Fmriprep html report missing anatomical section

1

Hi,

I am using fmriprep 1.4.1 and thing appear to be running correctly. The only issue is that the html reports only contains information on the functional data and is missing the section regarding the anatomical processing?

Thanks

Rob

2

Hi,

I’m still having this issue and wondered if anyone else had ran into a similar problem. I’m now using fmriprep and the command I give is:

singularity run --cleanenv ${HOME}/singularity_images/fmriprep-1.5.3.simg
${data_folder} ${postprocessed_folder}
participant
–participant-label ${file}
–fs-license-file ${HOME}/license.txt
-w ${working_folder}
–output-spaces MNI152NLin2009cAsym MNI152NLin6Asym fsaverage5 fsnative
–use-syn-sdc
–ignore fieldmaps
–nthreads 4
–omp-nthreads 4
–mem_mb 30000
-t rest

It seems to run fine it is just the html report does not include the anatomical section, and I am just concerned if this suggest something may not have run correctly?

Thanks,

Rob

3

Hi, thanks for posting and sorry for missing this. Can you list your output directory?

4

Thanks! I’ve attachedfmriprep_output.txt (33.0 KB) p.s. one of the subjects was run with --fs-no-reconall

5

Well, there are definitely no anatomical figures for the report generator to pick up. Are you sure you didn’t get any errors at the bottom of your HTML reports?

6

Thanks, no errors it states: No errors to report!

It appears that there are anatomical figures in the working directory?:

reportlets/:
fmriprep

reportlets/fmriprep:
sub-507 sub-508

reportlets/fmriprep/sub-507:
anat ses-A ses-B

reportlets/fmriprep/sub-507/anat:
sub-507_desc-about_T1w.html sub-507_desc-summary_T1w.html sub-507_space-MNI152NLin2009cAsym_T1w.svg
sub-507_desc-conform_T1w.html sub-507_dseg.svg sub-507_space-MNI152NLin6Asym_T1w.svg

reportlets/fmriprep/sub-507/ses-A:
func

reportlets/fmriprep/sub-507/ses-A/func:
sub-507_ses-A_task-CA_run-1_desc-carpetplot_bold.svg sub-507_ses-A_task-CA_run-2_desc-rois_bold.svg
sub-507_ses-A_task-CA_run-1_desc-compcorvar_bold.svg sub-507_ses-A_task-CA_run-2_desc-summary_bold.html
sub-507_ses-A_task-CA_run-1_desc-confoundcorr_bold.svg sub-507_ses-A_task-CA_run-2_desc-validation_bold.html
sub-507_ses-A_task-CA_run-1_desc-flirtbbr_bold.svg sub-507_ses-A_task-rest_run-1_desc-carpetplot_bold.svg
sub-507_ses-A_task-CA_run-1_desc-rois_bold.svg sub-507_ses-A_task-rest_run-1_desc-compcorvar_bold.svg
sub-507_ses-A_task-CA_run-1_desc-summary_bold.html sub-507_ses-A_task-rest_run-1_desc-confoundcorr_bold.svg
sub-507_ses-A_task-CA_run-1_desc-validation_bold.html sub-507_ses-A_task-rest_run-1_desc-flirtbbr_bold.svg
sub-507_ses-A_task-CA_run-2_desc-carpetplot_bold.svg sub-507_ses-A_task-rest_run-1_desc-rois_bold.svg
sub-507_ses-A_task-CA_run-2_desc-compcorvar_bold.svg sub-507_ses-A_task-rest_run-1_desc-summary_bold.html
sub-507_ses-A_task-CA_run-2_desc-confoundcorr_bold.svg sub-507_ses-A_task-rest_run-1_desc-validation_bold.html
sub-507_ses-A_task-CA_run-2_desc-flirtbbr_bold.svg

