JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for FSL Archives


FSL Archives

FSL Archives


FSL@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

FSL Home

FSL Home

FSL  August 2018

FSL August 2018

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: epi_reg error

From:

Matthew Webster <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 6 Aug 2018 13:23:56 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (1 lines)

Hello Karen, 
		   Can you try the following commands ( in the folder with c22061_MPRAGEreorient_.nii ) 
 
file=c22061_MPRAGEreorient_.nii  
absfile=`$FSLDIR/bin/fsl_abspath $file` 
cp ${absfile} test 
 
And let me know if there are any errors ( and if test.nii.gz is created ).  
 
Kind Regards 
Matthew 
-------------------------------- 
Dr Matthew Webster 
FMRIB Centre  
John Radcliffe Hospital 
University of Oxford 
 
> On 6 Aug 2018, at 14:03, Karen Seymour <[log in to unmask]> wrote: 
>  
> Matthew, 
>  
> Just checking in about any thoughts for this problem..... 
>  
> Thanks! 
>  
> Karen 
>  
> On Fri, Aug 3, 2018 at 12:39 PM, Karen Seymour <[log in to unmask]> wrote: 
> Matthew, 
>  
> I actually deleted the files since I wasn't sure if they were "valid", but saved a list of them: 
>  
>  
> 2061_MB_run1CoregSource_fieldmap2str_init.mat 
> 2061_MB_run1CoregSource_fieldmap2str.mat 
> 2061_MB_run1CoregSource_fieldmap2str.nii.gz 
> 2061_MB_run1CoregSource_fieldmaprads2str_dilated.nii.gz 
> 2061_MB_run1CoregSource_fieldmaprads2str_pad0.nii.gz 
> 2061_MB_run1CoregSource_fieldmaprads2str.nii.gz 
> 2061_MB_run1CoregSource_init.mat 
>  
> On Fri, Aug 3, 2018 at 11:43 AM, Matthew Webster <[log in to unmask]> wrote: 
> Hi Karen, 
> Thank you, it would be very useful to also know the exact filenames ( e.g. obtained with ls in the folder containing ra2061_MB_run1CoregSource.nii.gz ) to see how far epi_reg had progressed. 
>  
> Kind Regards 
> Matthew 
> -------------------------------- 
> Dr Matthew Webster 
> FMRIB Centre  
> John Radcliffe Hospital 
> University of Oxford 
>  
>> On 3 Aug 2018, at 15:56, Karen Seymour <[log in to unmask]> wrote: 
>>  
>> Sure, individual folders for each participant labelled with their subject id. Within those folders are all the files being called by epi_reg. I am using a bash script to batch epi_reg (see attached). I have a larger script that does this for 2 runs and then applies the warps, but was getting a lot of error messages so broke it down into smaller scripts. 
>>  
>> ks 
>>  
>> On Fri, Aug 3, 2018 at 10:50 AM, Matthew Webster <[log in to unmask]> wrote: 
>> Hi Karen, 
>> Thank you - can you let me know the contents of the directory as well? 
>>  
>> Kind Regards 
>> Matthew 
>> -------------------------------- 
>> Dr Matthew Webster 
>> FMRIB Centre  
>> John Radcliffe Hospital 
>> University of Oxford 
>>  
>>> On 3 Aug 2018, at 15:11, Karen Seymour <[log in to unmask]> wrote: 
>>>  
>>> directory listing is: 
>>>  
>>> path=/Volumes/DCN_DATA$/fmri/UMD_collaboration/ADHD_BA_Study/Moneybags/Data_New 
>>>  
>>> DCN_DATA$ is a server 
>>>  
>>> I will try to run without the extension and let you know what happens 
>>>  
>>> ks 
>>>  
>>> On Fri, Aug 3, 2018 at 9:40 AM, Matthew Webster <[log in to unmask]> wrote: 
>>> Hello,  
>>> Can you let me know the directory listing for the location where you are running this? Also can you try rerunning with —out just set to 2061_MB_run1CoregSource ( e.g. without extension ) and see if the error messages change at all? 
>>>  
>>> Kind Regards 
>>> Matthew 
>>> -------------------------------- 
>>> Dr Matthew Webster 
>>> FMRIB Centre  
>>> John Radcliffe Hospital 
>>> University of Oxford 
>>>  
>>>> On 3 Aug 2018, at 14:22, Karen Seymour <[log in to unmask]> wrote: 
>>>>  
>>>> Hi all, 
>>>>  
>>>> I am using epi_reg to apply field maps to my EPI data, but keep getting errors when I run the script. Here is the command I am running: 
>>>>  
>>>> epi_reg --epi=ra2061_MB_run1CoregSource.nii.gz  --t1=m2061_MPRAGEreorient.nii \ 
>>>> --t1brain=2061_MPRAGEreorient_brain_4.nii.gz --wmseg=c22061_MPRAGEreorient_.nii \ 
>>>> --fmap=2061smoothfieldmapinRad.nii.gz --fmapmag=2061unwarped4DSEmean.nii.gz --fmapmagbrain=2061unwarpedSEbrain.nii.gz \ 
>>>> --echospacing=0.0007 --pedir=y --out=2061_MB_run1CoregSource.nii.gz 
>>>>  
>>>> Of note, the T1 (bias-corrected) and WM segmentation are from SPM.  
>>>>  
>>>> The error I keep getting is: 
>>>>  
>>>> Cannot open volume 2061_MB_run1CoregSource_fast_wmseg for reading! 
>>>>  
>>>> which is then followed by a whole set of errors about not being able to open matrix files: 
>>>>  
>>>> Could not open matrix file 2061_MB_run1CoregSource.mat.  
>>>> Cannot read input-matrix 
>>>> Could not open matrix file 2061_MB_run1CoregSource_inv.mat 
>>>> Cannot read concat-matrix 
>>>> Could not open matrix file 2061_MB_run1CoregSource_fieldmaprads2epi.mat 
>>>>  
>>>> I assume all the errors are stemming from the first.  
>>>>  
>>>> Any help or advice would be greatly appreciated! 
>>>>  
>>>> Thanks 
>>>>  
>>>> Karen 
>>>>  
>>>> ######################################################################## 
>>>>  
>>>> To unsubscribe from the FSL list, click the following link: 
>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 
>>>  
>>>  
>>> To unsubscribe from the FSL list, click the following link: 
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 
>>>  
>>>  
>>>  
>>> To unsubscribe from the FSL list, click the following link: 
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 
>>>  
>>  
>>  
>> To unsubscribe from the FSL list, click the following link: 
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 
>>  
>>  
>>  
>> To unsubscribe from the FSL list, click the following link: 
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 
>>  
>> <UMD_ADHD_BA_Epi_reg_run1.sh> 
>  
>  
> To unsubscribe from the FSL list, click the following link: 
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 
>  
>  
>  
>  
> To unsubscribe from the FSL list, click the following link: 
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 
>  
 
 
######################################################################## 
 
To unsubscribe from the FSL list, click the following link: 
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager