[Freesurfer] hello experts
Hello experts. I have some question to you. I used SurfStat statistical tool to analyze the two group(control, patient) When i click the surf in fsaverage folder and then show up lh.pial and lh.pial_avg. What is the differences between lh.pial and lh.pial_avg ? lh.pial_avg means that real subjects's average pial? plz reply. ___ 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.
Re: [Freesurfer] hello freesurfer developer~
hello experts i solve the problem always thanks your reply 2016-04-30 0:18 GMT+09:00 A-reum Min <naniy...@gmail.com>: > hi experts > > i have some problem using qdec > > when i enter the qdec and then 'Generate Stats Data Tables' > > show up these sentences > > asegstats2table --common-segs --meas volume --tablefile > /usr/local/freesurfer/subjects/HCP_sleep/qdec/stats_tables/aseg.volume.stats.dat > --statsfile=aseg.stats --subjects con_1 con_2 con_3 con_4 con_5 con_6 con_7 > con_8 con_9 con_10 con_11 con_12 con_13 con_14 con_15 con_16 con_17 con_18 > con_19 con_20 con_21 con_22 con_23 con_24 con_25 con_26 con_27 con_28 > con_29 con_30 con_31 con_32 con_33 con_34 con_35 con_36 con_37 con_38 > con_39 con_40 con_41 con_42 con_43 con_44 dep_1 dep_2 dep_3 dep_4 dep_5 > dep_6 dep_7 dep_8 dep_9 dep_10 dep_11 dep_12 dep_13 dep_14 dep_15 dep_16 > dep_17 dep_18 dep_19 dep_20 dep_21 dep_22 > SUBJECTS_DIR : /usr/local/freesurfer/subjects/HCP_sleep > Parsing the .stats files > ERROR: The stats file > /usr/local/freesurfer/subjects/HCP_sleep/con_12/stats/aseg.stats is not > found or is too small to be a valid statsfile > Use --skip flag to automatically skip bad stats files > > > and show up error box(fig1.jpg) > > > how can i to do.. plz help me. > > my data information is > > 1 diagnosis discrete 2 > 1 Control > 2 Deprivation > 2 age continuous 0 > Continuous Factors: Mean: StdDev: > --- - --- > age28.167 3.280 > > Number of subjects: 66 > Number of factors:2 (1 discrete, 1 continuous) > Number of classes:2 > Number of regressors: 4 > > rh--Avg-thickness-age-Cor.mtx and lh-Avg-thickness-age-Cor.mtx contain (1 > -1 0 0) > > > 2016-03-05 0:36 GMT+09:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > >> for asymmetryc, see >> https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi >> >> On 03/04/2016 09:28 AM, A-reum Min wrote: >> > hello experts >> > >> > i have some question to you >> > >> > Question 1. >> > i want to compare two groups(patients group VS control groups) for >> > cortical thickness asymmetry. >> > so.. am i using a lh.thickness.fsaverage.mgh and >> > rh.thickness.fsaverage.mgh for each group subjects right..? >> > >> > Question 2. >> > >> > Left hemisphere whole vertices were extracted using a matlab. ( i read >> > lh.thickness.fsaverage.mgh) >> > i was wondering why vertex# 9(cortical thickness) value is zero? >> > (fig1.png) >> > what is that mean? plz answer me. >> > >> > 2016-02-13 5:19 GMT+09:00 A-reum Min <naniy...@gmail.com >> > <mailto:naniy...@gmail.com>>: >> > >> > hello experts >> > >> > i have some question to you >> > >> > What is the meaning about cortical thickness alteration (increase >> > or decrease) >> > >> > a few days ago i read these sentences >> > >> > Deviations from these patterns can be used as diagnostic >> > indicators for brain disorders >> > <http://en.citizendium.org/wiki/Brain_disorder>: While Alzheimer's >> > disease <http://en.citizendium.org/wiki/Alzheimer%27s_disease>, >> > even very early on, is characterized by pronounced cortical >> > thinning^[4] >> > < >> http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Dickerson2009-4 >> > >> > , Williams syndrome >> > < >> http://en.citizendium.org/wiki?title=Williams_syndrome=edit=1> >> patients >> > exhibit an increase in cortical thickness of about 5-10% in some >> > regions ^[5] >> > < >> http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Thompson2005-5 >> > >> > , and lissencephalic >> > <http://en.citizendium.org/wiki/Lissencephalic> patients show >> > drastic thickening, up to several centimetres in occipital >> > regions^[6] >> > < >> http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Guerrini2006-6 >> > >> > . from wiki >> > >> > i wonder increased or reduced cortex depended on disorder? >> > >> > plz answer me >> > >> > 2016-02-06 0:27 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu >> > <mailto:fis...@nmr.mgh.harvard.edu>>
Re: [Freesurfer] hello freesurfer developer~
