be run to Set Origin & Reorient for every image in the group. But I just cannot work out a way to do it (Set Origin & Reorient are in Display, I have to click it for every image to do it. I can assign a fixed origin coordinate for all the images. And Batch Editor does not give selection on setting Origin & Reorient). Any suggestions? Thank you very much in advance.
Regards,
Suhuai Luo
From: Suhuai Luo
Sent: Monday, 19 March 2018 10:10 PM
To: 'John Ashburner' <[log in to unmask]>
Cc: SPM <[log in to unmask]>
Subject: RE: [SPM] How to make SPM12 Segment work to get Grey Matter etc. - Re-posted
Thank you very much, John. I’ll have a look.
Regards,
Suhuai
From: John Ashburner [mailto:[log in to unmask]]
Sent: Monday, 19 March 2018 9:59 PM
To: Suhuai Luo <[log in to unmask]>
Cc: SPM <[log in to unmask]>
Subject: Re: [SPM] How to make SPM12 Segment work to get Grey Matter etc. - Re-posted
The origin was wrong by about 20 inches.
Best regards,
-John
On 16 March 2018 at 22:34, Suhuai Luo <[log in to unmask]> wrote:
Hi John,
Many thanks for your help. Seems I tried bit on origin before, but I’ll try it thoroughly in 2 days.
Just a point: “…by about half a metre”, what do you exactly mean “metre”?
Regards,
Suhuai
From: John Ashburner [mailto:[log in to unmask]]
Sent: Saturday, 17 March 2018 12:00 AM
To: Suhuai Luo <[log in to unmask]>
Cc: SPM <[log in to unmask]>
Subject: Re: [SPM] How to make SPM12 Segment work to get Grey Matter etc. - Re-posted
Try moving the origin in the header by about half a metre. SPM uses starting estimates taken from the header in order to register the images with MNI space. If the origin is way off, then this fails.
You can use the Display button to do this re-positioning.
Best regards,
-John
On 16 March 2018 at 04:39, Suhuai Luo <[log in to unmask]> wrote:
Dear SPM Experts and Users,
I posted the following content 2 weeks ago, since the issue has not been solved, hope you could read it again if you havenot got a chance before, thanks.
I am trying to get grey matter (and other matters) out of t1 MRI using SPM12. It worked on one group of the images, but not at all for another group of files. So far I cannot figure out why, just can see some difference between the two groups – the not working group has different original coordinates and maybe less contrast, and the working group may have gone through different preprocessing which I am not sure. For the NOT working group I tried to adjust almost all the parameters in SPM12, just got all 0’s as segment out.
Note: I tried another segment tool, it worked for the both group, but with too much redundant areas for both comparing to SPM. So I do want SPM work.
I will appreciate it very much if you could help solving the issue (e.g., tell exactly what parameters to choose, or how to pre-adjust the images, etc.), or offer any hints. For your possible trying on, I upload the two files (about 40Mb, File1 belongs to not working group, File2 belongs to working group) to owncloud, the link:
https://owncloud.newcastle.edu.au/index.php/s/tFtd6iqUNdPeJMZ; and pw is 2018.
Regards,
Suhuai Luo
The University of Newcastle
https://www.newcastle.edu.au/profile/suhuai-luo
--
Prof John Ashburner
Professor of Imaging Science
UCL Institute of Neurology
Queen Square
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square, London, WC1N 3BG
E: [log in to unmask] T: +44 (0)20 3448 4365
http://www.fil.ion.ucl.ac.uk/
--
Prof John Ashburner
Professor of Imaging Science
UCL Institute of Neurology
Queen Square
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square, London, WC1N 3BG
E: [log in to unmask] T: +44 (0)20 3448 4365
http://www.fil.ion.ucl.ac.uk/