Re: [Freesurfer] PET processing seg fault with mri_glmfit --mrtm1

Can you send the full terminal output? ie, evverything that is printed to the screen until the program exists? Also, can you send the nii.gz, .dat, and time.dat file?

On 11/13/2017 03:16 PM, Conchy PF wrote:

Dear Douglas,

I checked km.ref.tac.dat and these are the values (I also copied the values from km.hb.tac.dat):

hb        ref 26.73126411 -4.761529326 -51.51094818 9.139505029 -44.41317749 -30.22258914 220.9154358 14.15057564 -148.9746399 -43.47668242 616.010437 693.7505493 3824.406494 1780.615295 5860.389648 4099.188477 9274.21582 7107.838867 13033.90234 11014.56836 20199.89453 15320.79248 26479.21094 19191.92676 22497.46875 22564.60352 33364.9375 23562.50488 32399.6543 25423.65039 30375.87891 27588.76758 31598.69531 28611.44141 36040.28125 28856.04297 33941.47266 29354.62598 36371.19922 29652.85645 36864.45313 29824.78809 36461.71875 30356.99902 37141.31641 29621.66504 35989.77734 29284.03418 34920.16406 28383.14063 32570.80273 27048.52637 31181.25195 26152.96777 30228.48438 24923.17285 30397.92188 23731.39355 27963.25391 22931.38672 27626.80859 21669.00781 27317.41406 20714.75098 24818.10352 19908.15332 25746.88867 18791.90332 23731.32227 17453.33691 21670.56445 16185.16846 20853.60156 14717.54785 19521.11523 13301.76416 18291.18164 12331.82324 17112.03125 11231.87012 16750.16797 10366.62256 15137.30078 8969.751953 12795.11328 7273.169434 11052.7207 5976.648193 9589.397461 4914.908691 7955.464844 3755.181274 6104.589844 2690.000854 4789.041016 1954.52179 3701.868652 1439.027466 2905.178223 1106.310547 2309.740967 834.9413757 1885.463867 654.3575439 1415.454956 498.8769073 1100.553345 413.3814087 930.8244629 313.5371246 754.6965332 260.3549805 633.7663574 190.4842987 523.4249878 171.7433548

The output is this one:

MacBook-Pro:~ usr$ cd $SUBJECTS_DIR

MacBook-Pro:~ usr$ mri_glmfit.bin --y gtmpvc/km.hb.tac.nii.gz --mrtm1 gtmpvc/km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz

Segmentation fault: 11

Unfortunately, there is no more information.

I am running the command on a Mac OS X 10.9.5.

What do you think?

Thank you and kind regards,

CP

On Mon, Nov 13, 2017 at 4:18 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

Please check the reference TAC. Also, please send the full
terminal output


On 11/11/2017 06:07 AM, Conchy PF wrote:
> Dear Douglas,
>
> I had the same problem as Jonathan described in his post "PET
> processing seg fault with mri_glmfit --mrtm1"
>
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043144.html
<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043144.html>).
>
> In my case, I used this command:
>
> mri_glmfit --y gtmpvc/km.hb.tac.nii.gz --mrtm1 gtmpvc/km.ref.tac.dat
> time.dat --o mrtm1 --no-est-fwhm --nii.gz
>
> And I got this message:
>
> /Applications/freesurfer/bin/mri_glmfit: line 3: 27756 Segmentation
> fault: 11mri_glmfit.bin "$@"
>
> Following your advice, I checked if km.hb.tac.nii.gz was all 0 using
>
> hb = fast_vol2mat( MRIread('km.hb.tac.nii.gz'));
> plot(hb)
>
> in matlab, but that is not the case
>
> Inline image 1
>
> I also checked the table.dat format and it was correct, and I tried
> using mri_glmfit.bin command insted, but it did not work.
>
> Could you give me some advice, so I can keep running the PET surfer
> pipeline?
>
> Thank you in advance and kind regards,
>
> CP
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline
<http://www.partners.org/complianceline> . If the e-mail was sent
to you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer