Replies: 9 comments 4 replies
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Hey Devin! I'm taking a look at this, I should have an answer here soon |
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The It looks like FEAT didn't successfully generate the |
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OK good to know regarding the structural processing, thanks. Here is the FEAT log as requested, it doesn't really contain much... bb_feat_rfMRI_ns_sub-A00028845.log STANDARD OUT: STANDARD ERROR: |
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No worries. It's one of the holdovers from the original implementation - probably worth removing at some point to eliminate any confusion :) Oh right, it just points you to the MELODIC report. Would you mind pasting the contents of |
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Sure thing! Here it is. Just curious, do you have way to view .html files on Compute Canada? I usually download and then look with firefox but figured there must be a module to load that could view them. Progress Report / Log Main script /bin/cp /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.fsf design.fsf mkdir .files;cp /opt/fsl/doc/fsl.css .files;cp -r /opt/fsl/doc/images .files/images /opt/fsl/bin/fsl_sub -T 10 -l logs -N feat1a_init /opt/fsl/bin/feat /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.ica/design.fsf -D /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.ica -I 1 -init /opt/fsl/bin/fsl_sub -T 250 -l logs -N feat2_pre -j 108601 /opt/fsl/bin/feat /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.ica/design.fsf -D /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.ica -I 1 -prestats /opt/fsl/bin/fsl_sub -T 180 -l logs -N feat4_ica -j 108912 /opt/fsl/bin/melodic -i filtered_func_data -o filtered_func_data.ica -v --nobet --bgthreshold=3 --tr=1.400000 --report --guireport=../../report.html -d 0 --mmthresh=0.5 /opt/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 112439 /opt/fsl/bin/feat /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.ica/design.fsf -D /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.ica -stop Initialisation /opt/fsl/bin/fslmaths /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI prefiltered_func_data -odt float /opt/fsl/bin/fslroi prefiltered_func_data prefiltered_func_data 4 400 /opt/fsl/bin/fslmaths /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI_SBREF.nii.gz example_func Preprocessing:Stage 1 /opt/fsl/bin/mainfeatreg -F 6.00 -d /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.ica -l /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.ica/logs/feat2_pre -R /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.ica/report_unwarp.html -r /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.ica/report_reg.html -i /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.ica/example_func.nii.gz -n 10 -h /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/symlink/T1_brain.nii.gz -w BBR -x 90 -s /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 Registration /bin/mkdir -p /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/rfMRI.ica/reg /opt/fsl/bin/fslmaths /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/symlink/T1_brain highres /opt/fsl/bin/fslmaths /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/symlink/T1.nii.gz highres_head /opt/fsl/bin/fslmaths /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/symlink/T1_brain_wmseg highres_wmseg Checking for /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/symlink/T1_brain2MNI152_T1_2mm_brain_warp and /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/symlink/T1_brain2MNI152_T1_2mm_brain.mat /opt/fsl/bin/fslmaths /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/symlink/T1_brain2MNI152_T1_2mm_brain_warp highres2standard_warp cp /scratch/soddev/Rockland/pipeline_testing_June2022/Raw_BIDS/sub-A00028845/fMRI/symlink/T1_brain2MNI152_T1_2mm_brain.mat highres2standard.mat did not find file: example_func2highres.mat. Generating transform. /opt/fsl/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres /opt/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat /opt/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 ; /opt/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 ; /opt/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 ; /opt/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 ; /opt/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 Preprocessing:Stage 2 /opt/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 /opt/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 /opt/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 /opt/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 /opt/fsl/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func /opt/fsl/bin/bet2 mean_func mask -f 0.3 -n -m; /opt/fsl/bin/immv mask_mask mask /opt/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet /opt/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98 /opt/fsl/bin/fslmaths prefiltered_func_data_bet -thr 172.99729 -Tmin -bin mask -odt char /opt/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50 /opt/fsl/bin/fslmaths mask -dilF mask /opt/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh /opt/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func /opt/fsl/bin/susan prefiltered_func_data_thresh 791.70245325 2.12314225053 3 1 1 mean_func 791.70245325 prefiltered_func_data_smooth /opt/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth /opt/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 9.47325598047 prefiltered_func_data_intnorm /opt/fsl/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean /opt/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 35.7142857143 -1 -add tempMean prefiltered_func_data_tempfilt /opt/fsl/bin/imrm tempMean /opt/fsl/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data /opt/fsl/bin/fslmaths filtered_func_data -Tmean mean_func /bin/rm -rf prefiltered_func_data* Stats Melodic Version 3.15 Melodic results will be in filtered_func_data.ica Create mask ... done Data size : 400 x 236269 Starting PCA ... done Starting ICA estimation using symm Step no. 1 change : 0.999937 Sorting IC maps Writing results to : Running Mixture Modelling on Z-transformed IC maps ... Writing results to : To view the output report point your web browser at filtered_func_data.ica/report/00index.html finished! |
