[RESOLVED] Fc_compute_roifc problems

Issues
1

Description:

I am looking at changes in fc among several regions from pre-task rest through several repetitions of the task to post task rest. fc_compute_roifc. seems to be perfect for my purposes. However, I have difficulties running it.

Call:

RAStudy="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA"
cd $RAStudy

qunex_container fc_compute_roifc \
--bolds="rest|$RAStudy/sessions/pb1719/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii" \
--roiinfo="$RAStudy/GlasserParcellation/ROIs/SN_DMN.GlasserParcellation.names" \
--frames="$RAStudy/sessions/pb1719/images/functional/events/restfc.fidl|RS:rest:s0:e0" \
--targetf="$RAStudy/analysis/fcROI" \
--options="roimethod=mean|eventdata=all|ignore=use,fidl|badevents=use|fcmeasure=r|saveind=txt|verbose=true|debug=true|fcname=DMN_SN" \
--container="/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-0.97.3.sif"

Error message:

Running:
>>> fc_compute_roifc('rest|/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/GlasserParcellation/ROIs/SN_DMN.GlasserParcellation.names', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/events/restfc.fidl|RS:rest:s0:e0', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI', 'roimethod=mean|eventdata=all|ignore=use,fidl|badevents=use|fcmeasure=r|saveind=txt|verbose=true|debug=true|fcname=DMN_SN')


Options used:
------------
 roimethod: mean
 eventdata: all
    ignore: use,fidl
 badevents: use
 fcmeasure: r
   saveind: txt
   verbose: true
     debug: true
    fcname: DMN_SN

Checking ...
... found results folder (/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI)
     ... creating ROI mask
     ... reading image file(s) ... 420 frames read, done.
     ... generating extraction sets ...
Options used:
------------
    ignore: use,fidl
 badevents: use
   verbose: true
     debug: true
 roimethod: mean
 eventdata: all
 fcmeasure: r
   saveind: {txt}
    fcname: DMN_SN

Matlab Error! Processing Failed!
bsxfun: dimensions of A and B must match


ERROR: fc_compute_roifc failed! Please check output / log!

Logs:

No log files produced

** For an example of how to report an issue, please refer to this post.

2

Helen, hi!

I reviewed the files on grace and it seems there are two issues. First, your fidl file is not a valid fidl file. If you want the FC to be computed on the whole timeseries, then use “0” as input to --frames parmeter. Second, there seems to be a bug in the code and the default value for subjectname is not set, so it needs to be set explicitly. I have a problem running singularity on grace, but I tested the changed command on our severs, an this should work:

qunex_container fc_compute_roifc \
--bolds="rest|$RAStudy/sessions/pb1719/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii" \
--roiinfo="$RAStudy/GlasserParcellation/ROIs/SN_DMN.GlasserParcellation.names" \
--frames="0" \
--targetf="$RAStudy/analysis/fcROI" \
--options="roimethod=mean|eventdata=all|ignore=use,fidl|badevents=use|fcmeasure=r|saveind=txt|verbose=true|debug=true|fcname=DMN_SN|subjectname=" \
--container="/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-0.97.3.sif"

Please, give it a try and let me know if issues persist.

In the upcoming version of QuNex (> 0.99.3) the issue with subjectname is already addressed.

3

Hi Grega,
Unfortunately this did not help.
I tried several different versions of parameters.
Setting frames to “0”

qunex_container fc_compute_roifc \
--bolds="rest|$RAStudy/sessions/pb1719/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii" \
--roiinfo="$RAStudy/GlasserParcellation/ROIs/SN_DMN.GlasserParcellation.names" \
--frames="0" \
--targetf="$RAStudy/analysis/fcROI" \
--options="roimethod=mean|eventdata=all|ignore=use,fidl|badevents=use|fcmeasure=r|saveind=txt|verbose=true|debug=true|fcname=DMN_SN|subjectname=" \
--container="/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-0.97.3.sif"

produced this error:

... could not find fidlfile (0), please check your paths!
Matlab Error! Processing Failed!
ERROR: Fidl file was not found. Please check the path!\n\n
ERROR: fc_compute_roifc failed! Please check output / log!

Setting subjectname=pb1719 produced the same error.

