Hello,
Can you run
/usr/local/fsl/bin/bet2 mean_func test -f 0.3 -n -m
in the FEAT directory, and let me know if test_mask looks OK ( you might need to copy it elsewhere again )?
Also can you run
fslstats prefiltered_func_data_st -r R
and let me know the results?
Kind Regards
Matthew
> On 1 Aug 2016, at 19:59, Bloodworth, Natasha <[log in to unmask]> wrote:
>
> Hi Matthew,
>
> Thank you for that. I have opened the two together and it is not possible to even see the mask in fsl view, despite it showing that it has loaded correctly etc.
>
> Best wishes,
> Natasha
>
>> On 1 Aug 2016, at 13:43, Matthew Webster <[log in to unmask]> wrote:
>>
>> Hi Natasha,
>> FSLview is automatically trying to run in “FEAT” mode and load in the filtered_func_data ( which doesn’t exist yet as the run has failed! ) can you copy the prefiltered_func_data_st and mask images to another directory and view them there?
>>
>> Kind Regards
>> Matthew
>>
>>> On 26 Jul 2016, at 13:37, Bloodworth, Natasha <[log in to unmask]> wrote:
>>>
>>> Hi Matthew,
>>>
>>> When I try and load prefiltered_func_data_st.nii.gz in fslview, I get the following error:
>>>
>>> psy-05036:~ nlb206$ ** ERROR (nifti_image_read): failed to find header file for '/Users/nlb206/Desktop/Study2/Study2MRIAnalysis/guess_FEAT/Participant24.feat/filtered_func_data'
>>> ** ERROR: nifti_image_open(/Users/nlb206/Desktop/Study2/Study2MRIAnalysis/guess_FEAT/Participant24.feat/filtered_func_data): bad header info
>>> ERROR: failed to open file /Users/nlb206/Desktop/Study2/Study2MRIAnalysis/guess_FEAT/Participant24.feat/filtered_func_data
>>>
>>> This is only occurring on a few of my participants, so I really am not sure what is going on…
>>>
>>> Thank you for all of your help!
>>>
>>> Best wishes,
>>> Natasha
>>>
>>>
>>>> On 26 Jul 2016, at 11:21, Matthew Webster <[log in to unmask]> wrote:
>>>>
>>>> Hi Natasha,
>>>> It looks like there is a problem either with the range of your data, or possibly brain extraction - the line
>>>>
>>>> /usr/local/fsl/bin/fslstats prefiltered_func_data_st -k mask -p 50
>>>> 0.000
>>>>
>>>> shows that the median intensity in the brain mask is 0 - which is very wrong! Can you load prefiltered_func_data_st.nii.gz and mask.nii.gz into fslview and check the mask fits the brain well?
>>>>
>>>> Kind Regards
>>>> Matthew
>>>>> On 21 Jul 2016, at 13:39, Bloodworth, Natasha <[log in to unmask]> wrote:
>>>>>
>>>>> Hi Mark,
>>>>>
>>>>> The file was there, but when I changed the directory and ran the command I received the following error:
>>>>>
>>>>> psy-05036:~ nlb206$ cd /Users/nlb206/Desktop/Study2/Study2MRIAnalysis/guess_FEAT/Participant24.feat
>>>>> psy-05036:Participant24.feat nlb206$ /usr/local/fsl/bin/susan prefiltered_func_data_thresh 0.0 2.12314225053 3 1 1 mean_func 0.0 prefiltered_func_data_smooth
>>>>> Segmentation fault: 11
>>>>>
>>>>> ??
>>>>>
>>>>> Best wishes,
>>>>> Natasha
>>>>>
>>>>>> On 21 Jul 2016, at 09:15, Mark Jenkinson <[log in to unmask]> wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> It is odd that it is failing on relatively straightforward data.
>>>>>> The error that you got from running the command indicates that you either were not in the right directory (the feat output directory) or that the necessary file (prefiltered_func_data_thresh.nii.gz) has been deleted. If you can find the file prefiltered_func_data_thresh.nii.gz in your directory then do "cd" into that directory and re-run the command. If you don't have that file then it makes it harder to track down, so let us know if that's the case or not.