hello experts i have some question to you Question 1. i want to compare two groups(patients group VS control groups) for cortical thickness asymmetry. so.. am i using a lh.thickness.fsaverage.mgh and rh.thickness.fsaverage.mgh for each group subjects right..? Question 2. Left hemisphere whole vertices were extracted using a matlab. ( i read lh.thickness.fsaverage.mgh) i was wondering why vertex# 9(cortical thickness) value is zero? (fig1.png) what is that mean? plz answer me. 2016-02-13 5:19 GMT+09:00 A-reum Min <naniy...@gmail.com>: > hello experts > > i have some question to you > > What is the meaning about cortical thickness alteration (increase or > decrease) > > a few days ago i read these sentences > > Deviations from these patterns can be used as diagnostic indicators for brain > disorders <http://en.citizendium.org/wiki/Brain_disorder>: While Alzheimer's > disease <http://en.citizendium.org/wiki/Alzheimer%27s_disease>, even very > early on, is characterized by pronounced cortical thinning[4] > <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Dickerson2009-4> > , Williams syndrome > <http://en.citizendium.org/wiki?title=Williams_syndrome=edit=1> > patients > exhibit an increase in cortical thickness of about 5-10% in some regions > [5] > <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Thompson2005-5>, > and lissencephalic <http://en.citizendium.org/wiki/Lissencephalic> patients > show drastic thickening, up to several centimetres in occipital regions[6] > <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Guerrini2006-6>. > from wiki > > i wonder increased or reduced cortex depended on disorder? > > plz answer me > > 2016-02-06 0:27 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > >> Hi A-reum >> >> we use average Euclidean distance from gray to white and visa-versa. >> There are other (variational) techniques that we have messed around with, >> but none of our experiments have shown that they are any better, so we have >> stuck with the simplest thing. >> >> cheers >> Bruce >> >> >> On Fri, 5 Feb 2016, A-reum Min wrote: >> >> hello experts >>> >>> i have some question to you >>> >>> What method do you use when measuring the cortical thickness? >>> >>> (ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal >>> equation?) >>> >>> plz answer me. >>> >>> 2016-01-17 0:53 GMT+09:00 A-reum Min <naniy...@gmail.com>: >>> Thank you for u r answer. >>> I have some question to you. >>> >>> i compared two groups(patients VS control) >>> >>> How can i extract the total vertices(ex.#1 vertex : cortical thickness >>> value) to 1 subject(patient) and average of patients ? >>> I want to compared asymmetry of brain (lateralization). So, i really >>> necessary above value(cortical thickness value of vertex). >>> >>> plz answer me. >>> >>> Thank you. >>> >>> >>> 2016-01-17 0:22 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>> Hi Areum >>> >>> every brain will have a somewhat different number of >>> vertices depending on size and geometry. If you want them >>> to be comparable you need to map them into the fsaverage >>> space using e.g. the -qcache switch to recon-all (or >>> mri_surf2surf directly if you prefer). >>> >>> cheers >>> Bruce >>> >>> >>> On Sat, 16 Jan 2016, A-reum Min wrote: >>> >>> Hello expert. >>> I'm Areum. >>> >>> I have some question to you. >>> >>> A weeks ago, i compared two groups (OSA >>> patients VS control) and then the >>> number of vertices were confirmed. >>> >>> Each group has the same number of >>> vertices.(176416) -experiment 1. >>> >>> And yesterday, i compared two groups(partial >>> sleep deprivation:PSD VS >>> control) and then the number of vertices were >>> confirmed. >>> >>> Each group has the same number of >>> vertices(169548) -experiment 2. >>> >>> >>> 1) Why isn't the same number of total >>> vertices? is it related rain size? >>> >>
Re: [Freesurfer] hello freesurfer developer~
hello experts i have some question to you What is the meaning about cortical thickness alteration (increase or decrease) a few days ago i read these sentences Deviations from these patterns can be used as diagnostic indicators for brain disorders <http://en.citizendium.org/wiki/Brain_disorder>: While Alzheimer's disease <http://en.citizendium.org/wiki/Alzheimer%27s_disease>, even very early on, is characterized by pronounced cortical thinning[4] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Dickerson2009-4> , Williams syndrome <http://en.citizendium.org/wiki?title=Williams_syndrome=edit=1> patients exhibit an increase in cortical thickness of about 5-10% in some regions [5] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Thompson2005-5>, and lissencephalic <http://en.citizendium.org/wiki/Lissencephalic> patients show drastic thickening, up to several centimetres in occipital regions[6] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Guerrini2006-6>. from wiki i wonder increased or reduced cortex depended on disorder? plz answer me 2016-02-06 0:27 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi A-reum > > we use average Euclidean distance from gray to white and visa-versa. There > are other (variational) techniques that we have messed around with, but > none of our experiments have shown that they are any better, so we have > stuck with the simplest thing. > > cheers > Bruce > > > On Fri, 5 Feb 2016, A-reum Min wrote: > > hello experts >> >> i have some question to you >> >> What method do you use when measuring the cortical thickness? >> >> (ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal >> equation?) >> >> plz answer me. >> >> 2016-01-17 0:53 GMT+09:00 A-reum Min <naniy...