Hi Mark,


Sorry about the slow reply.

I've attached my concatenated bvars file and design matrix and a few bvars files.

I have included the two design matrices I have tried. Originally, I only created a t-test, but today I also tried an f-test via Glm, just to see if that makes a difference...which it didn't. 

It look as though you may not be able to access the .mat files..?



Thanks,

Rosie

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Mark Jenkinson <[log in to unmask]>
Sent: 12 March 2018 13:49:35
To: [log in to unmask]
Subject: Re: [FSL] Problem if vertex anaylsis on FSL FIRST
 
Hi,

I'm still really puzzled as to what is going on.
Can you send me (off the list) a couple of example single-subejct bvars files, your concatenated bvars file and the design matrix you are using?

All the best,
Mark



On 12 Mar 2018, at 11:21, Rosie Mogridge <[log in to unmask]> wrote:

Hi, 

I understand, does seem an odd error. 
The output was; 

-rwxr-xr-x 1 nobody nobody 36320875 May 27  2009 /cubric/software/fsl/data/first/models_336_bin/05mm/R_Thal_05mm.bmv

thanks, 

Rosie
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Niels Bergsland <[log in to unmask]>
Sent: 12 March 2018 10:32:36
To: [log in to unmask]
Subject: Re: [FSL] Problem if vertex anaylsis on FSL FIRST
 
Hi Rosie,
I don’t have any other great ideas off the top of my head  but what is the output of 

ls -l /cubric/software/fsl/data/first/models_336_bin/05mm/R_Thal_05mm.bmv


It seems rather unlikely you would have been able to get this far without having other issues but figure it doesn’t hurt to double check...

On Mon, Mar 12, 2018 at 11:16 Rosie Mogridge <[log in to unmask]> wrote:
Hi, 

I am not sure if I missed your response the other day, but have you had any thoughts about our problem? 
I am still waiting on a reply for the IT department my end. 

Many thanks, 
Rosie 
From: Rosie Mogridge
Sent: 09 March 2018 11:01:58

To: [log in to unmask]
Subject: Re: [FSL] Problem if vertex anaylsis on FSL FIRST
Hi, 

Sorry about that. Is this information what you are looking for

 uname -a
Linux l048.cubric.cf.ac.uk 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 14:09:15 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.2.1511 (Core) 
Release: 7.2.1511
Codename: Core

thanks, 

Rosie
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Mark Jenkinson <[log in to unmask]>
Sent: 08 March 2018 17:44:43
To: [log in to unmask]
Subject: Re: [FSL] Problem if vertex anaylsis on FSL FIRST
 
Hi,

What's crucial here is what type of Linux is being used on the remote system.

All the best,
Mark


On 8 Mar 2018, at 16:22, Rosie Mogridge <[log in to unmask]> wrote:

I am working on a windows 10 but usually Remote Desktop via nomachine to a Linux network

Rosie 

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From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Mark Jenkinson <[log in to unmask]>
Sent: Thursday, March 8, 2018 11:15:11 AM
To: [log in to unmask]
Subject: Re: [FSL] Problem if vertex anaylsis on FSL FIRST
 
Hi,

Can you tell details about your system?
In particular, what OS are you using?

All the best,
Mark


On 8 Mar 2018, at 09:31, Rosie Mogridge <[log in to unmask]> wrote:

Hi Mark, 

I got the same error. 
We were wondering if it is a local issue with our FSLDIR?

Many thanks, 
Rosie 

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From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Mark Jenkinson <[log in to unmask]>
Sent: Wednesday, March 7, 2018 10:50:40 PM
To: [log in to unmask]
Subject: Re: [FSL] Problem if vertex anaylsis on FSL FIRST
 
Hi,

Can use try the first_utils command with --useReconMNI instead of --useReconNative --useRigidAlign, just to see if you still get the same error?  It could be a problem related to find other relevant files.

All the best,
Mark

On 7 Mar 2018, at 13:15, Rosie Mogridge <[log in to unmask]> wrote:

Hi 

the output of head -n2

head -n2 171011-50+6221_FIRST-R_Thal_first.bvars
this is a bvars file
/cubric/software/fsl/data/first/models_336_bin/05mm/R_Thal_05mm.bmv

The output of echo FSLDIR

/cubric/software/fsl


thanks, 
Rosie
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Niels Bergsland <[log in to unmask]>
Sent: 07 March 2018 11:45:48
To: [log in to unmask]
Subject: Re: [FSL] Problem if vertex anaylsis on FSL FIRST
 
Hi,
What is the output of running 

head -n2 

On your bvars file?

