----- Weitergeleitete Nachricht von [log in to unmask] -----
Datum: Tue, 23 Jun 2015 19:15:59 -0600
Von: Kulpreet Cheema <[log in to unmask]>
Antwort an: Kulpreet Cheema <[log in to unmask]>
Betreff: RE: [SPM] getting error while doing all 3 jobs in one
batch window for VBM preprocessing
An: Volkmar Glauche <[log in to unmask]>
Hello Volkmar,Thanks so much for the reply. I am sending the
screenshot of the batch jobs I did for the preprocessing. For the 3rd
option "Normalise to MNI space" , when I do the jobs separately, I
select "urc1*.nii" images in Flow fields option (as outlined in manual
too) but when doing the jobs together, I don't see the ""urc1*.nii"
images in the dependency option(the image to the right in 1st picture)
but I see the option of Flow Fields which doesn't work. What I want to
see is the picture titled "preferred_flowfields_option" which is what
I see when I run the 3rd option on its own but not when I run all the
3 jobs together. I am doing everything else similar to what you
outlined and as outlined in the manual. I selected the DARTEL created
flowfields which is created as the dependency and the use the c1
images for the IMAGES option. But when I do these 3 jobs together, it
never works beyond the 2nd job.I guess the main problem is the
inability to see the u_rc1 images in the 3rd job (Normalise to MNI
space) dependency option which should be seen and this is causing all
the problems. Thanks again for all your help!
Kulpreet Cheema
BSc. Psychology (Science)
University of Alberta,
2015
LinkedIn: ca.linkedin.com/pub/kulpreet-cheema/53/69/2b4/
> Date: Tue, 23 Jun 2015 13:59:02 +0100
> From: [log in to unmask]
> Subject: Re: [SPM] getting error while doing all 3 jobs in one batch
> window for VBM preprocessing
> To: [log in to unmask]
>
> Dear Kulpreet Cheema,
>
> since you did not attach your batch job, it is difficult to guess
> what you were trying to do and went wrong. As the error message
> suggests, the number of flow fields did not match the number of
> images to normalise using "Normalise to MNI space". You would want
> to use the "Many subjects" option in for "Normalise to MNI space".
> Then, you would enter the DARTEL created flow fields as a dependency
> for "Flow Fields". For each set of images to normalise, you would
> then add a new "Images" item and select files for each subject or
> use a dependency for e.g. c1 or c2 images. Each images item should
> contain exactly one image per subject in the order of the DARTEL
> flow fields.
>
> Hope this helps,
>
> Volkmar
----- Ende der weitergeleiteten Nachricht -----
--
Freiburg Brain Imaging
http://fbi.uniklinik-freiburg.de/
Tel. +761 270-54110
Fax. +761 270-53100
Hello Volkmar,Thanks so much for the reply. I am sending the screenshot of the batch jobs I did for the preprocessing. For the 3rd option "Normalise to MNI space" , when I do the jobs separately, I select "urc1*.nii" images in Flow fields option (as outlined in manual too) but when doing the jobs together, I don't see the ""urc1*.nii" images in the dependency option(the image to the right in 1st picture) but I see the option of Flow Fields which doesn't work. What I want to see is the picture titled "preferred_flowfields_option" which is what I see when I run the 3rd option on its own but not when I run all the 3 jobs together. I am doing everything else similar to what you outlined and as outlined in the manual. I selected the DARTEL created flowfields which is created as the dependency and the use the c1 images for the IMAGES option. But when I do these 3 jobs together, it never works beyond the 2nd job.I guess the main problem is the inability to see the u_rc1 images in the 3rd job (Normalise to MNI space) dependency option which should be seen and this is causing all the problems. Thanks again for all your help!
Kulpreet Cheema
BSc. Psychology (Science)
University of Alberta,
2015
LinkedIn: ca.linkedin.com/pub/kulpreet-cheema/53/69/2b4/
> Date: Tue, 23 Jun 2015 13:59:02 +0100
> From: [log in to unmask]
> Subject: Re: [SPM] getting error while doing all 3 jobs in one batch window for VBM preprocessing
> To: [log in to unmask]
>
> Dear Kulpreet Cheema,
>
> since you did not attach your batch job, it is difficult to guess what you were trying to do and went wrong. As the error message suggests, the number of flow fields did not match the number of images to normalise using "Normalise to MNI space". You would want to use the "Many subjects" option in for "Normalise to MNI space". Then, you would enter the DARTEL created flow fields as a dependency for "Flow Fields". For each set of images to normalise, you would then add a new "Images" item and select files for each subject or use a dependency for e.g. c1 or c2 images. Each images item should contain exactly one image per subject in the order of the DARTEL flow fields.
>
> Hope this helps,
>
> Volkmar
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