Freesurfer May 2016

freesurfer@nmr.mgh.harvard.edu

135 participants
197 discussions

Re: [Freesurfer] hello freesurfer developer~
by A-reum Min 27 Sep '16

27 Sep '16

hello experts. I have a question to you... I'm doing recon-all stage... but errors showed up (fig.1) how can i to do? plz, help me 2015-09-16 23:56 GMT+09:00 Douglas Greve <greve(a)nmr.mgh.harvard.edu>: > don't use .hdr. When you have a .hdr/.img pair, just use the .img file. > > > On 9/16/15 10:51 AM, A-reum Min wrote: > > hello, experts > I have some question. > > I want to use analyze format instead of DICOM file. > > So, i type this sentence > > recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i > /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001 > > > and then error occured.... > > ERROR: cannot determine file type for > /usr/local/freesurfer/subjects/test_han/I0071579.hdr > 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 han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015 > > For more details, see the log file > /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > How can i to do using analyze format? > > > 2015-08-27 23:55 GMT+09:00 Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: > >> Specify something for --seg. It just needs to be a surface overlay of >> the same size as the input. >> >> On 08/27/2015 01:49 AM, A-reum Min wrote: >> > Hello doug >> > >> > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' >> > then, error occured --> ERROR: must specify a segmentation volume >> > >> > >> > 2015-08-27 12:50 GMT+09:00 Douglas Greve <greve(a)nmr.mgh.harvard.edu >> > <mailto:greve@nmr.mgh.harvard.edu>>: >> > >> > don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 >> > >> > >> > On 8/26/15 9:22 PM, A-reum Min wrote: >> >> Hello developer, >> >> >> >> I have some question to you. >> >> >> >> How can i get the significant vertices value using Qdec result? >> >> >> >> When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> >> --avgwf out.dat', then error ouccured --> ERROR : Option out.dat >> >> unknown. >> >> >> >> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> >> --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. >> >> >> >> How can i fix it? >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00 Douglas Greve >> >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >> >> >> >> >> >> >> >> On 8/25/15 9:35 AM, A-reum Min wrote: >> >>> Hello developers >> >>> >> >>> I have some question to you. >> >>> >> >>> 1.In fig.png, how many vertices were composed of cluster at >> >>> least? >> >> I'm not sure what you mean. it does not look like there are >> >> any clusters there >> >>> >> >>> 2. How to change Area Threshold(fig.png)? >> >> The area is controlled by the clusterwise threshold (--cwp) >> >> to mri_glmfit-sim >> >>> >> >>> 3. How to change CSD thresh(fig.png)? >> >> That is controlled by the threshold when specifying "--cache >> >> threshold sign" to mri_glmfit-sim >> >>> >> >>> 4. What is the difference between two words(Area Threshold, >> >>> CSD thresh)? >> >> One is the cluster-pvalue and the other is the >> >> cluster-forming thershold >> >>> >> >>> 5. What is the exactly mean two words(Area Threshold, CSD >> >>> thresh)? >> >> See above >> >> >> >>> >> >>> Thank you >> >>> >> >>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve >> >>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu >> >>: >> >>> >> >>> >> >>> >> >>> 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 >> >>> <naniyaah(a)gmail.com <mailto:naniyaah@gmail.com> >> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@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 >> >>> <naniyaah(a)gmail.com <mailto:naniyaah@gmail.com> >> >>> > <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com>>>: >> >>> > >> >>> > Hello bruce >> >>> > >> >>> > I solve this problem(12.png) >> >>> > >> >>> > Thank you >> >>> > >> >>> > 2015-07-27 13:03 GMT+09:00 dgw >> >>> <dgwakeman(a)gmail.com <mailto:dgwakeman@gmail.com> >> >>> > <mailto:dgwakeman@gmail.com >> >>> <mailto:dgwakeman@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 >> >>> > <fischl(a)nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu>> >> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@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 >> >>> > <naniyaah(a)gmail.com >> >>> <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com>> >> >>> > > <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com> >> >>> > <mailto:naniyaah@gmail.com <mailto: >> naniyaah(a)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 >> >>> > <naniyaah(a)gmail.com >> >>> <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com>> >> >>> > > <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com> >> >>> > <mailto:naniyaah@gmail.com <mailto: >> naniyaah(a)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 >> >>> > > <fischl(a)nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu>> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@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 >> >>> > > <fischl(a)nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu>> >> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@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 >> >>> > > >> >>> > > <fischl(a)nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu>> >> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@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 >> >>> > > >> >>> > > <naniyaah(a)gmail.com >> >>> <mailto:naniyaah@gmail.com> >> >>> > <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com> >> >>> > <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@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 >> >>> > > >> >>> > > <zkaufman(a)nmr.mgh.harvard.edu >> >>> <mailto:zkaufman@nmr.mgh.harvard.edu> >> >>> > <mailto:zkaufman@nmr.mgh.harvard.edu >> >>> <mailto:zkaufman@nmr.mgh.harvard.edu>> >> >>> > > <mailto:zkaufman@nmr.mgh.harvard.edu >> >>> <mailto:zkaufman@nmr.mgh.harvard.edu> >> >>> > <mailto:zkaufman@nmr.mgh.harvard.edu >> >>> <mailto:zkaufman@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: >> >>> > > > >> >>> >> > ... > > [메일의 일부입니다.] > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > >

3 27

Coordinates in TRACULA group analysis
by Anri WATANABE 03 Aug '16

03 Aug '16

Dear experts, I use TRACULA to examine a measure (FA) at each voxel in one pathway. pathstats.byvoxel.txt files show coordinates in native space and after converting those the new files don't show any coordinates which are in MNI space. Could you tell me how can I know MNI coordinate values? Thank you! Regards, Anri ********************************************************************** 京都府立医科大学附属病院精神科・心療内科渡辺杏里 ********************************************************************** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine **********************************************************************

2 21

ERROR: dimension mismatch between input volume and seg
by Kari Parsons 25 Jul '16

25 Jul '16

Hi, I'm trying to get some cortical thickness volumes for an ROI that I have (I'm pretty much following the instructions at https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness verbatim), but for some of my subjects I'm getting errors that look like this when I run mdi_segstats: ERROR: dimension mismatch between input volume and seg input 1 1 145283 seg 145283 1 1 Does anyone have any thoughts on how to trouble-shoot this one? Thanks!

3 7

matlab crashes on selxavg
by S.V.Shepherd [work] 20 Jun '16

20 Jun '16

Hello, When running more than 3 analyses in parallel in FreeSurfer 5.3, I am getting matlab crashes. Mathworks has politely declined to provide support unless I can replicate outside FsFAST. The errors are variants of """ OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable [...] MATLAB is exiting because of fatal error Killed ------------------------------------------ ERROR: fast_selxavg3() failed\n """ thread_monitor Resource temporarily unavailable in pthread_create *** glibc detected *** /usr/local/MATLAB/R2015b/bin/glnxa64/MATLAB: double free or corruption (!prev): 0x00007f585308c390 *** Segmentation fault (core dumped) """ I have copied Matlab version info below. Any tips on how to troubleshoot? ---------------------------------------------------------------------------------------------------- MATLAB Version: 8.6.0.267246 (R2015b) MATLAB License Number: 1098672 Operating System: Linux 2.6.32-573.18.1.el6.x86_64 #1 SMP Wed Jan 6 11:20:49 EST 2016 x86_64 Java Version: Java 1.7.0_60-b19 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode ---------------------------------------------------------------------------------------------------- MATLAB Version 8.6 (R2015b) Computer Vision System Toolbox Version 7.0 (R2015b) Image Processing Toolbox Version 9.3 (R2015b) Optimization Toolbox Version 7.3 (R2015b) Signal Processing Toolbox Version 7.1 (R2015b) Statistics and Machine Learning Toolbox Version 10.1 (R2015b) *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699