@gmail.com>: >> Thank you for u r answer. >> I have some question to you. >> >> i compared two groups(patients VS control) >> >> How can i extract the total vertices(ex.#1 vertex : cortical thickness >> value) to 1 subject(patient) and average of patients ? >> I want to compared asymmetry of brain (lateralization). So, i really >> necessary above value(cortical thickness value of vertex). >> >> plz answer me. >> >> Thank you. >> >> >> 2016-01-17 0:22 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >> Hi Areum >> >> every brain will have a somewhat different number of >> vertices depending on size and geometry. If you want them >> to be comparable you need to map them into the fsaverage >> space using e.g. the -qcache switch to recon-all (or >> mri_surf2surf directly if you prefer). >> >> cheers >> Bruce >> >> >> On Sat, 16 Jan 2016, A-reum Min wrote: >> >> Hello expert. >> I'm Areum. >> >> I have some question to you. >> >> A weeks ago, i compared two groups (OSA >> patients VS control) and then the >> number of vertices were confirmed. >> >> Each group has the same number of >> vertices.(176416) -experiment 1. >> >> And yesterday, i compared two groups(partial >> sleep deprivation:PSD VS >> control) and then the number of vertices were >> confirmed. >> >> Each group has the same number of >> vertices(169548) -experiment 2. >> >> >> 1) Why isn't the same number of total >> vertices? is it related rain size? >> >> >> 2) How can i extract the number of total >> vertices(ex.#1 vertex : cortical >> thickness value) to 1 subject(PSD) and average >> of PSD ? >> I want to compared asymmetry of brain >> (lateralization). So, i really >> necessary above value(cortical thickness value >> of vertex). >> >> plz answer me. >> >> Thank you. >> >> >> 2016-01-07 3:52 GMT+09:00 Bruce Fischl >> <fis...@nmr.mgh.harvard.edu>: >> Hi A-reum >> >> did you talk to the Wash U group? If you >> have nifti files they >> can be processed using recon-all (i.e. >> recon-all -i > to nifti file> -s -sd >> > subject
Re: [Freesurfer] hello freesurfer developer~
hello experts i have some question to you What method do you use when measuring the cortical thickness? (ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal equation?) plz answer me. 2016-01-17 0:53 GMT+09:00 A-reum Min <naniy...@gmail.com>: > Thank you for u r answer. > > I have some question to you. > > i compared two groups(patients VS control) > > How can i extract the total vertices(ex.#1 vertex : cortical thickness > value) to 1 subject(patient) and average of patients ? > I want to compared asymmetry of brain (lateralization). So, i really > necessary above value(cortical thickness value of vertex). > > plz answer me. > > Thank you. > > > 2016-01-17 0:22 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > >> Hi Areum >> >> every brain will have a somewhat different number of vertices depending >> on size and geometry. If you want them to be comparable you need to map >> them into the fsaverage space using e.g. the -qcache switch to recon-all >> (or mri_surf2surf directly if you prefer). >> >> cheers >> Bruce >> >> >> On Sat, 16 Jan 2016, A-reum Min wrote: >> >> Hello expert. >>> I'm Areum. >>> >>> I have some question to you. >>> >>> A weeks ago, i compared two groups (OSA patients VS control) and then the >>> number of vertices were confirmed. >>> >>> Each group has the same number of vertices.(176416) -experiment 1. >>> >>> And yesterday, i compared two groups(partial sleep deprivation:PSD VS >>> control) and then the number of vertices were confirmed. >>> >>> Each group has the same number of vertices(169548) -experiment 2. >>> >>> >>> 1) Why isn't the same number of total vertices? is it related rain size? >>> >>> >>> 2) How can i extract the number of total vertices(ex.#1 vertex : cortical >>> thickness value) to 1 subject(PSD) and average of PSD ? >>> I want to compared asymmetry of brain (lateralization). So, i really >>> necessary above value(cortical thickness value of vertex). >>> >>> plz answer me. >>> >>> Thank you. >>> >>> >>> 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>> Hi A-reum >>> >>> did you talk to the Wash U group? If you have nifti files they >>> can be processed using recon-all (i.e. recon-all -i >> to nifti file> -s -sd >> subjects> -all) >>> >>> cheers >>> Bruce >>> >>> >>> On Tue, 29 Dec 2015, A-reum Min wrote: >>> >>> hello experts!my name is areum. >>> i have some question to you.i have never seen before >>> these NIFTI >>> format(fig.1.png) >>> I want to see these data subjects's cortical >>> thickness using qdec. >>> how can i to do? plz answer me >>> >>> 2015-12-25 2:16 GMT+09:00 Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu>: >>> Hi A-reum >>> >>> you should probably ask the Wash U HCP group. >>> I'll cc Matt >>> Glasser who might be able to answer your >>> question >>> cheers >>> Bruce >>> >>> On Thu, 24 Dec 2015, A-reum Min wrote: >>> >>> hello experts!my name is areum. >>> i have some question to you. >>> a few days ago i was down load HCP(human >>> connectom >>> project) data. >>> but.. how can i use these HCP format. >>> i have never seen before these >>> format(fig.1.png) >>> I want to see HCP data subjects's >>> cortical thickness >>> using qdec. >>> how can i to do? >>> plz answer me >>> >>> 2015-11-10 7:49 GMT+09:00 A-reum Min >>> <naniy...