There is not time.dat file. CAn you send it?
On 11/13/17 4:28 PM, Conchy PF wrote:
Dear Douglas,
I did not save the full output from the beginning when I processed
this subject. I can send you what I get when I run the
mri_glmfit command. If you need this output, I can run another subject
from the beginning. Please, find attached the original pet data,
.nii.gz, time.dat, and .dat files.
PIB.nii.gz
<https://drive.google.com/file/d/1SR07tXZnqeTiJEAuLS3JlXutSx-IEmh4/view?usp=drive_web>
Thank you,
CP
Last login: Mon Nov 13 20:00:09 on ttys001
-------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR/Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR /usr/local/fsl
MacBook-Pro:~ usr$ export
SUBJECTS_DIR=/Volumes/usr/STUDY/Raw_PET/TP1/subject
MacBook-Pro:~ usr$
MacBook-Pro:~ usr$ cd $SUBJECTS_DIR
MacBook-Pro:subject usr$ 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
MacBook-Pro:subject usr$
On Mon, Nov 13, 2017 at 8:37 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
Can you send the full terminal output? ie, evverything that is printed
to the screen until the program exits? 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
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@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>
>
<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
> >
> >
> > _______________________________________________
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422
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