Sorry, I forgot the time.dat file. Here it goes. Thank you,
CP On Mon, Nov 13, 2017 at 9:28 PM, Conchy PF <conchipaf...@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/ > 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> 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>> 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 >> > gr...@nmr.mgh.harvard.edu <mailto:gr...@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:freesur...@nmr.mgh.har >> vard.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 >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@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/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >
time.dat
Description: Binary data
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