>>>>>>
>>>>>> All the best,
>>>>>> Mark
>>>>>>
>>>>>> Mark Jenkinson, BSc BE DPhil
>>>>>> Professor of Neuroimaging
>>>>>> FMRIB Centre, University of Oxford
>>>>>>
>>>>>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>>>>>> +44 (0) 1865 222782 (fax 222717)
>>>>>>
>>>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~mark
>>>>>>
>>>>>>
>>>>>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of "Bloodworth, Natasha" <[log in to unmask]>
>>>>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>>>>> Date: Tuesday, 19 July 2016 at 21:26
>>>>>> To: "[log in to unmask]" <[log in to unmask]>
>>>>>> Subject: Re: [FSL] SUSAN segmentation violation - please help!
>>>>>>
>>>>>> Dear Mark,
>>>>>>
>>>>>> Thank you for your speedy response!
>>>>>>
>>>>>> The data isn’t particularly large and it is similar to a previous dataset on which the analysis ran perfectly, so I do not think that is the problem. When I run the command on its own I get the following:
>>>>>>
>>>>>> psy-05036:~ nlb206$ /usr/local/fsl/bin/susan prefiltered_func_data_thresh 0.0 2.12314225053 3 1 1 mean_func 0.0 prefiltered_func_data_smooth
>>>>>> Cannot open volume prefiltered_func_data_thresh for reading!
>>>>>>
>>>>>>
>>>>>> Thank you for your help,
>>>>>> Natasha
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 19 Jul 2016, at 08:22, Mark Jenkinson <[log in to unmask]> wrote:
>>>>>>
>>>>>> Dear Natasha,
>>>>>>
>>>>>> For some reason your email was blank in my mail but I found the contents on jiscmail. Check your jiscmail/email settings to try and see what happened and avoid that in future.
>>>>>>
>>>>>> As for your problem, it isn't clear to me why this would be happening and in such an intermittent way. Is your data particularly large or unusual in some way? Also, what happens if you just try and re-run the last command on its own from the terminal; that is:
>>>>>>
>>>>>> /usr/local/fsl/bin/susan prefiltered_func_data_thresh 0.0 2.12314225053 3 1 1 mean_func 0.0 prefiltered_func_data_smooth
>>>>>>
>>>>>> ?
>>>>>>
>>>>>> Let us know about your data and what happens with the above command as this will hopefully give us some idea as to what might be going wrong.
>>>>>>
>>>>>> All the best,
>>>>>> Mark
>>>>>>
>>>>>>
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I am trying to run the first level FEAT analysis on some fMRI data, this has worked for some participants, but for several the analysis has crashed. On some occasions, just rerunning the analysis has worked, but not in every case and I cannot work out why. This has happened on two different machines - my own mac and a linux desktop. I have copied the log below - any help would be greatly appreciated!
>>>>>>
>>>>>> Natasha
>>>>>>
>>>>>> Feat main script
>>>>>>
>>>>>>
>>>>>> /bin/cp /tmp/feat_DqPoGS.fsf design.fsf
>>>>>>
>>>>>> /usr/local/fsl/bin/feat_model design
>>>>>>
>>>>>> mkdir .files;cp /usr/local/fsl/doc/fsl.css .files;cp -r /usr/local/fsl/doc/images .files/images
>>>>>>
>>>>>> /usr/local/fsl/bin/fsl_sub -T 10 -l logs -N feat0_init /usr/local/fsl/bin/feat /Users/nlb206/Desktop/guess_FEAT/Participant24.feat/design.fsf -D /Users/nlb206/Desktop/guess_FEAT/Participant24.feat -I 1 -init
>>>>>> 3120
>>>>>>
>>>>>> /usr/local/fsl/bin/fsl_sub -T 57 -l logs -N feat2_pre -j 3120 /usr/local/fsl/bin/feat /Users/nlb206/Desktop/guess_FEAT/Participant24.feat/design.fsf -D /Users/nlb206/Desktop/guess_FEAT/Participant24.feat -I 1 -prestats
>>>>>> child killed: segmentation violation
>>>>>> while executing
>>>>>> "if { [ catch {
>>>>>>
>>>>>> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>>>>>> switch -- [ lindex $argv $argindex ] {
>>>>>>
>>>>>> -I {
>>>>>> incr arginde..."
