Anderson,

 

Thanks for the advice.  My IT guys have modified the file so that it now specifies the correct queue, but I’m now getting the following error:

 

Generating 40 fragments for  2  contrasts with  100 permutations per fragment. Allocating 30 minutes per fragment.

The total number of permutations per contrast will be 2000 .

done 1

done 2

done 3

done 4

done 5

done 6

done 7

done 8

done 9

done 10

done 11

done 12

done 13

done 14

done 15

done 16

done 17

done 18

done 19

done 20

The command you have requested cannot be found or is not executable

 

I see the line in fsl_sub which is generating this error, but not sure how this is happening after it is obviously able to run some of the permutations.  Note that I have run the same exact command which I am running with randomise_parallel using randomise, just to make sure that it’s not the files that are the issue.  That runs just fine.

 

Thanks for the help!

 

Mark

 

____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email: [log in to unmask]

 

This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

 

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Anderson M. Winkler
Sent: Monday, January 29, 2018 9:06 AM

To: [log in to unmask]
Subject: Re: [FSL] randomise error

 

Hi Mark,

 

You can edit randomise_parallel too. Maybe the expected timing is causing the job to be send to a queue that isn't there (in this case, it seems it's, short.q).

 

I'd think though that just changing fsl_sub to match your environment should fix the problem.

 

All the best,

 

Anderson

 

 

On 29 January 2018 at 08:48, Mark Wagshul <[log in to unmask]> wrote:

Thanks!  I thought I would be able to get around this by specifying the queue name in fsl_sub, but this did not work.  So, I am still not sure why modifying the code in fsl_sub would solve the problem.  It seemed like there was something internal to randomise_parallel which was using short.q, in which case modifying fsl_sub would not solve the problem.

 

Best,

 

Mark

 

____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email: [log in to unmask]

 

This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

 

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Anderson M. Winkler
Sent: Sunday, January 28, 2018 11:37 PM

To: [log in to unmask]
Subject: Re: [FSL] randomise error

 

Hi Mark,

 

You'd either have to make sure a short.q exists in your SGE or edit fsl_sub to replace short.q for some other queue that exists in your system.

 

All the best,

 

Anderson

 

 

On 26 January 2018 at 12:56, Mark Wagshul <[log in to unmask]> wrote:

Thanks.  That was the problem, I forgot to binarize it.

I have another, unrelated question, wrt randomise.  I am trying to run randomise_parallel, and running into problems because it can't find the queue short.q.  This happens even if I run it through fsl_sub and specify the queue.  Is this queue hard-coded into this function, and if so, how can I get around this problem?

Thanks,

Mark

____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: [log in to unmask]


This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Matthew Webster
Sent: Friday, January 26, 2018 12:18 PM
To: [log in to unmask]
Subject: Re: [FSL] randomise error

Hello,
          Can you check that your mask only contains the values 0 and 1 and no other ( e.g. fractional ) values?

Kind regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford

> On 26 Jan 2018, at 16:58, Mark Wagshul <[log in to unmask]> wrote:
>
> Hi.  I am running randomise with a very similar configuration to what I have used successfully dozens of times before and running into an error.  It is a group analysis of DTI data, 146 subjects, with 6 covariates.  Here are the contrast files, and the top of the design matrix file (not printing it all to save space):
>
> CONTRAST
> /ContrastName1 group mean
> /NumWaves 7
> /NumContrasts 2
> /PPheights 0.5
> /RequiredEffect 1.0
>
> /Matrix
> 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00
> 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
>
> DESIGN MATRIX:
> /NumWaves 7
> /NumPoints 146
> /PPheights 27.3904 0.684932 9.34932 0.181063 3.37671 32.8493 0.5
>
> /Matrix
> 19.3904 0.6849 3.3493 0.1811 -0.6233 32.8493 -0.5000
> 17.3904 -0.3151 1.3493 0.0811 -0.6233 24.8493 -0.5000
> 0.3904 -0.3151 1.3493 0.1811 -0.6233 20.8493 -0.5000
> 0.3904 0.6849 0.3493 0.1811 1.3767 20.8493 -0.5000
> 1.3904 -0.3151 2.3493 -0.0295 0.3767 20.8493 -0.5000
> -0.6096 -0.3151 1.3493 -0.0189 -0.6233 5.8493 -0.5000
>
> I've checked the input file, and it is indeed 146 volumes.
>
> Here is the error I'm getting:
> Loading Data: ERROR: Program failed
>
> An exception has been thrown
> Logic error:- detected by Newmat: index error: requested indices = 1, 355544
>
> MatrixType = Rect   # Rows = 146; # Cols = 355543
>
> Exiting.
>
> Any thoughts about what might be going wrong here.  The only thing I can think of is something with the mask file, it is a bit odd because it's volume is 370422, which is a bit off from the column size reported here.
>
> Thanks.
>
> Mark Wagshul