@gmail.com>: >>> Hello experts! >>> I have some question to you.. >>> >>> I don't need to
Re: [Freesurfer] hello freesurfer developer~
Hello expert. I'm Areum. I have some question to you. A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed. Each group has the same number of vertices.(176416) -experiment 1. And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed. Each group has the same number of vertices(169548) -experiment 2. 1) Why isn't the same number of total vertices? is it related rain size? 2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi A-reum > > did you talk to the Wash U group? If you have nifti files they can be > processed using recon-all (i.e. recon-all -i -s > -sd -all) > > cheers > Bruce > > > On Tue, 29 Dec 2015, A-reum Min wrote: > > hello experts!my name is areum. >> i have some question to you.i have never seen before these NIFTI >> format(fig.1.png) >> I want to see these data subjects's cortical thickness using qdec. >> how can i to do? plz answer me >> >> 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >> Hi A-reum >> >> you should probably ask the Wash U HCP group. I'll cc Matt >> Glasser who might be able to answer your question >> cheers >> Bruce >> >> On Thu, 24 Dec 2015, A-reum Min wrote: >> >> hello experts!my name is areum. >> i have some question to you. >> a few days ago i was down load HCP(human connectom >> project) data. >> but.. how can i use these HCP format. >> i have never seen before these format(fig.1.png) >> I want to see HCP data subjects's cortical thickness >> using qdec. >> how can i to do? >> plz answer me >> >> 2015-11-10 7:49 GMT+09:00 A-reum Min >> <naniy...@gmail.com>: >> Hello experts! >> I have some question to you.. >> >> I don't need to show up so small blue regions(fig.1 >> blue region) >> >> How can i control these? >> >> 2015-11-10 7:41 GMT+09:00 Douglas N Greve >> <gr...@nmr.mgh.harvard.edu>: >> Hi, please create a new thread since this is a >> new topic. >> Also, I don't >> understand your question so please elaborate. >> >> On 11/09/2015 05:34 AM, A-reum Min wrote: >> > Hello experts! >> > >> > i have some question to you.. >> > >> > How can i control the cluster size? >> > >> > My cluster threshold is 1. >> > >> > then, too many blue regions (as shown >> fig.1). >> > >> > so, i want to control cluster threshold 1--> >> cluster >> threshold 5. >> > >> > 2015-11-08 20:44 GMT+09:00 A-reum Min >> <naniy...@gmail.com >> > <mailto:naniy...@gmail.com>>: >> > >> > Hello bruce! >> > >> > I solve the problem for your answer. >> > >> > And.. i have some question to you.. >> > >> > How can i control the cluster size? >> > >> > My cluster threshold is 1. >> > >> > then, too many blue regions (as shown >> fig.1). >> > >> > so, i want to control cluster threshold >> 1--> cluster >> threshold 5. >> > >> > How can i to do? >> > >> > >> > >> >
Re: [Freesurfer] hello freesurfer developer~
Hello expert. I'm Areum. I have some question to you. A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed. Each group has the same number of vertices.(176416) -experiment 1. And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed. Each group has the same number of vertices(169548) -experiment 2. 1) Why isn't the same number of total vertices? is it related brain size? 2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-16 23:39 GMT+09:00 A-reum Min <naniy...@gmail.com>: > Hello expert. > > I'm Areum. > > I have some question to you. > > A weeks ago, i compared two groups (OSA patients VS control) and then the > number of vertices were confirmed. > > Each group has the same number of vertices.(176416) -experiment 1. > > And yesterday, i compared two groups(partial sleep deprivation:PSD VS > control) and then the number of vertices were confirmed. > > Each group has the same number of vertices(169548) -experiment 2. > > > 1) Why isn't the same number of total vertices? is it related rain size? > > > 2) How can i extract the number of total vertices(ex.