---------- Forwarded message ----------
From: "Erin W." <[log in to unmask]>
To: [log in to unmask], Rachelle Ho <[log in to unmask]>
Cc: "Erin W." <[log in to unmask]>
Bcc: 
Date: Tue, 17 Apr 2018 16:29:53 +0100
Subject: Re: Failure to generate example_func2highres.png
Hi Rachelle,

Apologies, I must have missed your reply last week!

Yes, I have that file, as well as the .mat file (and others that result from the standard registration process, e.g., *wmedge.nii).

Input is the functional run (for a respective participant). For registration, the Main Structural is the skull-stripped (robust fov, then bet) anatomical file, and standard space is set to default MNI.

As I said, when we change the Main Structural to a Freesurfer skull-stripped brain, we do not have this issue. Hence, was wondering if this is related to using robust fov / bet?

Thanks,
Erin

--------

Hi Erin,

What are the files you're inputting into the analysis? It seems like the issue might be in creating the example_func2highres.mat file. Do you have a transformed example_func2highres.nii file?

Best,
Rachelle

On Mon, Apr 9, 2018 at 7:10 PM, Erin Walsh <[log in to unmask]> wrote:
Hi again,

Just resubmitting this question in case anyone can provide any input. Thank you for your time!

Warmly,
Erin


On Mon, Apr 2, 2018 at 4:01 PM, Erin W. <[log in to unmask]> wrote:
Hi all,

I cannot find an answer on previous threads. I have noticed an issue in preprocessing where example_func2highres.png file is not generated. However, all other example_func2highres files are in the reg directory (e.g., .mat, *fast_wmseg) and seem reasonable upon viewing.

Report log specific to example_func2highres is posted below.

For this particular dataset (7T scanner), we have had to use robustfov, then bet, to improve skullstripping.

To note, when we use a Freesurfer skull stripped brain as input for the main structural, we do not receive any such errors or issue generating the .png file.

Thanks for any insight or assistance,
Erin

-------------
Error:

did not find file: example_func2highres.mat. Generating transform.

/nas/longleaf/apps/fsl/5.0.10/fsl/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres
Running FAST segmentation FLIRT pre-alignment Running BBR 0.487216 0.998850 -0.030615 0.036900 0.000000 0.030626 0.999531 0.000260 0.000000 -0.036891 0.000870 0.999319 0.000000 0.557750 5.505235 -0.433015 1.000000

/nas/longleaf/apps/fsl/5.0.10/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat


/nas/longleaf/apps/fsl/5.0.10/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 ; /nas/longleaf/apps/fsl/5.0.10/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 ; /nas/longleaf/apps/fsl/5.0.10/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 ; /nas/longleaf/apps/fsl/5.0.10/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 ; /nas/longleaf/apps/fsl/5.0.10/fsl/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png example_func2highres2.png
Images aren't the same size!

 Cannot open sla.png for reading
sh: line 1: 29511 Segmentation fault      /nas/longleaf/apps/fsl/5.0.10/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
Images aren't the same size!

 Cannot open sla.png for reading
sh: line 1: 29515 Segmentation fault      /nas/longleaf/apps/fsl/5.0.10/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

 Cannot open example_func2highres1.png for reading
sh: line 1: 29516 Segmentation fault      /nas/longleaf/apps/fsl/5.0.10/fsl/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png


/bin/rm example_func2highres1.png
/bin/rm: cannot remove 'example_func2highres1.png': No such file or directory