Hi, Bruce When i use a Qdec, this message(12.png) show up.. How can i solve this problem?
2015-07-23 22:57 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > 1. No, each subject has a different #. You can map to fsaverage (this is > what -qcache does if you specify it for recon-all), then they will have the > same #. > > 2. What result data do you mean? > > 3. Yes, although I'll leave the details to Doug (since I don't remember > how his cluster code works). > > 4. The significance doesn't depend on the cluster size unless you do > multiple comparison corrections (and even then only if you do them a > certain way) > > cheers > Bruce > > > On Thu, 23 Jul 2015, A-reum Min wrote: > > HELLO developer >> I have some question to you.. >> >> 1. Every patient is given to the same number of vertex? >> >> 2. When i use a Qdec, How can I get the subject result data? >> >> 3. Could i get the significant vertex’s number, extent of the >> significant area and gray matter volume? >> >> 4. Is it significant blue color which how many connected vertex? >> >> >> 2015-05-29 2:03 GMT+09:00 A-reum Min <naniy...@gmail.com>: >> hello developer~ >> reconstruction is well done, so i'm doing on 'qdec' step.. >> Actually, i don't know how to treat the Design menu exactly.. >> >> --------------------------------------------------------------------------- >> Discrete(fixed factors) : diagnosis >> continuous (covariate) : age , Left-Lateral-Ventricle >> >> --------------------------------------------------------------------------- >> which one click before analyze? >> >> age range is 12years~24years/ >> all subjects are adolescent. >> and no outlier in age range.. so.. age (continuous factor) does not >> nasessart? >> >> >> 2015-05-29 1:19 GMT+09:00 A-reum Min <naniy...@gmail.com>: >> hello developer~ >> reconstruction is well done, so i'm doing on 'qdec' step.. >> Actually, i don't know how to treat the Design menu exactly.. >> >> --------------------------------------------------------------------------- >> Discrete(fixed factors) : diagnosis >> continuous (covariate) : age , Left-Lateral-Ventricle >> >> --------------------------------------------------------------------------- >> which one click before analyze? >> >> >> >> 2015-04-05 21:41 GMT+09:00 Bruce Fischl >> <fis...@nmr.mgh.harvard.edu>: >> I'm glad it worked out >> Bruce >> On Sun, 5 Apr 2015, A-reum Min wrote: >> >> Hello Bruce~ >> You're right.. my PISA dicom file header >> is too short >> so, freesurfer didn't read it. >> >> Therefore I use another subjects dicom >> file and then freesurfer read it! >> >> thank you for u r adavice to me. >> >> I really appreciate u >> >> 2015-04-05 7:08 GMT+09:00 Bruce Fischl >> <fis...@nmr.mgh.harvard.edu>: >> Hi A-reum >> >> the problem is that newer versions >> of scanner software compress >> dicoms and the version of FS you >> have doesn't know how to read >> it. So you need to decompress them >> before passing them to >> recon-all >> >> cheers >> Bruce >> On Sun, 5 Apr 2015, A-reum Min >> wrote: >> >> Hello developer~ >> >> Can you summarize what the >> problem is? >> ==> >> my problem is recon-all -i >> didn't working... >> so, if i type the recon-all >> -i~then show up theses >> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> ERROR: 32512, see >> >> /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out >> for >> more details >> Linux localhost.localdomain >> 2.6.32-504.el6.x86_64 #1 >> SMP Wed Oct 15 04:27:16 >> UTC 2014 x86_64 x86_64 >> x86_64 GNU/Linux >> >> dcmdjpeg.fs: error while >> loading shared libraries: >> libijg8.so.3.6: cannot >> open shared object file: No >> such file or directory >> >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >> then, i click the >> >> root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, >> show >> up >> these >> dcmdjpeg.fs: error while >> loading shared libraries: >> libijg8.so.3.6: cannot >> open shared object file: No >> such file or directory >> >> Are you trying to read >> compressed dicom? >> ==> >> Am i trying to read >> compressed dicom? >> I send my 10071579.dicom(i >> use this) to you, >> using -i, convert the dicom >> file to mgh file. i just >> know that dicom file >> convert to mgz format using >> -i /my data path >> Is it right..?? >> >> >> If so, Can you try running >> dcmdjpeg on it to create >> a new (uncompressed) >> series and give that to >> recon-all? >> ==> (actually, i didn't >> understand your sentence >> means perfectly..) >> zeke tomeaurl( >> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/c >> >> en >> t >> os6_x86_64/dcmdjpeg.fs) >> and then, replace my >> existing >> >> $FREESURFER_HOME/bin/dcmdjpeg.fs file. >> Also, make sure it is set to >> executable by typing >> the following in a >> terminal window: >> $> chmod a+x >> $FREESURFER_HOME/bin/dcmdjpeg.fs >> >> >> 2015-04-05 2:30 GMT+09:00 >> Bruce Fischl >> >> <fis...