>>>>>> (file "/usr/local/fsl/bin/feat" line 309)
>>>>>>
>>>>>> FATAL ERROR ENCOUNTERED:
>>>>>> COMMAND:
>>>>>> /usr/local/fsl/bin/fsl_sub -T 57 -l logs -N feat2_pre -j 3120 /usr/local/fsl/bin/feat /Users/nlb206/Desktop/guess_FEAT/Participant24.feat/design.fsf -D /Users/nlb206/Desktop/guess_FEAT/Participant24.feat -I 1 -prestats
>>>>>> ERROR MESSAGE:
>>>>>> child process exited abnormally
>>>>>> END OF ERROR MESSAGE
>>>>>> Initialisation
>>>>>>
>>>>>> /usr/local/fsl/bin/fslmaths /Users/nlb206/Desktop/Study2/Study2MRIData/24/20160407_121223WIPPS_29_fMRI_1SENSEs005a001 prefiltered_func_data -odt float
>>>>>> Total original volumes = 270
>>>>>>
>>>>>> /usr/local/fsl/bin/fslroi prefiltered_func_data example_func 135 1
>>>>>> Preprocessing:Stage 1
>>>>>>
>>>>>> /usr/local/fsl/bin/mainfeatreg -F 6.00 -d /Users/nlb206/Desktop/guess_FEAT/Participant24.feat -l /Users/nlb206/Desktop/guess_FEAT/Participant24.feat/logs/feat2_pre -R /Users/nlb206/Desktop/guess_FEAT/Participant24.feat/report_unwarp.html -r /Users/nlb206/Desktop/guess_FEAT/Participant24.feat/report_reg.html -i /Users/nlb206/Desktop/guess_FEAT/Participant24.feat/example_func.nii.gz -h /Users/nlb206/Desktop/Study2/Study2MRIData/24/20160407_121223WIPsT1W3DFFESENSEs003a001_brain -w BBR -x 90 -s /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
>>>>>> Option -F ( FEAT version parameter ) selected with argument "6.00"
>>>>>> Option -d ( output directory ) selected with argument "/Users/nlb206/Desktop/guess_FEAT/Participant24.feat"
>>>>>> Option -l ( logfile )input with argument "/Users/nlb206/Desktop/guess_FEAT/Participant24.feat/logs/feat2_pre"
>>>>>> Option -R ( html unwarping report ) selected with argument "/Users/nlb206/Desktop/guess_FEAT/Participant24.feat/report_unwarp.html"
>>>>>> Option -r ( html registration report ) selected with argument "/Users/nlb206/Desktop/guess_FEAT/Participant24.feat/report_reg.html"
>>>>>> Option -i ( main input ) input with argument "/Users/nlb206/Desktop/guess_FEAT/Participant24.feat/example_func.nii.gz"
>>>>>> Option -h ( high-res structural image ) selected with argument "/Users/nlb206/Desktop/Study2/Study2MRIData/24/20160407_121223WIPsT1W3DFFESENSEs003a001_brain"
>>>>>> Option -w ( highres dof ) selected with argument "BBR"
>>>>>> Option -x ( highres search ) selected with argument "90"
>>>>>> Option -s ( standard image ) selected with argument "/usr/local/fsl/data/standard/MNI152_T1_2mm_brain"
>>>>>> Option -y ( standard dof ) selected with argument "12"
>>>>>> Option -z ( standard search ) selected with argument "90"
>>>>>> Registration
>>>>>>
>>>>>> /bin/mkdir -p /Users/nlb206/Desktop/guess_FEAT/Participant24.feat/reg
>>>>>>
>>>>>>
>>>>>> /usr/local/fsl/bin/fslmaths /Users/nlb206/Desktop/Study2/Study2MRIData/24/20160407_121223WIPsT1W3DFFESENSEs003a001_brain highres
>>>>>>
>>>>>>
>>>>>> /usr/local/fsl/bin/fslmaths /Users/nlb206/Desktop/Study2/Study2MRIData/24/20160407_121223WIPsT1W3DFFESENSEs003a001 highres_head
>>>>>>
>>>>>>
>>>>>> /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain standard
>>>>>>
>>>>>> did not find file: example_func2highres.mat. Generating transform.
