[RESOLVED] Setting up connectivity analysis

Use Questions
21

Hi Grega,

Thanks for your help! Unfortunately, it doesn’t work. It seems to add an extra-path “roifc_/home/aca/qunex/quickstart/processing/lists/session_HCPA001_r” after my target path, which makes the output path strange.

Matlab Error! Processing Failed!
save: unable to open output file '/home/aca/Desktop/roifc_/home/aca/qunex/quickstart/processing/lists/session_HCPA001_r'

aca@aca-virtual-machine:~/qunex$ 

ERROR: fc_compute_roifc failed! Please check output / log!
22

Acacius, hi!

I am sorry, I was focused on the target folder specification and did not notice the values supplied to --flist parameter:

--flist="listname:/home/aca/qunex/quickstart/processing/lists/session.list|session id:HCPA001|file:/home/aca/qunex/quickstart/sessions/HCPA001/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d_lpss.dtseries.nii|roi:/home/aca/qunex/data/null_lL_WG33/S900.sulc_MSMAll.32k_fs_LR.dscalar.nii"

For the flist parameter you have two options. One option is to provide a path to the .list file. In this case, the path is the only value to submit, e.g.:

--flist="/home/aca/qunex/quickstart/processing/lists/session.list"

The second option is to construct a string that is the content of the .list file in this case, you need to first specify the list name, and then the following information. An example would be:

--flist="listname:HCPA001|session id:HCPA001|file:/home/aca/qunex/quickstart/sessions/HCPA001/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d_lpss.dtseries.nii"

In this case I have also omitted the roi specification, as you do not provide a names file as an input to roiinfo parameter and so individual roi specification is not used.

If you specify --flist="listname:<name_of_the_list>, `name of the list is appended to the results file name. In your case above, the name of the list was a path, so it appended a path to the target file path, which led to an error.

To correct this you could do either:

qunex_container fc_compute_roifc \
    --sessionsfolder="${STUDY_FOLDER}/sessions" \
    --flist="/home/aca/qunex/quickstart/processing/lists/session.list" \
    --roiinfo="/home/aca/qunex/data/null_lL_WG33/Gordon333_FreesurferSubcortical.32k_fs_LR.dlabel.nii" \
    --targetf="/home/aca/Desktop" \
    --options="sessions=all|roimethod=mean|eventdata=all|ignore=use,fidl|badevents=use|fcmeasure=r|debug=false|saveind=mat,long,wide_single|itargetf:gfolder" \
    --frames_info="5" \
    --container="${QUNEX_CONTAINER}"

or

qunex_container fc_compute_roifc \
    --sessionsfolder="${STUDY_FOLDER}/sessions" \
    --flist="listname:HCPA001|session id:HCPA001|file:/home/aca/qunex/quickstart/sessions/HCPA001/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d_lpss.dtseries.nii" \
    --roiinfo="/home/aca/qunex/data/null_lL_WG33/Gordon333_FreesurferSubcortical.32k_fs_LR.dlabel.nii" \
    --targetf="/home/aca/Desktop" \
    --options="sessions=all|roimethod=mean|eventdata=all|ignore=use,fidl|badevents=use|fcmeasure=r|debug=false|saveind=mat,long,wide_single|itargetf:gfolder" \
    --frames_info="5" \
    --container="${QUNEX_CONTAINER}"

I’m not sure, which one you intended to use and what is correct for your environment.

I hope this helps and resolves the issue.

All the best,

Grega

23

Hi Grega,

Thanks for your generous help! I have tried the second option, it works now!

Best,
Acacius

24

Acacius, hi!

That’s great! Let us know if you run into any other issues or need further help.

All the best,

Grega