Revising fidl file and including subjectname produced the same error as before.
So, it does look like it is about the fidl file.
Do you have a sample fidl file to share? I tried many-many different formats.
Thank you.

4

If I use a fidl file:

0.8	rest	
0	0	336

and a call

qunex_container fc_compute_roifc \
--bolds="rest|/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii" \
--roiinfo="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/GlasserParcellation/ROIs/SN_DMN.GlasserParcellation.names" \
--frames="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/events/restfc.fidl|rest:s0:e0" \
--targetf="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI" \
--options="roimethod=mean|eventdata=all|ignore=use|badevents=use|fcmeasure=r|saveind=txt|verbose=true|debug=true|fcname=DMN_SN|subjectname=pb1719" \
--container="/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-0.98.6a.sif"

I get this error:

Running:
>>> fc_compute_roifc('rest|/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/GlasserParcellation/ROIs/SN_DMN.GlasserParcellation.names', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/events/restfc.fidl|rest:s0:e0', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI', 'roimethod=mean|eventdata=all|ignore=use|badevents=use|fcmeasure=r|saveind=txt|verbose=true|debug=true|fcname=DMN_SN|subjectname=pb1719')

Options used:
------------
   roimethod: mean
   eventdata: all
      ignore: use
   badevents: use
   fcmeasure: r
     saveind: txt
     verbose: true
       debug: true
      fcname: DMN_SN
 subjectname: pb1719

Checking ...
... found results folder (/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI)
     ... creating ROI mask
     ... reading image file(s) ... 420 frames read, done.
     ... generating extraction sets ...
Options used:
------------
      ignore: use
   badevents: use
     verbose: true
       debug: true
   roimethod: mean
   eventdata: all
   fcmeasure: r
     saveind: {txt}
      fcname: DMN_SN
 subjectname: pb1719

Matlab Error! Processing Failed!
operator /: nonconformant arguments (op1 is 1x1, op2 is 0x0)

ERROR: fc_compute_roifc failed! Please check output / log!
5

I see you are using an older version of the container, did you try with the latest release one - 0.99.2d?

Jure

6

Yes, I tried many different containers, including this one.

qunex_container fc_compute_roifc \
--bolds="rest|/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii" \
--roiinfo="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/GlasserParcellation/ROIs/SN_DMN.GlasserParcellation.names" \
--frames="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/events/restfc.fidl|rest:s0:e0" \
--targetf="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI" \
--options="roimethod=mean|eventdata=all|ignore=use|badevents=use|fcmeasure=r|saveind=txt|verbose=true|debug=true|fcname=DMN_SN|subjectname=pb1719" \
--container="/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-0.99.2d.sif"

Same error.


Running:
>>> fc_compute_roifc('rest|/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/GlasserParcellation/ROIs/SN_DMN.GlasserParcellation.names', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/events/restfc.fidl|rest:s0:e0', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI', 'roimethod=mean|eventdata=all|ignore=use|badevents=use|fcmeasure=r|saveind=txt|verbose=true|debug=true|fcname=DMN_SN|subjectname=pb1719')


Options used:
------------
   roimethod: mean
   eventdata: all
      ignore: use
   badevents: use
   fcmeasure: r
     saveind: txt
     verbose: true
       debug: true
      fcname: DMN_SN
 subjectname: pb1719

Checking ...
... found results folder (/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI)
     ... creating ROI mask
     ... reading image file(s) ... 420 frames read, done.
     ... generating extraction sets ...
Options used:
------------
      ignore: use
   badevents: use
     verbose: true
       debug: true
   roimethod: mean
   eventdata: all
   fcmeasure: r
     saveind: {txt}
      fcname: DMN_SN
 subjectname: pb1719

Matlab Error! Processing Failed!
operator /: nonconformant arguments (op1 is 1x1, op2 is 0x0)

Or

qunex_container fc_compute_roifc \
--bolds="rest|/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii" \
--roiinfo="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/GlasserParcellation/ROIs/SN_DMN.GlasserParcellation.names" \
--frames="0" \
--targetf="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI" \
--options="roimethod=mean|eventdata=all|ignore=use|badevents=use|fcmeasure=r|saveind=txt|verbose=true|debug=true|fcname=DMN_SN|subjectname=pb1719" \
--container="/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-0.99.2d.sif"

