Thanks Rali:
I did an additional step of preproc that was not needed. It created
redundant files. Once I skipped that step, it ran without problems.
cheers,
Alan
On Fri, Sep 20, 2013 at 6:44 AM, Rali Dimitrova
<[log in to unmask]>wrote:
> I don't have FSL at the moment to look at the script but I would suggest
> to make sure you check whether
>
> - you are running the command from the right dir (the one that contains
> the ./FA/ and ./L1/ directories where your maps are)
> - that you have named the directories and the FA/L1 maps appropriately
> (how are your FA/L1 maps named?)
>
> Have you followed the exact instructions on the wiki?
> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/UserGuide
>
> also check:
>
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1304&L=FSL&P=R77267&1=FSL&9=A&J=on&X=186B624BC66D6AAFAC&Y=ralicavdimitrova%40gmail.com&d=No+Match%3BMatch%3BMatches&z=4
>
> All best,
> Rali
>
>
> On 19 September 2013 19:48, Alan Francis <[log in to unmask]> wrote:
>
>> Hi Rali/ FSL:
>>
>> For some reason the command *tbss_non_FA L1 *gives me an error
>> message. I am running TBSS on mytbss folder with the L1 data present. I
>> enclose the error message. Any help is deeply appreciated:
>>
>> [cerebro:mytbss_3] (nmr-stable53-env) tbss_non_FA L1
>> using pre-chosen registration target: target
>> upsampling alternative images into standard space
>> G1_valera_bi_103_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G1_valera_bi_103_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27107 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G1_valera_bi_105_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G1_valera_bi_105_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27112 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G1_valera_bi_106_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G1_valera_bi_106_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27117 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G1_valera_bi_107_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G1_valera_bi_107_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27122 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G1_valera_bi_109_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G1_valera_bi_109_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27127 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G1_valera_bi_113_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G1_valera_bi_113_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27132 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G1_valera_bi_117_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G1_valera_bi_117_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27137 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G1_valera_bi_118_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G1_valera_bi_118_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27142 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G1_valera_bi_119_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G1_valera_bi_119_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27147 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G1_valera_bi_120_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G1_valera_bi_120_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27152 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G1_valera_bi_122_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G1_valera_bi_122_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27157 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G2_valera_bi_102_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G2_valera_bi_102_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27162 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G2_valera_bi_104_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G2_valera_bi_104_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27167 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G2_valera_bi_108_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G2_valera_bi_108_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27172 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G2_valera_bi_110_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G2_valera_bi_110_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27177 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G2_valera_bi_111_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G2_valera_bi_111_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27182 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G2_valera_bi_112_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G2_valera_bi_112_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27187 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G2_valera_bi_114_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G2_valera_bi_114_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27192 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G2_valera_bi_116_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G2_valera_bi_116_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27197 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G2_valera_bi_121_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G2_valera_bi_121_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27202 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G2_valera_bi_124_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G2_valera_bi_124_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27207 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G2_valera_bi_125_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G2_valera_bi_125_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27212 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> G2_valera_bi_126_dti_FA
>> Image Exception : #22 :: ERROR: Could not open image
>> ../L1/G2_valera_bi_126_dti_FA
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 91: 27217 Aborted
>> (core dumped) $FSLDIR/bin/applywarp -i ../${ALTIM}/$f -o
>> ${f}_to_target_${ALTIM} -r $FSLDIR/data/standard/FMRIB58_FA_1mm -w
>> ${f}_FA_to_${best}_warp $postaffine
>> merging all upsampled L1 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
>> Cannot open volume all_L1 for reading!
>> projecting all_L1 onto mean FA skeleton
>> Image Exception : #22 :: ERROR: Could not open image all_L1
>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>> /usr/pubsw/packages/fsl/5.0.0/bin/tbss_non_FA: line 104: 27223 Aborted
>> (core dumped) ${FSLDIR}/bin/tbss_skeleton -i mean_FA -p
>> $thresh mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm
>> all_FA all_${ALTIM}_skeletonised -a all_$ALTIM
>> now run stats - for example:
>> randomise -i all_L1_skeletonised -o tbss_L1 -m mean_FA_skeleton_mask -d
>> design.mat -t design.con -n 500 --T2 -V
>> (after generating design.mat and design.con)
>> [cerebro:mytbss_3] (nmr-stable53-env)
>>
>>
>>
>>
>>
>> On Thu, Sep 19, 2013 at 2:05 PM, Rali Dimitrova <
>> [log in to unmask]> wrote:
>>
>>> The script/command in terminal is *tbss_non_FA L1.*
>>>
>>> Bw,
>>> Rali
>>>
>>>
>>> On 19 September 2013 18:45, Alan Francis <[log in to unmask]>wrote:
>>>
>>>> Hi FSL community:
>>>>
>>>> I am following the TBSS index on the FSL website. I am specifically
>>>> trying to merge all subjects' warped L1 data into a 4D file
>>>> stats/all_L1.
>>>>
>>>> The website says "use the tbss_non_FA script". Do you know where I can
>>>> locate this script?
>>>>
>>>>
>>>> thanks,
>>>>
>>>> Alan
>>>>
>>>
>>>
>>
>
>
> --
> Best wishes,
> Rali Dimitrova
>
> Division of Psychiatry,
> University of Edinburgh
>