#1 vertex : cortical > thickness value) to 1 subject(PSD) and average of PSD ? > I want to compared asymmetry of brain (lateralization). So, i really > necessary above value(cortical thickness value of vertex). > > plz answer me. > > Thank you. > > > 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > >> Hi A-reum >> >> did you talk to the Wash U group? If you have nifti files they can be >> processed using recon-all (i.e. recon-all -i -s >> -sd -all) >> >> cheers >> Bruce >> >> >> On Tue, 29 Dec 2015, A-reum Min wrote: >> >> hello experts!my name is areum. >>> i have some question to you.i have never seen before these NIFTI >>> format(fig.1.png) >>> I want to see these data subjects's cortical thickness using qdec. >>> how can i to do? plz answer me >>> >>> 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>> Hi A-reum >>> >>> you should probably ask the Wash U HCP group. I'll cc Matt >>> Glasser who might be able to answer your question >>> cheers >>> Bruce >>> >>> On Thu, 24 Dec 2015, A-reum Min wrote: >>> >>> hello experts!my name is areum. >>> i have some question to you. >>> a few days ago i was down load HCP(human connectom >>> project) data. >>> but.. how can i use these HCP format. >>> i have never seen before these format(fig.1.png) >>> I want to see HCP data subjects's cortical thickness >>> using qdec. >>> how can i to do? >>> plz answer me >>> >>> 2015-11-10 7:49 GMT+09:00 A-reum Min >>> <naniy...@gmail.com>: >>> Hello experts! >>> I have some question to you.. >>> >>> I don't need to show up so small blue regions(fig.1 >>> blue region) >>> >>> How can i control these? >>> >>> 2015-11-10 7:41 GMT+09:00 Douglas N Greve >>> <gr...@nmr.mgh.harvard.edu>: >>> Hi, please create a new thread since this is a >>> new topic. >>> Also, I don't >>> understand your question so please elaborate. >>> >>> On 11/09/2015 05:34 AM, A-reum Min wrote: >>> > Hello experts! >>> > >>> > i have some question to you.. >>> > >>> > How can i control the cluster size? >>> > >>> > My cluster threshold is 1. >>> > >>> > then, too many blue regions (as shown >>> fig.1). >>> > >>> > so, i want to control cluster threshold 1--> >>>
Re: [Freesurfer] hello freesurfer developer~
Thank you for u r answer. I have some question to you. i compared two groups(patients VS control) How can i extract the total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(patient) and average of patients ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-17 0:22 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Areum > > every brain will have a somewhat different number of vertices depending on > size and geometry. If you want them to be comparable you need to map them > into the fsaverage space using e.g. the -qcache switch to recon-all (or > mri_surf2surf directly if you prefer). > > cheers > Bruce > > > On Sat, 16 Jan 2016, A-reum Min wrote: > > Hello expert. >> I'm Areum. >> >> I have some question to you. >> >> A weeks ago, i compared two groups (OSA patients VS control) and then the >> number of vertices were confirmed. >> >> Each group has the same number of vertices.(176416) -experiment 1. >> >> And yesterday, i compared two groups(partial sleep deprivation:PSD VS >> control) and then the number of vertices were confirmed. >> >> Each group has the same number of vertices(169548) -experiment 2. >> >> >> 1) Why isn't the same number of total vertices? is it related rain size? >> >> >> 2) How can i extract the number of total vertices(ex.#1 vertex : cortical >> thickness value) to 1 subject(PSD) and average of PSD ? >> I want to compared asymmetry of brain (lateralization). So, i really >> necessary above value(cortical thickness value of vertex). >> >> plz answer me. >> >> Thank you. >> >> >> 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >> Hi A-reum >> >> did you talk to the Wash U group? If you have nifti files they >> can be processed using recon-all (i.e. recon-all -i > to nifti file> -s -sd > subjects> -all) >> >> cheers >> Bruce >> >> >> On Tue, 29 Dec 2015, A-reum Min wrote: >> >> hello experts!my name is areum. >> i have some question to you.i have never seen before >> these NIFTI >> format(fig.1.png) >> I want to see these data subjects's cortical >> thickness using qdec. >> how can i to do? plz answer me >> >> 2015-12-25 2:16 GMT+09:00 Bruce Fischl >> <fis...@nmr.mgh.harvard.edu>: >> Hi A-reum >> >> you should probably ask the Wash U HCP group. >> I'll cc Matt >> Glasser who might be able to answer your >> question >> cheers >> Bruce >> >> On Thu, 24 Dec 2015, A-reum Min wrote: >> >> hello experts!my name is areum. >> i have some question to you. >> a few days ago i was down load HCP(human >> connectom >> project) data. >> but.. how can i use these HCP format. >> i have never seen before these >> format(fig.1.png) >> I want to see HCP data subjects's >> cortical thickness >> using qdec. >> how can i to do? >> plz answer me >> >> 2015-11-10 7:49 GMT+09:00 A-reum Min >> <naniy...@gmail.com>: >> Hello experts! >> I have some question to you.. >> >> I don't need to show up so small blue >> regions(fig.1 >> blue region) >> >> How can i control these? >> >> 2015-11-10 7:41 GMT+09:00 Douglas N >> Greve >> <gr...@nmr.mgh.harvard.edu>: >> Hi, please create a new thread >> since this is a >> new topic. >> Also, I don't >> understand your question so please >> elaborate. >> >> On 11/09/2015 05:34 AM, A-reum Min >>
