Freesurfer April 2016

freesurfer@nmr.mgh.harvard.edu

122 participants
173 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

-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

Improve normalization with own average subject
by pfannmoelj＠uni-greifswald.de 25 May '16

25 May '16

Dear Experts, I am currently working with the non-linear FreeSurfer normalization. We have a small group of subjects N = 12 and in each brain we identified a single position with a fMRI localizer. The task is a group comparison of the individual results for this position. Therefore, the coordinates of each position in FSaverage was determined using mri_label2label. The radius of the region is an important quantity in my investigations. A smaller radius would help me a lot in my data processing. I tried to decrease the radius by generating a new group space template from my 12 subjects with make_average_subject. Then I used mri_label2label to determine the coordinates in the new group space template. Unfortunately, there was no difference in the radius. The intention behind this procedure was to achieve an improved normalization of the subjects. I have read much about this topic in the mailing list, but there are many details in the processing which I am not yet aware of. So, my question is if I proceeded the best possible way or if there is a better alternative to improve the normalization. Would it help to generate a new template as outlined in the second part on this web tutorial (chapter: Creating a registration template from scratch): https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates or do I need to use mris_register with my new template and my 12 subjects instead of mri_label2label in order to benfit from my new template as generated by make_average_subject (also outlined in the web tutorial in the chapter: Creating a registration template initialized with FreeSurfer template)? Even a small decrease in the radius would help to improve my results. Thanks in advance pfannmoe

2 2

Extracting BOLD from a flattened surface
by Taha Abdullah 20 May '16

20 May '16

Hello Freesurfer Experts, Long story short--I would like to extract BOLD values from each TR across all vertices for one subjects flattened surface Following is a brief overview of my steps and at the end you can see where I am stuck. First, after *recon-all I* followed the steps to cut the lh inflated surface, saved as a patch, ran *mris_flatten, *converted patch into asc file. Second, I used read_patch.m to extract all spatial information and a net loss of approximately 10k vertices (127k to 116k) We had all functional images processed in FSL, the 4D file has 64x64x36x240 dimensions (voxels are 3.4x3.4x3.0). Next, co-registered the functional and anatomicals together via the following cmd: * bbregister --s cbp001_v1 --mov filtered_func_data.nii.gz --bold --init-fsl --reg dummy1.da*t. Afterwards, converted the volume to a surface using the following cmd*: mri_vol2surf --mov filtered_func_data.nii.gz --reg dummy1.dat --projfrac 0.5 --interp trilinear --hemi lh --o ./lh.func.vol2surf.mgh. *THe dimensions are 127027 x 1 x 1 x 240. Visually no problem when using* tksurfer cbp001_v1 lh inflated -patch /path to flattened patch/ -overlay /lh.func.vol2surf.mgh/ -timecourse lh.func.vol2surf.mgh;* click on the patch and shows the timecourse for that selected vertex. Using the View>Configure>overlay I can shuffle through the TRs to inspect the change in raw BOLD signal per vertex. I have been perusing the email web server searching for how to extract the hemodynamic waveform for each vertex across the flattened surface and ultimately will be using matlab to understand how the spatial transformation is happening. As well I have all the matlab files that seemed relevant to my query (read_surf.m, read_patch.m, and readMRI.m). I was hoping that I would be able to have a text file with all the vertices (127K not the flattened 116k) in rows and each column would have the TRs; I ran this command;* mri_segstats --slabel cbp001_v1 lh /home/share/freesurfer/subjects/cbp001_v1/label/lh.cortex.label --avgwf mri_seg_stats.dat --i lh.func.vol2surf.mgh*, output was the 240 TRs as rows and seems like the average global BOLD signal in the single column corresponding with each TR. Excuse my naiveness, I just recently (1 month ago) started using freesurfer and I feel like I have exhausted as much of the information available on the FS wiki and email server. Any information or advice would be great! I put the commands just to give an idea of my workflow (most of the command lines are from the email server or the FS Wiki) and if there are any issues with my steps please let me know so I can correct them before starting the group analysis. Best, Taha -- Taha Abdullah Department of Physiology Northwestern University Masters of Science Physiology and Biophysics, Georgetown University 2015

3 4

Tracula Pathway reconstruction
by Peggy Skelly 20 May '16

20 May '16

Hi Tracula Experts, How do you determine if a pathway reconstructed well? I've been examining the merged pathways (<subj>/dpath/merged_avg33_mni_bbr.mgz) in freeview, and if the pathway looked too small when viewing with the default threshold, I would reinitialize those pathways. Most of the time, the new pathway would look ok upon re-inspection. A few pathways, however, still appear too small when viewed at the default threshold in Freeview, but at lower thresholds, they begin to look ok. I've encountered 1 pathway that still appears too small in Freeview, but the output in pathstats.overall.txt and pathstats.byvoxel.txt seem reasonable. On the other hand, its path distribution (path.pd.nii.gz) does not look like a distribution, but a single path -- there are a 38 voxels with values of 4000, and all others are 0. This doesn't seem right. What could cause this to happen? What objective measure can I use to determine if a pathway is reconstructed well enough? Thanks, Peggy

2 1

bvals bvecs Error
by Marissa Pifer 20 May '16

20 May '16

Hi freesurfers, I'm having a problem the bvals and bvecs for one of my subject's DTI data. When I try to run the first step of tracula I get this error message: "Error: data and bvals/bvecs do not contain the same number of entries" I have checked, the bvals and bvecs do contain the same amount of entries (42), and they are in the proper format (bvals one line, bvecs three lines). The entries in the bvals/bvecs matches the number of images within the DTI file as well. Looking online, I saw that this was part of the FAQs on tracula. It suggested making sure the locale settings were correct, which it is (en_US.UTF-8). I've run tracula on every other subject and have not run into this problem, but the same subject had an error with multiple frames when we were processing the T2 images. Could this be related? Any idea about what is going on, or how I can fix it? Thanks in advance, Marissa

2 1

REPOST: TRACULA dev version: Error message
by Elijah Mak 20 May '16

20 May '16

Hi Freesurfer, Sorry about reposting this email from earlier: I can't seem to get the TRACULA in the dev version of FS6 to run. mv -f /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs mv: rename /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs to /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs: No such file or directory The contents of that folder are: dwi_orig.mghdti.bvals dwi_orig.mghdti.bvecs dwi_orig.nii.gz dwi_orig_flip.nii.gz xfms The full error message is enclosed with this email. Thanks! Best Wishes, Elijah

2 1

External ROI for fcseed
by Martin Juneja 04 May '16

04 May '16

Hi all, I am trying to perform step-3 from the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… But I do not have segid because the LookUp table FreeSurfer creates after running recon-all doesn't have the area I am interested in. So I defined the ROI externally, converted it into surface using vol2surf and further into .label file using cor2label. I was wondering how can I use this externally created ROI (either in vol format, or surface format or label format) in this command: fcseed-config. I made sure that the external ROI is perfectly aligned where it was supposed to be. Thanks. MJ

2 1

Cortical Parcellation
by Heidi Foo 02 May '16

02 May '16

Dear FreeSurfer Experts, I am currently trying to run cortical parcellation on my subjects. However, I am getting error messages that the --outdir is unknown. This is the command I ran *mri_annotation2label --s FS_PD002_1.nii --hemi lh --lobesStrict --outdir ./label* Is there a way I can resolve this issue? Thank you so much for your kind attention. Best Regards, Heidi Foo

2 2

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