HI expert ! My name is Areum. I have some question to you.
1. Does FreeSurfer offer a effect size? if that offer, how can i use effect size? 2. I was wondering about the stats.dat file in stats_table (in Qdec folder). Stats.dat file’s value mean that each area’s average (include whole vertex) or each area’s average (only significant vertex)? 3. Can I get whole vertex value or significant vertex value? Because, I want to compare two groups correlation using SPSS. In addition, I want to compare thickness, volume and surface area correlation within the one group using SPSS. 4. I currently use the default cluster size(significant area threshold is 0mm^2). So, I want to control cluster size larger than default cluster size. How can I control the cluster size? 5. In FreeSurfer manual, GLM and Qdec have a same results. But when I use the both(GLM, Qdec) group analysis program results are not same. What is differences between two analysis program? How can I get same result while GLM and Qdec? 6. How can I get surface area and volume using GLM(group analysis program)? plz reply to me 2015-08-10 21:35 GMT+09:00 A-reum Min <naniy...@gmail.com>: > Hello developer~ > > I have some questions to you. > > > > 1. Does FreeSurfer offer a effect size? if that offer, how can i use > effect size? > > > > 2. I was wondering about the stats.dat file in stats_table (in Qdec > folder). > > Stats.dat file’s value mean that each area’s average (include whole > vertex) or each > > area’s average (only significant vertex)? > > > > 3. Can I get whole vertex value or significant vertex value? Because, I > want to > > compare two groups correlation using SPSS. In addition, I want to compare > > thickness, volume and surface area correlation within the one group using > SPSS. > > > > 4. I currently use the default cluster size(significant area threshold is > 0mm^2). So, I > > want to control cluster size larger than default cluster size. How can I > control the > > cluster size? > > > > 5. In FreeSurfer manual, GLM and Qdec have a same results. But when I use > the > > both(GLM, Qdec) group analysis program results are not same. What is > differences > > between two analysis program? How can I get same result while GLM and Qdec? > > > > 6. How can I get surface area and volume using GLM(group analysis program)? > > > thanks for your help > > 2015-07-27 14:28 GMT+09:00 A-reum Min <naniy...@gmail.com>: > >> Hello bruce >> >> I solve this problem(12.png) >> >> Thank you >> >> 2015-07-27 13:03 GMT+09:00 dgw <dgwake...@gmail.com>: >> >>> Hi A-reum, >>> >>> I think you may be able to get a faster response if you include some >>> details about your setup: I would start with the following: >>> >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> and run bugr. >>> >>> hth >>> D >>> >>> On 7/26/15 5:17 PM, A-reum Min wrote: >>> > 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 >>> > <mailto: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 >>> > <mailto: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 >>> > <mailto: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 <mailto: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 >>> > <mailto: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 >>> > <mailto: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 <mailto: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 >>> > <mailto: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 >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> > > >>> > >>> > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> > >>> > >>> > _______________________________________________ >>> > Freesurfer >>> > mailing list >>> > >>> > Freesurfer@nmr.mgh.harvard.edu >>> > <mailto: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 >>> > <mailto: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 >>> > <mailto: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 >>> > <mailto: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 <mailto: >>> 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 >>> >> >> >
_______________________________________________ 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.