Returns this

>>> fc_compute_roifc('rest|/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/GlasserParcellation/ROIs/SN_DMN.GlasserParcellation.names', '0', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI', 'roimethod=mean|eventdata=all|ignore=use|badevents=use|fcmeasure=r|saveind=txt|verbose=true|debug=true|fcname=DMN_SN|subjectname=pb1719')


Options used:
------------
   roimethod: mean
   eventdata: all
      ignore: use
   badevents: use
   fcmeasure: r
     saveind: txt
     verbose: true
       debug: true
      fcname: DMN_SN
 subjectname: pb1719

Checking ...
... found results folder (/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI)
     ... creating ROI mask
     ... reading image file(s) ... 420 frames read, done.
     ... generating extraction sets ...
Options used:
------------
      ignore: use
   badevents: use
     verbose: true
       debug: true
   roimethod: mean
   eventdata: all
   fcmeasure: r
     saveind: {txt}
      fcname: DMN_SN
 subjectname: pb1719
... could not find fidlfile (0), please check your paths!

Matlab Error! Processing Failed!
ERROR: Fidl file was not found. Please check the path!\n\n


ERROR: fc_compute_roifc failed! Please check output / log!
7

Helen,

Try changing your fidl file to:

0.8 rest
0 0 336
8

I tried it:

0.8 rest
0 0 336

But getting the same error:

type or Running:
>>> fc_compute_roifc('rest|/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/GlasserParcellation/ROIs/SN_DMN.GlasserParcellation.names', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/events/restfc.fidl|rest:s0:e0', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI', 'roimethod=mean|eventdata=all|ignore=use|badevents=use|fcmeasure=r|saveind=txt|verbose=true|debug=true|fcname=DMN_SN|subjectname=pb1719')


Options used:
------------
   roimethod: mean
   eventdata: all
      ignore: use
   badevents: use
   fcmeasure: r
     saveind: txt
     verbose: true
       debug: true
      fcname: DMN_SN
 subjectname: pb1719

Checking ...
... found results folder (/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI)
     ... creating ROI mask
     ... reading image file(s) ... 420 frames read, done.
     ... generating extraction sets ...
Options used:
------------
      ignore: use
   badevents: use
     verbose: true
       debug: true
   roimethod: mean
   eventdata: all
   fcmeasure: r
     saveind: {txt}
      fcname: DMN_SN
 subjectname: pb1719

Matlab Error! Processing Failed!
operator /: nonconformant arguments (op1 is 1x1, op2 is 0x0)

ERROR: fc_compute_roifc failed! Please check output / log!paste code here
9

Helen,

I will need to get help fixing my access to singularity on grace, so that I can run the same container in your environment and resolve the issue. Let me come back with a fix for you.

10

Thank you Grega - I really appreciate your time.

11

Ok! Mysteries resolved.

First, your fidl file started with non-ascii characters. It might be, that it was written in an app that added BOM to the file. To resolve that, I created a new file w/o BOM:

/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/events/restfc_g.fidl

Second, in your frames parameter, the name of the extraction set was missing. The full specification of the extraction has to be:

'<fidlfile>|<extraction name>:<event list>:<extraction start>:<extraction end>'

I corrected the specification to:

--frames="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/events/restfc_g.fidl|rest:rest:s0:e0"

And third, e0 denotes the first frame after the end of the event. This was now outside of the timeseries, so the event was skipped. The correct specification is:

--frames="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/events/restfc_g.fidl|rest:rest:s0:e-1"

and the full command call:

qunex_container fc_compute_roifc \
--bolds="rest|/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii" \
--roiinfo="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/GlasserParcellation/ROIs/SN_DMN.GlasserParcellation.names" \
--frames="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1719/images/functional/events/restfc_g.fidl|rest:rest:s0:e-1" \
--targetf="/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/fcROI" \
--options="roimethod=mean|eventdata=all|ignore=use|badevents=use|fcmeasure=r|saveind=txt|verbose=true|debug=true|fcname=DMN_SN|subjectname=pb1719" \
--container="/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-0.99.2d.sif"

I have tested it out and it works.

12 
===> Successful completion of task

Grega - Thank you so much!!!

13

Grega, thanks for your deep dive into this!