Re: [Freesurfer] hello freesurfer developer~
HI expert ! My name is Areum. I have some question to you. 1. 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)? 2. 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. 3. 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? plz reply to me 2015-08-11 11:06 GMT+09:00 A-reum Min naniy...@gmail.com: 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
Re: [Freesurfer] hello freesurfer developer~
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
Re: [Freesurfer] hello freesurfer developer~
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
Re: [Freesurfer] hello freesurfer developer~
Hi, Bruce When i use a Qdec, this message(12.png) show up.. How can i solve this problem? 2015-07-23 22:57 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: 1. No, each subject has a different #. You can map to fsaverage (this is what -qcache does if you specify it for recon-all), then they will have the same #. 2. What result data do you mean? 3. Yes, although I'll leave the details to Doug (since I don't remember how his cluster code works). 4. The significance doesn't depend on the cluster size unless you do multiple comparison corrections (and even then only if you do them a certain way) cheers Bruce On Thu, 23 Jul 2015, A-reum Min wrote: HELLO developer I have some question to you.. 1. Every patient is given to the same number of vertex? 2. When i use a Qdec, How can I get the subject result data? 3. Could i get the significant vertex’s number, extent of the significant area and gray matter volume? 4. Is it significant blue color which how many connected vertex? 2015-05-29 2:03 GMT+09:00 A-reum Min naniy...@gmail.com: hello developer~ reconstruction is well done, so i'm doing on 'qdec' step.. Actually, i don't know how to treat the Design menu exactly.. --- Discrete(fixed factors) : diagnosis continuous (covariate) : age , Left-Lateral-Ventricle --- which one click before analyze? age range is 12years~24years/ all subjects are adolescent. and no outlier in age range.. so.. age (continuous factor) does not nasessart? 2015-05-29 1:19 GMT+09:00 A-reum Min naniy...@gmail.com: hello developer~ reconstruction is well done, so i'm doing on 'qdec' step.. Actually, i don't know how to treat the Design menu exactly.. --- Discrete(fixed factors) : diagnosis continuous (covariate) : age , Left-Lateral-Ventricle --- which one click before analyze? 2015-04-05 21:41 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: I'm glad it worked out Bruce On Sun, 5 Apr 2015, A-reum Min wrote: Hello Bruce~ You're right.. my PISA dicom file header is too short so, freesurfer didn't read it. Therefore I use another subjects dicom file and then freesurfer read it! thank you for u r adavice to me. I really appreciate u 2015-04-05 7:08 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi A-reum the problem is that newer versions of scanner software compress dicoms and the version of FS you have doesn't know how to read it. So you need to decompress them before passing them to recon-all cheers Bruce On Sun, 5 Apr 2015, A-reum Min wrote: Hello developer~ Can you summarize what the problem is? == my problem is recon-all -i didn't working... so, if i type the recon-all -i~then show up theses ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory + then, i click the root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, show up these dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory Are you trying to read compressed dicom? == Am i trying to read compressed dicom? I send my 10071579.dicom(i use this) to you
Re: [Freesurfer] hello freesurfer developer~
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
Re: [Freesurfer] hello freesurfer developer~
hello developer~ reconstruction is well done, so i'm doing on 'qdec' step.. Actually, i don't know how to treat the Design menu exactly.. --- Discrete(fixed factors) : diagnosis continuous (covariate) : age , Left-Lateral-Ventricle --- which one click before analyze? 