3 5

-hippocampal-subfields-T1T2
by Daniele Orlandi 15 Jun '16

15 Jun '16

Dear All, I'm trying to run the flag -hippocampal-subfields-T1T2 with the new FS v6.0 but I get the following error: >Fitting mesh to synthetic image from ASEG took 217.8633 seconds >Transforming points >Transforming points >ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta): can't open file >No such file or directory >ERROR: Reading transform from file /media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta Do you have any suggestion? thank you all for your collaboration Daniele _______________________________________________________________________________ Daniele Orlandi, PsyD, Research Assistant Laboratory of Epidemiology, Neuroimaging Alzheimer IRCCS Centro San Giovanni di Dio, Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel:+39 030/3501563 cell: +39 3495119685 <%2B39%20030%2F3501563> email: dorlandi(a)fatebenefratelli.it; daniele.orlandi.psy(a)gmail.com (http://www.centroalzheimer.org/sito/chi_staff_e.php)

3 2

Symmetric label on fsaverage
by Alexandre Routier 10 Jun '16

10 Jun '16

Hello everyone, We used tksurfer to draw a specific region on the left hemisphere of fsaverage subject and we would like to automatically register the label from the left hemisphere to the right hemisphere. Since FreeSurfer provides tools to compute a symmetric fsaverage ( https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi) I was wondering if there was any command to have the manually drawn label on the left hemisphere to the right hemisphere. Thanks in advance for your help. Alexandre

2 5

Brainmask edit error
by Sabrina Yu 09 Jun '16

09 Jun '16

Hello, I'm having problems with regenerating the surfaces for stroke cases after editing the brainmask.mgz file. In the aseg.mgz file, the brain matter around lesion area is correctly classified as brain matter. In the pial surface, this brain matter is not included. I've tried to edit the brainmask.mgz file to include this region, but when I run: recon-all -subjid <SUBJECT> -autorecon2-pial, the surfaces generated are not changed at all. I have attached some images to this email. I'm new to Freesurfer, so any help would be greatly appreciated. Thank you.

3 13

errors in wm and pial boundaries
by Corinna Bauer 07 Jun '16

07 Jun '16

Hello all, We are analyzing data from our collaborators and are running into some difficulties with the accuracy of the pial and wm boundaries. The wm.mgz appears to follow the actual WM, independent of the wm surface boundary. Attached is an example showing two types of problems. 1. the WM surface is inaccurate regardless of the number of control points used. 2. The pial surface is inaccurate, missing a bunch of the sulcal and gyral patterns of the left parietal lobe (see area around cursor). For completeness, I have also included the wm.mgz at the same slice. I should mention that these problems has been occurring in multiple subjects. Any suggestions?? Thanks Corinna

2 4

glmdir question
by Clara Kühn 02 Jun '16

02 Jun '16

Dear FreeSurfer Experts, when running the Monte Carlo correction on a GLM I specify this command: mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp 0.05 --2spaces This assumes that my mgh file that I used as input for the GLM is in lh.gender_age.glmdir. That means though, that everytime I calculate a GLM and create a new folder for this GLM I have to copy the mgh file into the glmdir to run the Monte Carlo correction. Is there a way to specify where that mgh is located so that I don't have a bunch of copies of it in all my glmdirs? Thanks for your help! Cheers Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

3 11

Group Analysis: Two Groups and Two Covariates.
by Hanbyul Cho 01 Jun '16

01 Jun '16

Dear FreeSurfer Team, I processed the Group analysis by FreeSurfer 5.3.0 Our data has two groups (Patient, Control) and two covariate values (age, extra value) mtx, contrast is 1 -1 0 0 0 0 The mris_preproc, and mri_surf2surf command were completed without error. mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi lh --meas thickness --out lh.**G2V2.dods.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.**G2V2.dods.mgh --fwhm 15 --cortex --tval lh.**G2V2.dods_sm15.mgh mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C **G2V2.mtx --surf fsaverage lh --cortex --glmdir lh.**G2V2.dods_sm15.glmdir After mri_glmfit command, I saw the error message. ========================================================= ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C **G2V2.mtx --surf fsaverage lh --cortex --glmdir lh.**G2V2.dods_sm15.glmdir 2. The FSGD file (if using one) 3. And the design matrix above ========================================================= I think our fsgd and mtx compositions are equal to the g2v2.fsgd which FreeSurfer wiki example. (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V) In this situation, how can I correct my fsgd or mtx files? Is there any other command option? Best Regards, Han

2 9

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