>>>>>>
>>>>>> /usr/local/fsl/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres
>>>>>> Running FAST segmentation FLIRT pre-alignment Running BBR 0.931240 0.999555 0.018898 -0.023072 0.000000 -0.017991 0.999081 0.038912 0.000000 0.023786 -0.038480 0.998976 0.000000 1.906857 1.878921 -6.370079 1.000000
>>>>>>
>>>>>> /usr/local/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat
>>>>>>
>>>>>>
>>>>>> /usr/local/fsl/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/local/fsl/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/local/fsl/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/local/fsl/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/local/fsl/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png example_func2highres2.png
>>>>>>
>>>>>>
>>>>>> /bin/rm example_func2highres1.png
>>>>>>
>>>>>> did not find file: highres2standard.mat. Generating transform.
>>>>>>
>>>>>> /usr/local/fsl/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/local/fsl/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat
>>>>>>
>>>>>>
>>>>>> /usr/local/fsl/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/local/fsl/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/local/fsl/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/local/fsl/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/local/fsl/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png highres2standard2.png
>>>>>>
>>>>>>
>>>>>> /bin/rm highres2standard1.png
>>>>>>
>>>>>>
>>>>>> /usr/local/fsl/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat
>>>>>>
>>>>>>
>>>>>> /usr/local/fsl/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear
>>>>>>
>>>>>> Found file: example_func2standard.mat.
>>>>>>
>>>>>> /usr/local/fsl/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat
>>>>>>
>>>>>>
>>>>>> /usr/local/fsl/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/local/fsl/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/local/fsl/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/local/fsl/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/local/fsl/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?.png example_func2standard2.png
>>>>>>
>>>>>> Preprocessing:Stage 2
>>>>>>
>>>>>> /usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final
>>>>>>
>>>>>> /bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc
>>>>>>
>>>>>> /usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png
>>>>>>
>>>>>> /usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png
>>>>>>
>>>>>> /usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png
>>>>>>
>>>>>> /usr/local/fsl/bin/slicetimer -i prefiltered_func_data_mcf --out=prefiltered_func_data_st -r 2.000000 --odd
>>>>>>
>>>>>> /usr/local/fsl/bin/fslmaths prefiltered_func_data_st -Tmean mean_func
>>>>>>
>>>>>> /usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /usr/local/fsl/bin/immv mask_mask mask
>>>>>>
>>>>>> /usr/local/fsl/bin/fslmaths prefiltered_func_data_st -mas mask prefiltered_func_data_bet
>>>>>>
>>>>>> /usr/local/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98
>>>>>> 0.000000 1339.503296
>>>>>>
>>>>>> /usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 133.9503296 -Tmin -bin mask -odt char
>>>>>>
>>>>>> /usr/local/fsl/bin/fslstats prefiltered_func_data_st -k mask -p 50
>>>>>> 0.000000
>>>>>>
>>>>>> /usr/local/fsl/bin/fslmaths mask -dilF mask
>>>>>>
>>>>>> /usr/local/fsl/bin/fslmaths prefiltered_func_data_st -mas mask prefiltered_func_data_thresh
>>>>>>
>>>>>> /usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func
>>>>>>
>>>>>> /usr/local/fsl/bin/susan prefiltered_func_data_thresh 0.0 2.12314225053 3 1 1 mean_func 0.0 prefiltered_func_data_smooth
>>>>>>
>>>>>> FATAL ERROR ENCOUNTERED:
>>>>>> COMMAND:
>>>>>> /usr/local/fsl/bin/susan prefiltered_func_data_thresh 0.0 2.12314225053 3 1 1 mean_func 0.0 prefiltered_func_data_smooth
>>>>>> ERROR MESSAGE:
>>>>>> child killed: segmentation violation
>>>>>> END OF ERROR MESSAGE
>>>>>> child killed: segmentation violation
>>>>>> while executing
>>>>>> "if { [ catch {
>>>>>>
>>>>>> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>>>>>> switch -- [ lindex $argv $argindex ] {
>>>>>>
>>>>>> -I {
>>>>>> incr arginde
>>>>>>
>>>>>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Natasha Bloodworth <[log in to unmask]>
>>>>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>>>>> Date: Monday, 18 July 2016 at 21:18
>>>>>> To: "[log in to unmask]" <[log in to unmask]>
>>>>>> Subject: [FSL] SUSAN segmentation violation - please help!
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>
|
