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  May 2018

FSL May 2018

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

tbss_3_postreg error

From:

Lara Foland-Ross <[log in to unmask]>

Reply-To:

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

Date:

Thu, 3 May 2018 17:38:24 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (190 lines)

Hi there, 

I'm running a TBSS analysis on a sample of adolescents. Thus far, I've run "tbss_1_preproc *.nii.gz" and "tbss_2_reg -n" successfully. However, "tbss_3_postreg -S" produces the following error (below). 

Could you please advise?

Many thanks,
Lara

tbss_3_postreg -S 
finding best target
cat: all.msf: No such file or directory
best target is  - now registering this to standard space
Usage: /Volumes/ToolsMac/fsl-5.0.8/bin/imcp <file1> <file2>
Usage: /Volumes/ToolsMac/fsl-5.0.8/bin/imcp <file1> <file2> ... <fileN> <directory>
  Copies images from file1 to file2 (including all extensions)
  NB: filenames can be basenames or include an extension
affine-registering target to MNI152 space
Cannot open volume target for reading!
Image Exception : #22 :: ERROR: Could not open image target
libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
/Volumes/ToolsMac/fsl-5.0.8/bin/tbss_3_postreg: line 176: 76090 Abort trap: 6           $FSLDIR/bin/flirt -in target -inweight target_mask -ref $FSLDIR/data/standard/FMRIB58_FA_1mm -omat target_to_MNI152.mat -out target_to_MNI152
transforming (and upsampling) all FA images into MNI152 space
c_16054_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_16054_dtifit_FA_FA_to__warp
An error occured while reading file: c_16054_dtifit_FA_FA_to__warp
c_18220_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_18220_dtifit_FA_FA_to__warp
An error occured while reading file: c_18220_dtifit_FA_FA_to__warp
c_18226_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_18226_dtifit_FA_FA_to__warp
An error occured while reading file: c_18226_dtifit_FA_FA_to__warp
c_18322_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_18322_dtifit_FA_FA_to__warp
An error occured while reading file: c_18322_dtifit_FA_FA_to__warp
c_18427_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_18427_dtifit_FA_FA_to__warp
An error occured while reading file: c_18427_dtifit_FA_FA_to__warp
c_18591_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_18591_dtifit_FA_FA_to__warp
An error occured while reading file: c_18591_dtifit_FA_FA_to__warp
c_18749_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_18749_dtifit_FA_FA_to__warp
An error occured while reading file: c_18749_dtifit_FA_FA_to__warp
c_18805_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_18805_dtifit_FA_FA_to__warp
An error occured while reading file: c_18805_dtifit_FA_FA_to__warp
c_18888_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_18888_dtifit_FA_FA_to__warp
An error occured while reading file: c_18888_dtifit_FA_FA_to__warp
c_19018_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_19018_dtifit_FA_FA_to__warp
An error occured while reading file: c_19018_dtifit_FA_FA_to__warp
c_19118_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_19118_dtifit_FA_FA_to__warp
An error occured while reading file: c_19118_dtifit_FA_FA_to__warp
c_19198_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_19198_dtifit_FA_FA_to__warp
An error occured while reading file: c_19198_dtifit_FA_FA_to__warp
c_19302_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_19302_dtifit_FA_FA_to__warp
An error occured while reading file: c_19302_dtifit_FA_FA_to__warp
c_19361_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_19361_dtifit_FA_FA_to__warp
An error occured while reading file: c_19361_dtifit_FA_FA_to__warp
c_19440_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_19440_dtifit_FA_FA_to__warp
An error occured while reading file: c_19440_dtifit_FA_FA_to__warp
c_20369_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_20369_dtifit_FA_FA_to__warp
An error occured while reading file: c_20369_dtifit_FA_FA_to__warp
c_20382_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image c_20382_dtifit_FA_FA_to__warp
An error occured while reading file: c_20382_dtifit_FA_FA_to__warp
n_19531_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_19531_dtifit_FA_FA_to__warp