2015-04-05 21:41 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: I'm glad it worked out Bruce On Sun, 5 Apr 2015, A-reum Min wrote: Hello Bruce~ You're right.. my PISA dicom file header is too short so, freesurfer didn't read it. Therefore I use another subjects dicom file and then freesurfer read it! thank you for u r adavice to me. I really appreciate u 2015-04-05 7:08 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi A-reum the problem is that newer versions of scanner software compress dicoms and the version of FS you have doesn't know how to read it. So you need to decompress them before passing them to recon-all cheers Bruce On Sun, 5 Apr 2015, A-reum Min wrote: Hello developer~ Can you summarize what the problem is? == my problem is recon-all -i didn't working... so, if i type the recon-all -i~then show up theses ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory + then, i click the root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, show up these dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory Are you trying to read compressed dicom? == Am i trying to read compressed dicom? I send my 10071579.dicom(i use this) to you, using -i, convert the dicom file to mgh file. i just know that dicom file convert to mgz format using -i /my data path Is it right..?? If so, Can you try running dcmdjpeg on it to create a new (uncompressed) series and give that to recon-all? == (actually, i didn't understand your sentence means perfectly..) zeke to meaurl( ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/cen t os6_x86_64/dcmdjpeg.fs) and then, replace my existing $FREESURFER_HOME/bin/dcmdjpeg.fs file. Also, make sure it is set to executable by typing the following in a terminal window: $ chmod a+x $FREESURFER_HOME/bin/dcmdjpeg.fs 2015-04-05 2:30 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi A-reum sorry, I'm coming into this late. Can you summarize what the problem is? Are you trying to read compressed dicom? If so, can you try running dcmdjpeg on it to create a new (uncompressed) series and give that to recon-all? cheers Bruec On Sat, 4 Apr 2015, A-reum Min wrote: Hello developers.. i type the recon-all -i~then show up theses ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory + error is occured (a little differntly..) then, i click the root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, show
Re: [Freesurfer] hello freesurfer developer~
hello developer~ reconstruction is well done, so i'm doing on 'qdec' step.. Actually, i don't know how to treat the Design menu exactly.. --- Discrete(fixed factors) : diagnosis continuous (covariate) : age , Left-Lateral-Ventricle --- which one click before analyze? age range is 12years~24years/ all subjects are adolescent. and no outlier in age range.. so.. age (continuous factor) does not nasessart? 2015-05-29 1:19 GMT+09:00 A-reum Min naniy...@gmail.com: hello developer~ reconstruction is well done, so i'm doing on 'qdec' step.. Actually, i don't know how to treat the Design menu exactly.. --- Discrete(fixed factors) : diagnosis continuous (covariate) : age , Left-Lateral-Ventricle --- which one click before analyze? 2015-04-05 21:41 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: I'm glad it worked out Bruce On Sun, 5 Apr 2015, A-reum Min wrote: Hello Bruce~ You're right.. my PISA dicom file header is too short so, freesurfer didn't read it. Therefore I use another subjects dicom file and then freesurfer read it! thank you for u r adavice to me. I really appreciate u 2015-04-05 7:08 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi A-reum the problem is that newer versions of scanner software compress dicoms and the version of FS you have doesn't know how to read it. So you need to decompress them before passing them to recon-all cheers Bruce On Sun, 5 Apr 2015, A-reum Min wrote: Hello developer~ Can you summarize what the problem is? == my problem is recon-all -i didn't working... so, if i type the recon-all -i~then show up theses ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory + then, i click the root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, show up these dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory Are you trying to read compressed dicom? == Am i trying to read compressed dicom? I send my 10071579.dicom(i use this) to you, using -i, convert the dicom file to mgh file. i just know that dicom file convert to mgz format using -i /my data path Is it right..?? If so, Can you try running dcmdjpeg on it to create a new (uncompressed) series and give that to recon-all? == (actually, i didn't understand your sentence means perfectly..) zeke to meaurl( ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/cen t os6_x86_64/dcmdjpeg.fs) and then, replace my existing $FREESURFER_HOME/bin/dcmdjpeg.fs file. Also, make sure it is set to executable by typing the following in a terminal window: $ chmod a+x $FREESURFER_HOME/bin/dcmdjpeg.fs 2015-04-05 2:30 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi A-reum sorry, I'm coming into this late. Can you summarize what the problem is? Are you trying to read compressed dicom? If so, can you try running dcmdjpeg on it to create a new (uncompressed) series and give that to recon-all? cheers Bruec On Sat, 4 Apr 2015, A-reum Min wrote: Hello developers.. i type the recon-all -i~then show up theses ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6
Re: [Freesurfer] hello freesurfer developer~
