On 08/10/2015 10:06 PM, A-reum Min wrote: > 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? > If you're doing a group analysis, you can compute fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o glmdir/contrast/effectsize.mgh > > 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)? > what stats.dat? if subject/stats/lh.aparc.stats, then the area is the total area for the ROI > > 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. > You can extract a given vertex with mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf vertexno.dat vertexno.dat will be a text file with number of rows equalt to thge number of subjects where the value is the data from the given (0-based) vertex no. y.mgh is the input to mri_glmfit > > 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? > I don't know what you mean. > > 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? > No way to know unless you tell us the specifics of what you did > > 6. How can I get surface area and volume using GLM(group analysis > program)? > surface area and volume are outputs of recon-all, not glm > > > plz reply to me > > > 2015-08-10 21:35 GMT+09:00 A-reum Min <naniy...@gmail.com > <mailto: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 > <mailto: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 > <mailto: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> > > <mailto: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> > > <mailto: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> > > <mailto: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> > <mailto: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> > > <mailto: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> > > <mailto: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> <mailto: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> > > <mailto: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> > > <mailto: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> > > <mailto: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> > > <mailto: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> > > <mailto: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> > > <mailto: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> > <mailto: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 > > > > > > > _______________________________________________ > 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
