Thanks for your reply.
Is this error due to missing fsf or EVs file? Then should I re-generate EVs and
fsf?
Best,
Bai Haohao
------------------ Original ------------------
From: "Glasser, Matthew";<glass...@wustl.edu>;
Date: Sat, Apr 29, 2017 12:47 PM
To: "--"<744652...@qq.com>; "hcp-users"<hcp-users@humanconnectome.org>;
Cc: "Brown, Tim"<tbbr...@wustl.edu>;
Subject: Re: [SPAM] Re: [SPAM] Re: [SPAM] Re:
[HCP-Users][TaskfMRILevel2]feat_modelerror
I see: The fsf file is a part of the preprocessed fMRI packages together with
the EVs.
We should probably make a more descriptive error message for missing fsf or
EVs.
Peace,
Matt.
From: -- <744652...@qq.com>
Date: Friday, April 28, 2017 at 10:51 PM
To: Matt Glasser <glass...@wustl.edu>, hcp-users
<hcp-users@humanconnectome.org>
Subject: [SPAM] Re: [SPAM] Re: [SPAM] Re: [HCP-Users]
[TaskfMRILevel2]feat_modelerror
Thanks, here is the code that calls TaskfMRIAnalysis.sh in
TaskfMRIAnalysisBatch.sh:
${queuing_command} ${HCPPIPEDIR}/TaskfMRIAnalysis/TaskfMRIAnalysis.sh \
--path=$StudyFolder \
--subject=$Subject \
--lvl1tasks=$LevelOneTasks \
--lvl1fsfs=$LevelOneFSFs \
--lvl2task=$LevelTwoTask \
--lvl2fsf=$LevelTwoFSF \
--lowresmesh=$LowResMesh \
--grayordinatesres=$GrayOrdinatesResolution \
--origsmoothingFWHM=$OriginalSmoothingFWHM \
--confound=$Confound \
--finalsmoothingFWHM=$FinalSmoothingFWHM \
--temporalfilter=$TemporalFilter \
--vba=$VolumeBasedProcessing
# The following lines are used for interactive debugging to set the
positional parameters: $1 $2 $3 ...
echo "set -- --path=$StudyFolder \
--subject=$Subject \
--lvl1tasks=$LevelOneTasks \
--lvl1fsfs=$LevelOneFSFs \
--lvl2task=$LevelTwoTask \
--lvl2fsf=$LevelTwoFSF \
--lowresmesh=$LowResMesh \
--grayordinatesres=$GrayOrdinatesResolution \
--origsmoothingFWHM=$OriginalSmoothingFWHM \
--confound=$Confound \
--finalsmoothingFWHM=$FinalSmoothingFWHM \
--temporalfilter=$TemporalFilter \
--vba=$VolumeBasedProcessing"
And the echo shows:
set -- --path=/home/baihaohao/Workingdir/Data/HcpData
--subject=100307 --lvl1tasks=tfMRI_EMOTION_RL@tfMRI_EMOTION_LR
--lvl1fsfs=tfMRI_EMOTION_RL@tfMRI_EMOTION_LR --lvl2task=tfMRI_EMOTION
--lvl2fsf=tfMRI_EMOTION --lowresmesh=32
--grayordinatesres=2 --origsmoothingFWHM=2 --confound=NONE
--finalsmoothingFWHM=2 --temporalfilter=200 --vba=NO
There is the code that calls TaskfMRILevel2.sh in TaskfMRIAnalysis.sh:
echo "set -- $Subject $ResultsFolder $DownSampleFolder $LevelOnefMRINames
$LevelOnefsfNames $LevelTwofMRIName $LevelTwofsfNames $LowResMesh
$FinalSmoothingFWHM $TemporalFilter $VolumeBasedProcessing"
${PipelineScripts}/TaskfMRILevel2.sh $Subject $ResultsFolder
$DownSampleFolder $LevelOnefMRINames $LevelOnefsfNames $LevelTwofMRIName
$LevelTwofsfNames $LowResMesh $FinalSmoothingFWHM $TemporalFilter
$VolumeBasedProcessing
And the echo shows:
set -- 100307
/home/baihaohao/Workingdir/Data/HcpData/100307/MNINonLinear/Results
/home/baihaohao/Workingdir/Data/HcpData/100307/MNINonLinear/fsaverage_LR32k
tfMRI_EMOTION_RL@tfMRI_EMOTION_LR tfMRI_EMOTION_RL@tfMRI_EMOTION_LR
tfMRI_EMOTION tfMRI_EMOTION 32 2 200 NO
And line56 of TaskfMRILevel2.sh is the red line here, which creates the error:
#Make design files
log_Msg "Make design files"
DIR=`pwd`
cd ${LevelTwoFEATDir}
feat_model ${LevelTwoFEATDir}/design
cd $DIR
The path in ${LevelTwoFEATDir}:
/home/baihaohao/Workingdir/Data/HcpData/100307/MNINonLinear/Results/tfMRI_EMOTION/tfMRI_EMOTION_hp200_s2_level2.feat
Under the path, I can only found design.fsf, no design, even cp design.fsf
design cannot fix this.
