Hello again Gwenaëlle,

I am trying to run randomise to compare two groups with the following code, but keep getting the following error. Thoughts?

randomise -i GM_mod_merg_s3 -m GM_mask -o fslvbm -d design.mat -t design.con -T -n 5000

randomise options: -i GM_mod_merg_s3 -m GM_mask -o fslvbm -d design.mat -t design.con -T -n 5000 
Loading Data: Image Exception : #22 :: ERROR: Could not open image GM_mod_merg_s3
ERROR: Program failed

An exception has been thrown
ERROR: Could not open image GM_mod_merg_s3Trace: read_volume4DROI.


Exiting

Thanks!
Ravi
On May 19, 2016, at 10:28 AM, Bhatt, Ravi <[log in to unmask]> wrote:

This worked!!! :D
On May 19, 2016, at 9:32 AM, Gwenaëlle DOUAUD <[log in to unmask]> wrote:

Yes, this most definitely should help!
 
------------------------------------------------------------------------------------------------------------------------
Gwenaëlle Douaud, PhD
Associate Professor & MRC Career Development Fellow

FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington
OX3 9DU Oxford UK
Switchboard: +44 (0) 1865 222 493
Fax: +44 (0) 1865 222 717

www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud
www.fmrib.ox.ac.uk/research/translational-image-analysis-group
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De : "Bhatt, Ravi" <[log in to unmask]>
À : [log in to unmask]
Envoyé le : Mercredi 18 mai 2016 21h20
Objet : Re: [FSL] FSLVBM_3_Proc

I read here that it may be a orientation issue. I ran fslreorient2std on all the images and am now trying to do it again. Maybe this will help?
On May 18, 2016, at 9:18 AM, Bhatt, Ravi <[log in to unmask]> wrote:

Hey Gwenaëlle,

Thanks for your response. It looks like all of the volumes in the 4D file are distorted; some less so than others, but still very distorted.

I’m attaching 3 pictures of one subjects template_GM image, GM_mod_merge image, and volume in the template_4D_GM. Things looked okay in the template_4D_GM I thought…?

http://imgur.com/a/AMILr

Hope this helps!

Thanks!
Ravi
On May 18, 2016, at 5:50 AM, Gwenaëlle DOUAUD <[log in to unmask]> wrote:

Hi Ravi,

I'm not sure: is this all of the volumes in your 4D file that look similarly distorted, or only one subject?

Assuming the latter, when looking at the very same subject's image struc_GM.nii.gz, or if this subject is part of the template, when looking at the corresponding volume in your template_4D_GM, did you see anything wrong?

Assuming the former, could you please take a snapshot of your template_GM image and one of your subject's struc_GM image?

Cheers,
Gwenaëlle
 
------------------------------------------------------------------------------------------------------------------------
Gwenaëlle Douaud, PhD
Associate Professor & MRC Career Development Fellow

FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington
OX3 9DU Oxford UK
Switchboard: +44 (0) 1865 222 493
Fax: +44 (0) 1865 222 717

www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud
www.fmrib.ox.ac.uk/research/translational-image-analysis-group
-----------------------------------------------------------------------------------------------------------------------


De : "Bhatt, Ravi" <[log in to unmask]>
À : [log in to unmask]
Envoyé le : Mardi 17 mai 2016 21h15
Objet : [FSL] FSLVBM_3_Proc

Hello everyone,

I’m currently using FSLVBM to run an analysis between two groups. I’m using the documentation online (hyperlinked) to guide me through this since I have not done it before.

I was having an issue at first with the BET tool since it was not extracting the entire brain of some subjects, but I went through the GUI and did each one manually by altering the f threshold. So then I had all of the “_struc” files in the “struc” folder. I ran the “fslvbm_2_template” script on this and it seemed to create a “template_GM_4D_image” just fine. This image looked okay.

But when I ran the “fslvbm_3_proc” script, I got a very distorted image for my “GM_mod_meg” files. I’ve attached a photo of it at this link. 


Is this a registration issue? If someone could please help me figure out why this is happening I would very much appreciate it! 

Thank you all! :)

Ravi


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