Thanks for your advice, I redo cp tfMRI_EMOTION_hp200_s4_level2.fsf file twice,
then it works now, I'm not sure whether it would crash again or not.
Best,
Bai Haohao
------------------ ???????? ------------------
??????: "Harms, Michael";<mha...@wustl.edu>;
????????: 2017??4??29??(??????) ????10:23
??????: "Glasser, Matthew"<glass...@wustl.edu>; "--"<744652...@qq.com>;
"hcp-users"<hcp-users@humanconnectome.org>;
????: Re: [HCP-Users] [SPAM] Re: [SPAM] Re: [SPAM] Re: [SPAM]
Re:[TaskfMRILevel2]feat_modelerror
To simplify your testing, once you have a design.fsf file, if
feat_model design
doesn??t work, then your fsf file was not set up correctly.
[Note that the feat_model command explicitly excludes the .fsf extension, and
it will not work if you try to call ??feat_model design.fsf??]
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: <hcp-users-boun...@humanconnectome.org> on behalf of "Glasser,
Matthew" <glass...@wustl.edu>
Date: Saturday, April 29, 2017 at 8:04 AM
To: -- <744652...@qq.com>, hcp-users <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] [SPAM] Re: [SPAM] Re: [SPAM] Re: [SPAM] Re:
[TaskfMRILevel2]feat_modelerror
Likely either could cause the error, but I would guess fsf.
Peace,
Matt.
From: -- <744652...@qq.com>
Date: Saturday, April 29, 2017 at 6:46 AM
To: Matt Glasser <glass...@wustl.edu>, hcp-users
<hcp-users@humanconnectome.org>
Subject: [SPAM] Re: [SPAM] Re: [SPAM] Re: [SPAM] Re:
[HCP-Users][TaskfMRILevel2]feat_modelerror
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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