@nmr.mgh.harvard.edu>: >> Hi A-reum >> >> sorry, I'm coming into >> this late. Can you >> summarize what the >> problem is? Are you >> trying to read compressed >> dicom? If so, can >> you try running >> dcmdjpeg on it to create a new >> (uncompressed) >> series and give that >> to recon-all? >> >> cheers >> Bruec >> >> >> >> On Sat, 4 Apr 2015, >> A-reum Min wrote: >> >> Hello >> developers.. >> >> i type the >> recon-all -i~then show up >> theses >> >> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> ERROR: 32512, >> see >> >> >> /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out >> for >> more details >> Linux >> localhost.localdomain >> 2.6.32-504.el6.x86_64 #1 >> SMP Wed Oct 15 >> 04:27:16 >> UTC 2014 x86_64 >> x86_64 x86_64 GNU/Linux >> >> dcmdjpeg.fs: >> error while loading shared >> libraries: >> libijg8.so.3.6: >> cannot >> open shared >> object file: No such file or >> directory >> >> >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >> error is occured >> (a little differntly..) >> then, i click >> the >> >> >> root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, >> show >> up >> these >> >> dcmdjpeg.fs: >> error while loading shared >> libraries: >> libijg8.so.3.6: >> cannot >> open shared >> object file: No such file or >> directory >> >> i'm so sorry..to >> bother you.. >> >> >> >> 2015-04-04 9:21 >> GMT+09:00 A-reum Min >> >> <naniy...@gmail.com>: >> hello >> >> i type the >> recon-all -i~ >> then show up >> theses >> >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >> >> >> +++++++ >> >> ERROR: 32256, >> see >> >> >> /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out >> for more details >> Linux >> localhost.localdomain >> 2.6.32-504.el6.x86_64 #1 >> SMP Wed Oct 15 >> 04:27:16 UTC >> 2014 x86_64 x86_64 x86_64 >> GNU/Linux >> >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >> >> >> +++++++ >> the error is >> occured (a little >> differntly..) >> then, i click >> the >> >> >> /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out, >> show iuo these >> >> sh: >> >> /usr/local/freesurfer/bin/dcmdjpeg.fs: >> >> /lib/ld-linux.so.2: bad ELF >> interpreter: No >> such file or directory >> >> plz help me >> 2015-04-04 4:12 >> GMT+09:00 >> >> <zkauf...@nmr.mgh.harvard.edu>: >> A-reum, >> >> Please >> download the following >> file: >> >> >> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_ >> >> >> >> >> x86_64/dcmdjpeg.fs >> >> And >> replace your existing >> >> $FREESURFER_HOME/bin/dcmdjpeg.fs >> file with >> the >> one from >> the link above. Also, >> make sure it is >> set to >> executable >> by typing >> the >> following in a terminal >> window: >> >> $> chmod >> a+x >> >> $FREESURFER_HOME/bin/dcmdjpeg.fs >> >> And then >> try again. >> >> -Zeke >> >> >> > Hi >> doug... recon-all dosen't >> working.. >> > >> > If i >> type the recon-all -i~ >> > then, >> error occured... >> > >> >> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> + >> + >> + >> ++ >> > >> > JPEG >> compressed, decompressing >> > cd >> >> >> /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01 >> > >> dcmdjpeg.fs +te >> >> >> >> /usr/local/freesurfer/subjects/PISA_FSPGR/1/I0071579.dcm >> > >> >> /tmp/root.tmp.decompressed.dcm.kBIYHL >& >> > >> >> >> /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out >> > ERROR: >> 32512, see >> >> >> >> /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out >> for >> > more >> details >> > Linux >> localhost.localdomain >> >> 2.6.32-504.el6.x86_64 #1 SMP >> Wed Oct 15 >> > 04:27:16 >> UTC 2014 x86_64 x86_64 >> x86_64 >> GNU/Linux >> > >> > >> recon-all -s subj01 exited with >> ERRORS at >> Fri Apr 3 >> 10:39:27 >> PDT 2015 >> > >> > For more >> details, see the log >> file >> > >> >> >> >> >> /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01/scripts/recon-all.log >> > To >> report a problem, see >> > >> >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > >> >> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> + >> + >> + >> +++ >> > >> > I copy >> the libdcmjpeg.so.3.6 and >> paste in >> >> FREESURFER_HOME/lib >> > after >> that type the setenv >> LD_LIBRARY_PATH >> >> $FREESURFER_HOME/lib >> > >> > but.. >> didn't working .. >> > >> > same >> error occured --> >> dcmdjpeg.fs: error >> while loading >> shared >> libraries: >> > >> libdcmjpeg.so.3.6: cannot open >> shared object >> file: No >> such file >> or >> > >> directory >> > >> > and i >> click the >> >> >> root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out >> then show up >> > these >> > >> > >> dcmdjpeg.fs: error while loading >> shared >> libraries: >> >> libdcmjpeg.so.3.6: >> > cannot >> open shared object file: >> No such file >> or >> directory >> > >> > how can i to >> do ㅜㅜ help me doug >> > >> >> _______________________________________________ >> > Freesurfer >> mailing list >> > >> Freesurfer@nmr.mgh.harvard.edu >> > >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> 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. >> >> >> >> >> >> >> _______________________________________________ >> 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. >> >> >> >> >> _______________________________________________ >> 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. >> >> >> >> >> _______________________________________________ >> 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. >> >> >> >> >> >> > _______________________________________________ > 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. > >
_______________________________________________ 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.