What is the output of echo $FSLDIR

best,
Niels 

On Wed, Mar 7, 2018 at 12:40 Rosie Mogridge <[log in to unmask]> wrote:
Hi, 

Just wondering if you have had any more thoughts. 

I ran the entire analysis again on a few subjects and still got the same error. 

Many thanks, 
Rosie
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Rosie Mogridge <[log in to unmask]>
Sent: 06 March 2018 13:46:43

To: [log in to unmask]
Subject: Re: [FSL] Problem if vertex anaylsis on FSL FIRST
Hi Mark, 

Ok that’s good to know. 
Yes I did the segmentation and the output looks good. 
I am using FSL 5.0.9

Many thanks, 
Rosie 

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From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Mark Jenkinson <[log in to unmask]>
Sent: Tuesday, March 6, 2018 1:32:19 PM
To: [log in to unmask]
Subject: Re: [FSL] Problem if vertex anaylsis on FSL FIRST
 
Hi,

It is crucial that the order of your concatenation matches the order of how you setup your design matrix.  Nothing will work properly if that is not the case.  However, I don't see why that would generate this _particular_ error message.

Did you generate the segmentations of the individual subjects with FIRST yourself?
Do the results look OK?
What version of FSL are you using?

All the best,
Mark


On 6 Mar 2018, at 13:24, Rosie Mogridge <[log in to unmask]> wrote:

Hi, 

Thank you for your prompt reply. 
I have run that step a number of times. I am wondering if the problems lies in how I am organising my bvars files.

Currently, I have created a t-test design matrix. I have age and sex matched controls. My bvars files are just listed subjects then controls but no particular order. Could this be causing a problem?

Many thanks

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From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Mark Jenkinson <[log in to unmask]>
Sent: Tuesday, March 6, 2018 12:46:27 PM
To: [log in to unmask]
Subject: Re: [FSL] Problem if vertex anaylsis on FSL FIRST
 
Hi,

Try running the concat_bvars stage again and see if that fixes things.
If not, let us know.

All the best,
Mark


On 6 Mar 2018, at 12:33, Rosie Mogridge <[log in to unmask]> wrote:

Hi, 

I emailed last week re. an error in performing vertex analysis. I have tried to resolve the error as suggested but I still haven't solved the second half of the error;

Not a vtk file (error in line 1).
Not a vtk file (error in line 1).

Do you have any thoughts on this?


Many thanks, 
Rosie 
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Niels Bergsland <[log in to unmask]>
Sent: 28 February 2018 11:52:24
To: [log in to unmask]
Subject: Re: [FSL] Problem if vertex anaylsis on FSL FIRST
 
Hi,
 It sounds like maybe different steps of your processing were done on machines with different $FSLDIR paths.  You can usually fix this by opening the bvars with a text editor and edit the top line to reflect the $FSLDIR of the machine running first_utils.




On Wed, Feb 28, 2018 at 11:50 AM, Rosie Mogridge <[log in to unmask]> wrote:
Hi, 

I am trying to perform vertex analysis with FSL FIRST. I am having an error at the first-utils stage and cannot understand where the problem is coming from. My error is

first_utils --vertexAnalysis --usebvars --useReconNative --useRigidAlign -i con-patients-LAccu.bvars -d ttest-design-matrix.mat -o LAccushapeanaylsis
Warning:  does not exist. Attempting to switch to: /cubric/software/fsl
Not a vtk file (error in line 1).
Not a vtk file (error in line 1).

Many thanks, 

Rosie 

  




-- 
Niels Bergsland
Integration Director / Research Assistant Professor of Neurology
Buffalo Neuroimaging Analysis Center / University at Buffalo
100 High St. Buffalo NY 14203
[log in to unmask]


-- 
Niels Bergsland
Integration Director / Research Assistant Professor of Neurology
Buffalo Neuroimaging Analysis Center / University at Buffalo
100 High St. Buffalo NY 14203
[log in to unmask]



-- 
Niels Bergsland
Integration Director / Research Assistant Professor of Neurology
Buffalo Neuroimaging Analysis Center / University at Buffalo
100 High St. Buffalo NY 14203
[log in to unmask]