An error occured while reading file: n_19531_dtifit_FA_FA_to__warp
n_19578_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_19578_dtifit_FA_FA_to__warp
An error occured while reading file: n_19578_dtifit_FA_FA_to__warp
n_20467_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_20467_dtifit_FA_FA_to__warp
An error occured while reading file: n_20467_dtifit_FA_FA_to__warp
n_21097_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21097_dtifit_FA_FA_to__warp
An error occured while reading file: n_21097_dtifit_FA_FA_to__warp
n_21099_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21099_dtifit_FA_FA_to__warp
An error occured while reading file: n_21099_dtifit_FA_FA_to__warp
n_21110_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21110_dtifit_FA_FA_to__warp
An error occured while reading file: n_21110_dtifit_FA_FA_to__warp
n_21113_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21113_dtifit_FA_FA_to__warp
An error occured while reading file: n_21113_dtifit_FA_FA_to__warp
n_21132_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21132_dtifit_FA_FA_to__warp
An error occured while reading file: n_21132_dtifit_FA_FA_to__warp
n_21174_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21174_dtifit_FA_FA_to__warp
An error occured while reading file: n_21174_dtifit_FA_FA_to__warp
n_21221_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21221_dtifit_FA_FA_to__warp
An error occured while reading file: n_21221_dtifit_FA_FA_to__warp
n_21224_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21224_dtifit_FA_FA_to__warp
An error occured while reading file: n_21224_dtifit_FA_FA_to__warp
n_21310_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21310_dtifit_FA_FA_to__warp
An error occured while reading file: n_21310_dtifit_FA_FA_to__warp
n_21513_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21513_dtifit_FA_FA_to__warp
An error occured while reading file: n_21513_dtifit_FA_FA_to__warp
n_21589_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21589_dtifit_FA_FA_to__warp
An error occured while reading file: n_21589_dtifit_FA_FA_to__warp
n_21592_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21592_dtifit_FA_FA_to__warp
An error occured while reading file: n_21592_dtifit_FA_FA_to__warp
n_21615_dtifit_FA_rs_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21615_dtifit_FA_rs_FA_to__warp
An error occured while reading file: n_21615_dtifit_FA_rs_FA_to__warp
n_21616_dtifit_FA_rs_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21616_dtifit_FA_rs_FA_to__warp
An error occured while reading file: n_21616_dtifit_FA_rs_FA_to__warp
n_21618_dtifit_FA_rs_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21618_dtifit_FA_rs_FA_to__warp
An error occured while reading file: n_21618_dtifit_FA_rs_FA_to__warp
n_21660_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21660_dtifit_FA_FA_to__warp
An error occured while reading file: n_21660_dtifit_FA_FA_to__warp
n_21695_dtifit_FA_FA
Could not open matrix file target_to_MNI152.mat
Image Exception : #22 :: ERROR: Could not open image n_21695_dtifit_FA_FA_to__warp
An error occured while reading file: n_21695_dtifit_FA_FA_to__warp
merging all upsampled FA images into single 4D image

Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds]
     -t : concatenate images in time
     -x : concatenate images in the x direction
     -y : concatenate images in the y direction
     -z : concatenate images in the z direction
     -a : auto-choose: single slices -> volume, volumes -> 4D (time series)
     -tr : concatenate images in time and set the output image tr to the final option value
creating valid mask and mean FA
Cannot open volume all_FA for reading!
Cannot open volume all_FA for reading!
Cannot open volume all_FA for reading!
skeletonising mean FA
Image Exception : #22 :: ERROR: Could not open image mean_FA
libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
/Volumes/ToolsMac/fsl-5.0.8/bin/tbss_3_postreg: line 197: 76146 Abort trap: 6           $FSLDIR/bin/tbss_skeleton -i mean_FA -o mean_FA_skeleton
now view mean_FA_skeleton to check whether the default threshold of 0.2 needs changing, when running:
tbss_4_prestats <threshold>

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