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 <conchipaf...@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 <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/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 < >> 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 >>> >> >> >
PET_Surfer
Description: Binary data
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