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

14 Nov 2017

      Dear Douglas,
I run another participant with PET Surfer. This time I converted the
original PET image from .hdr/.img to nii.gz using mri_convert. I had the
same problem when I run MRTM1. Please, find attached the log from the
beginning.
Thank you and kind regards,
CP
On Mon, Nov 13, 2017 at 9:36 PM, Conchy PF conchipafran@gmail.com wrote:
...
Sorry, I forgot the time.dat file. Here it goes.
Thank you,
CP
On Mon, Nov 13, 2017 at 9:28 PM, Conchy PF conchipafran@gmail.com 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/STUD
Y/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 <
greve@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
<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
>
>
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--
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>
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<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/>

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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