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Thanks for the log! Could you please post the contents of design.fsf (in the ica directory) and let us know which branch of the pipeline you adapted for your dataset? |
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Thanks for the help! Please below for the contents of design.fsf. I believe I'm working off the main branch of the pipeline, this is what I get when running the "git branch" command (i am not a github expert so please excuse if I'm misunderstanding...): |
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I don't think you're misunderstanding! git branch works great. Thanks for posting the design.fsf! Just an update - it looks like the |
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OK good to know re: git branch! Thanks for checking that out, in case this helps, here is the contents of my submit_subject.sh file: #!/bin/bash module load StdEnv/2020 gcc/9.3.0 afni/20.3.05 freesurfer/7.1.0 singularity run --nv -B /scratch -B /localscratch -B /cvmfs -B /project /home/soddev/projects/def-levine/soddev/Rockland/TVBukbb_pipeline/tvb-ukbb_latest.sif ${1} /home/soddev/projects/def-levine/soddev/Rockland/TVBukbb_pipeline/tvb-ukbb |
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Could you please share your |
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Sure thing, here is the init_vars: [soddev@cedar5 tvb-ukbb]$ cat init_vars Script name: init_varsDescription: Script to initalise the variables needed for the pipeline.Authors: Fidel Alfaro-Almagro, Stephen M. Smith & Mark JenkinsonCopyright 2017 University of OxfordLicensed under the Apache License, Version 2.0 (the "License");you may not use this file except in compliance with the License.You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing, softwaredistributed under the License is distributed on an "AS IS" BASIS,WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.See the License for the specific language governing permissions andlimitations under the License.########################################### USER MUST MODIFY THE INDICATED LINES########################################### UKBB ROOT DIR LOCATIONexport BBDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && cd ..; pwd )" #SETUP FSL #TODO implement this in the files option 1: true; use full-GPU probtrackx call. default.option 2: gpu_batch; split GPU probtrackx into 10 smaller batches.for low-memory systems.option 3: false: use CPU probtrackx split into 10 smaller batches.use for systems without CUDA GPUexport PROBTRACKX_GPU="true" #SETUP AFNI export AFNIDIR=/opt/afni #TO BE MODIFIED BY USERexport AFNIDIR="/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/gcc9/afni/20.3.05" #SETUP FREESURFER export FREESURFER_HOME=/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/freesurfer/5.3.0/bin/freesurfer #TO BE MODIFIED BY USERif usin on Compute Canada, load module firstsource $EBROOTFREESURFER/FreeSurferEnv.sh source $FREESURFER_HOME/SetUpFreeSurfer.sh > /dev/null#SETUP ANTS export SOFTDIR="/opt/tvb-pipeline" #TO BE MODIFIED BY USER (DEFAULT FOR SINGULARITY) SET UP MATLABexport MCROOT="/opt/mcr" #TO BE MODIFIED BY USER (DEFAULT FOR SINGULARITY) #Move $FSLDIR/bin before $FREESURFER_HOME in the path #SETUP EXTERNAL LIBRARIES #SET LOCALE FOR FLOATING POINT FORMATTING #ENV VARIABLES FOR BIOBANK export FSL_FIXDIR="$BB_BIN_DIR/bb_functional_pipeline/bb_fix_dir" set to 1 for single shell diffusion data and 2 for multi-shellexport DIFF_SHELL_TYPE="1" #INCLUDE 3 MAIN BIOBANK DIRECTORIES IN PATH #SET PATH FOR MCR export MATLAB_COMPILER_RUNTIME="$MCROOT/$MCRV" export XAPPLRESDIR="$MCROOT/$MCRV/X11/app-defaults" source activate $SOFTDIR/software/envsource activate $SOFTDIR/software/env And here is the bb_prepare_rfMRI log file: [soddev@cedar5 logs]$ cat bb_prepare_rfMRI_sub-A00028845.log STANDARD ERROR:
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Based off your
design_ICA.fsf calls the /usr/local/fsl, likely causing an error design_ICA_nonSmoothed.fsf on the other hand, refers to the appropriate FSLDIR defined in init_vars Depending on your needs, you may either edit to the |
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Ah OK, thanks so much. I'm using the smoothed version of the .fsf file so I think the easiest is to edit design_ICA.fsf so it calls the correct FSLDIR defined in init_vars. I'll try that out and let you know how it goes! |
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Dear Experts,
I'm noticing the following error in the bb_pipeline_struct for a subject, and I'm wondering if this is causing problems downstream in the functional pipeline. Please see below where I commented first on the two errors for the structural processing, flagged with "##"
Only errors are the following in structural processing log:
##The functional processing error I see is that it can't find a warp file called "example_func2standard_warp". Please see below for the output of the functional processing log, and below that, the contents of the transforms folder in the fMRI output folder
##contents of fMRI reg folder:
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