reportlets/fmriprep/sub-507/ses-B:
func

reportlets/fmriprep/sub-507/ses-B/func:
sub-507_ses-B_task-CA_run-1_desc-carpetplot_bold.svg sub-507_ses-B_task-CA_run-2_desc-rois_bold.svg
sub-507_ses-B_task-CA_run-1_desc-compcorvar_bold.svg sub-507_ses-B_task-CA_run-2_desc-summary_bold.html
sub-507_ses-B_task-CA_run-1_desc-confoundcorr_bold.svg sub-507_ses-B_task-CA_run-2_desc-validation_bold.html
sub-507_ses-B_task-CA_run-1_desc-flirtbbr_bold.svg sub-507_ses-B_task-rest_run-1_desc-carpetplot_bold.svg
sub-507_ses-B_task-CA_run-1_desc-rois_bold.svg sub-507_ses-B_task-rest_run-1_desc-compcorvar_bold.svg
sub-507_ses-B_task-CA_run-1_desc-summary_bold.html sub-507_ses-B_task-rest_run-1_desc-confoundcorr_bold.svg
sub-507_ses-B_task-CA_run-1_desc-validation_bold.html sub-507_ses-B_task-rest_run-1_desc-flirtbbr_bold.svg
sub-507_ses-B_task-CA_run-2_desc-carpetplot_bold.svg sub-507_ses-B_task-rest_run-1_desc-rois_bold.svg
sub-507_ses-B_task-CA_run-2_desc-compcorvar_bold.svg sub-507_ses-B_task-rest_run-1_desc-summary_bold.html
sub-507_ses-B_task-CA_run-2_desc-confoundcorr_bold.svg sub-507_ses-B_task-rest_run-1_desc-validation_bold.html
sub-507_ses-B_task-CA_run-2_desc-flirtbbr_bold.svg

reportlets/fmriprep/sub-508:
anat ses-A ses-B

reportlets/fmriprep/sub-508/anat:
sub-508_desc-about_T1w.html sub-508_desc-summary_T1w.html sub-508_space-MNI152NLin6Asym_T1w.svg
sub-508_desc-conform_T1w.html sub-508_dseg.svg
sub-508_desc-reconall_T1w.svg sub-508_space-MNI152NLin2009cAsym_T1w.svg

reportlets/fmriprep/sub-508/ses-A:
func

reportlets/fmriprep/sub-508/ses-A/func:
sub-508_ses-A_task-rest_run-1_desc-bbregister_bold.svg sub-508_ses-A_task-rest_run-1_desc-rois_bold.svg
sub-508_ses-A_task-rest_run-1_desc-carpetplot_bold.svg sub-508_ses-A_task-rest_run-1_desc-summary_bold.html
sub-508_ses-A_task-rest_run-1_desc-compcorvar_bold.svg sub-508_ses-A_task-rest_run-1_desc-validation_bold.html
sub-508_ses-A_task-rest_run-1_desc-confoundcorr_bold.svg

reportlets/fmriprep/sub-508/ses-B:
func

reportlets/fmriprep/sub-508/ses-B/func:
sub-508_ses-B_task-rest_run-1_desc-bbregister_bold.svg sub-508_ses-B_task-rest_run-1_desc-rois_bold.svg
sub-508_ses-B_task-rest_run-1_desc-carpetplot_bold.svg sub-508_ses-B_task-rest_run-1_desc-summary_bold.html
sub-508_ses-B_task-rest_run-1_desc-compcorvar_bold.svg sub-508_ses-B_task-rest_run-1_desc-validation_bold.html
sub-508_ses-B_task-rest_run-1_desc-confoundcorr_bold.svg

7

Dear @effigies

I’m still having this issue (now using fmriprep 20.0.5)

singularity run --cleanenv ${HOME}/singularity_images/fmriprep-20.0.5.simg \
    ${data_folder} ${postprocessed_folder}  \
    participant \
    --participant-label ${file} \
    --fs-license-file ${HOME}/license.txt \
    -w ${working_folder} \
    --use-syn-sdc \
    --cifti-output \
    --output-spaces MNI152NLin2009cAsym MNI152NLin6Asym fsaverage5 fsnative fsLR\
    --ignore fieldmaps\
    --nthreads 4 \
    --omp-nthreads 4 \
    --mem_mb 30000

and this occurs even after I have cleared output and working directories entirely. I wondered whether you or anyone else have any suggestions as to (a)why this may be, and (b) whether it is a cause for concern or can safely be ignored?

Many Thanks,

Rob