Hello,

Thanks for your help. I am running it through MELODIC.

I don´t know which files you need. If you refer to the input files, they are PARTICIPANT_ID/session1/xxx.nii

I have three sessions                                                                                                                                           /session2/xxx.nii

                                                                                                                                                                                    /session3/xxx.nii

I did find an error report in Registration, but as said, not in all participants (and I checked all the images and paths). I attach the error report:

Thanks

Yacila

Registration

….

did not find file: example_func2highres.mat. Generating transform.

/usr/share/fsl/5.0/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres

Error: failed to open file example_func2highres_fast_seg.nii.gz

Image Exception : #22 :: ERROR: Could not open image example_func2highres_fast_seg

terminate called after throwing an instance of 'RBD_COMMON::BaseException'

/usr/share/fsl/5.0/bin/epi_reg: line 312: 15758 Aborted                 $FSLDIR/bin/fast -o ${vout}_fast ${vrefbrain}

Cannot open volume example_func2highres_fast_pve_2 for reading!

Cannot open volume example_func2highres_fast_wmseg for reading!

Image Exception : #22 :: ERROR: Could not open image example_func2highres_fast_wmseg

terminate called after throwing an instance of 'RBD_COMMON::BaseException'

/usr/share/fsl/5.0/bin/epi_reg: line 378: 15798 Aborted                 $FSLDIR/bin/flirt -ref ${vrefhead} -in ${vepi} -dof 6 -cost bbr -wmseg ${vout}_fast_wmseg -init ${vout}_init.mat -omat ${vout}.mat -out ${vout} -schedule ${FSLDIR}/etc/flirtsch/bbr.sch

Could not open matrix file example_func2highres.mat

/usr/share/fsl/5.0/bin/epi_reg: line 378: 15799 Segmentation fault      $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} --premat=${vout}.mat --interp=spline

Running FAST segmentation FLIRT pre-alignment Running BBR

/usr/share/fsl/5.0/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres1.png ; /usr/share/fsl/5.0/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres2.png ; /usr/share/fsl/5.0/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png example_func2highres2.png

Image Exception : #22 :: ERROR: Could not open image example_func2highres

Cannot open sla.png for reading

Segmentation fault

Cannot open example_func2highres1.png for reading

Segmentation fault

Error in slicer input, exiting...

/bin/rm example_func2highres1.png

/bin/rm: cannot remove 'example_func2highres1.png': No such file or directory

did not find file: highres2standard.mat. Generating transform.

/usr/share/fsl/5.0/bin/flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear

/usr/share/fsl/5.0/bin/fnirt --iout=highres2standard_head --in=highres_head --aff=highres2standard.mat --cout=highres2standard_warp --iout=highres2standard --jout=highres2highres_jac --config=T1_2_MNI152_2mm --ref=standard_head --refmask=standard_mask --warpres=10,10,10

/usr/share/fsl/5.0/bin/applywarp -i highres -r standard -o highres2standard -w highres2standard_warp

/usr/share/fsl/5.0/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat

/usr/share/fsl/5.0/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard1.png ; /usr/share/fsl/5.0/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard2.png ; /usr/share/fsl/5.0/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png highres2standard2.png

/bin/rm highres2standard1.png

/usr/share/fsl/5.0/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat

Could not open matrix file example_func2highres.mat

Cannot read input-matrix

/usr/share/fsl/5.0/bin/convertwarp --ref=standard --premat=example_func2highres.mat --warp1=highres2standard_warp --out=example_func2standard_warp

Could not open matrix file example_func2highres.mat

terminate called after throwing an instance of 'NEWMAT::IncompatibleDimensionsException'

Aborted

did not find file: example_func2standard.mat. Generating transform.

/usr/share/fsl/5.0/bin/flirt -in example_func -ref standard -out example_func2standard -omat example_func2standard.mat -cost corratio -dof  -searchrx -  -searchry -  -searchrz -  -interp trilinear

Unrecognised option -

/usr/share/fsl/5.0/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard1.png ; /usr/share/fsl/5.0/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/share/fsl/5.0/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard2.png ; /usr/share/fsl/5.0/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png example_func2standard2.png

Image Exception : #22 :: ERROR: Could not open image example_func2standard

Cannot open sla.png for reading

Segmentation fault

Cannot open example_func2standard1.png for reading

Segmentation fault

Error in slicer input, exiting...

Sorry,

I just check and neither  the transformation matrices nor the masks for the example_func to highres and example_func to standard were produced. There is not error report though. What can it be?

Thanks

Yacila

 

Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Deza Araujo, Yacila Isabela
Gesendet: Sonntag, 10. Juli 2016 22:09
An: [log in to unmask]
Betreff: [FSL] BBR slicer is not produced

 

Dear FSL experts,

 

I am trying to perform the BBR algorithm in my data and prepare them for FIX. I am used to look at the registration output in the online report. For some reason, I can not see the Registration of example_func to high resolution and the registration of example_func to standard, but the highres_to standard is there. When I click the space where the images are supposed to be, an error report tells  me that they were deleted of moved (not by me) and there is not image in the reg folder. The strange thing is that this happens with some subjects, not with all. I tried in several browsers. What can be the reason? How can I know that the registration really worked for those images?

 

Thanks a lot for your attention

 

 

--
Yacila Deza Araujo, M.Sc. Neuropsych.
PhD Student

Technische Universität Dresden
Faculty of Medicine Carl Gustav Carus
Department of Psychiatry & Psychotherapy
Section of Systems Neuroscience

Würzburger Straße 35
01187 Dresden
Germany

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