Best,
Bai Haohao
------------------ Original ------------------
From: "Glasser, Matthew";<glass...@wustl.edu>;
Date: Thu, Apr 27, 2017 09:59 PM
To: "--"<744652...@qq.com>; "hcp-users"<hcp-users@humanconnectome.org>;
Subject: Re: [SPAM] Re: [SPAM] Re: [HCP-Users] [TaskfMRILevel2]feat_modelerror
Perhaps you can paste in how you are calling the TaskfMRIAnalysis pipeline
(not the run local part but rather what is in that script).
Peace,
Matt.
From: -- <744652...@qq.com>
Date: Thursday, April 27, 2017 at 8:48 AM
To: Matt Glasser <glass...@wustl.edu>, hcp-users
<hcp-users@humanconnectome.org>
Subject: [SPAM] Re: [SPAM] Re: [HCP-Users] [TaskfMRILevel2]feat_model error
The data and the Pipeline scripts are all included in the 2015 HCP Course,
and the subject ID is 100307.
Besides, I have already running three structural pipelines and two functional
pipelines.
Best,
Bai Haohao
------------------ Original ------------------
From: "Glasser, Matthew";<glass...@wustl.edu>;
Date: Thu, Apr 27, 2017 09:08 PM
To: "--"<744652...@qq.com>; "hcp-users"<hcp-users@humanconnectome.org>;
Subject: Re: [SPAM] Re: [HCP-Users] [TaskfMRILevel2]feat_model error
Are you using HCP data or your own task fMRI data?
Peace,
Matt.
From: -- <744652...@qq.com>
Date: Thursday, April 27, 2017 at 3:56 AM
To: Matt Glasser <glass...@wustl.edu>, hcp-users
<hcp-users@humanconnectome.org>
Subject: [SPAM] Re: [HCP-Users] [TaskfMRILevel2]feat_model error
Hello,
I modify the TaskfMRIAnalysisBatch.sh to change StudyFolder, Subjlist and
EnvironmentScript to my own file path.
Then I write a bash file to call copy_evs_into_results.sh and
generate_level1_fsf.sh to generate the files.
Followed Day4_Practical7_Task_fMRI tutorial, I install level2.fsf file.
After that, bash TaskfMRIAnalysisBatch.sh --runlocal
Best,
Bai Haohao
------------------ Original ------------------
From: "Glasser, Matthew";<glass...@wustl.edu>;
Date: Wed, Apr 26, 2017 11:43 PM
To: "--"<744652...@qq.com>;
"hcp-users@humanconnectome.org"<HCP-Users@humanconnectome.org>;
Subject: Re: [HCP-Users] [TaskfMRILevel2]feat_model error
How did you call the task analysis pipeline?
Peace,
Matt.
From: <hcp-users-boun...@humanconnectome.org> on behalf of --
<744652...@qq.com>
Date: Wednesday, April 26, 2017 at 10:35 AM
To: "hcp-users@humanconnectome.org" <HCP-Users@humanconnectome.org>
Subject: [HCP-Users] [TaskfMRILevel2]feat_model error
Hello HCP experts,
I get a fatal error during running Examples/Scripts/TaskfMRIAnalysisBatch.sh,
the error info(also see attached file):
terminate called after throwing an instance of 'NEWMAT::ProgramException'
/home/baihaohao/Workingdir/Pipelines-3.4.0/TaskfMRIAnalysis/scripts/TaskfMRILevel2.sh:
line 56: 79213 Aborted (core dumped) feat_model
${LevelTwoFEATDir}/design
and line56 of TaskfMRILevel2.sh is the red line here:
#Make design files
log_Msg "Make design files"
DIR=`pwd`
cd ${LevelTwoFEATDir}
feat_model ${LevelTwoFEATDir}/design
cd $DIR
I have done steps based on HCP Course Materials Day4_Practical7_Task_fMRI
tutorial, already install level1 and level2.
How can I fix it? Any suggestion would be helpful.
Thanks in advance,
Bai Haohao
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The materials in this message are private and may contain Protected Healthcare
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or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
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