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. > 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 > > -- > 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 >
km.hb.tac.dat
Description: Binary data
km.hb.tac.nii.gz
Description: GNU Zip compressed data
km.ref.tac.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.