Hello Bruce~ You're right.. my PISA dicom file header is too short so, freesurfer didn't read it. Therefore I use another subjects dicom file and then freesurfer read it! thank you for u r adavice to me. I really appreciate u 2015-04-05 7:08 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi A-reum the problem is that newer versions of scanner software compress dicoms and the version of FS you have doesn't know how to read it. So you need to decompress them before passing them to recon-all cheers Bruce On Sun, 5 Apr 2015, A-reum Min wrote: Hello developer~ Can you summarize what the problem is? == my problem is recon-all -i didn't working... so, if i type the recon-all -i~then show up theses ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory + then, i click the root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, show up these dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory Are you trying to read compressed dicom? == Am i trying to read compressed dicom? I send my 10071579.dicom(i use this) to you, using -i, convert the dicom file to mgh file. i just know that dicom file convert to mgz format using -i /my data path Is it right..?? If so, Can you try running dcmdjpeg on it to create a new (uncompressed) series and give that to recon-all? == (actually, i didn't understand your sentence means perfectly..) zeke to me aurl(ftp://surfer.nmr.mgh.harvard.edu//pub/dist/ freesurfer/dev_binaries/cent os6_x86_64/dcmdjpeg.fs) and then, replace my existing $FREESURFER_HOME/bin/dcmdjpeg.fs file. Also, make sure it is set to executable by typing the following in a terminal window: $ chmod a+x $FREESURFER_HOME/bin/dcmdjpeg.fs 2015-04-05 2:30 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi A-reum sorry, I'm coming into this late. Can you summarize what the problem is? Are you trying to read compressed dicom? If so, can you try running dcmdjpeg on it to create a new (uncompressed) series and give that to recon-all? cheers Bruec On Sat, 4 Apr 2015, A-reum Min wrote: Hello developers.. i type the recon-all -i~then show up theses ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory + error is occured (a little differntly..) then, i click the root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, show up these dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory i'm so sorry..to bother you.. 2015-04-04 9:21 GMT+09:00 A-reum Min naniy...@gmail.com: hello i type the recon-all -i~ then show up theses +++ +++ ERROR: 32256, see /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux +++ +++ the error is occured (a little differntly..) then, i click the /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out, show iuo these sh: /usr/local/freesurfer/bin/dcmdjpeg.fs: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory plz help me 2015-04-04 4:12 GMT+09:00 zkauf...@nmr.mgh.harvard.edu: A-reum, Please download the following file: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_ binaries/centos6_ x86_64/dcmdjpeg.fs
Re: [Freesurfer] hello freesurfer developer~
Hi developer So.. i can't use a freesurfer now..? Do i have to wait until May? I must use the freesurfer now.. because to write an abstract until april 8th ㅜㅜ so i really want to use a freesurfer... Is there any way I can use a freesurfer? Does not work. Can I get a old version? 2015-04-04 22:17 GMT+09:00 Z K zkauf...@nmr.mgh.harvard.edu: A-reum, Unfortunately it looks like the feature you require will not be fully implemented until the freesurfer v6 which is tentatively scheduled for release in May. -Zeke On Apr 4, 2015, at 1:49 AM, A-reum Min naniy...@gmail.com wrote: Hello developers.. i type the recon-all -i~ then show up theses ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory + error is occured (a little differntly..) then, i click the root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, show up these dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory i'm so sorry..to bother you.. 2015-04-04 9:21 GMT+09:00 A-reum Min naniy...@gmail.com: hello i type the recon-all -i~ then show up theses ++ ERROR: 32256, see /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux ++ the error is occured (a little differntly..) then, i click the /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out, show iuo these sh: /usr/local/freesurfer/bin/dcmdjpeg.fs: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory plz help me 2015-04-04 4:12 GMT+09:00 zkauf...@nmr.mgh.harvard.edu: A-reum, Please download the following file: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/dcmdjpeg.fs And replace your existing $FREESURFER_HOME/bin/dcmdjpeg.fs file with the one from the link above. Also, make sure it is set to executable by typing the following in a terminal window: $ chmod a+x $FREESURFER_HOME/bin/dcmdjpeg.fs And then try again. -Zeke Hi doug... recon-all dosen't working.. If i type the recon-all -i~ then, error occured... + JPEG compressed, decompressing cd /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01 dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_FSPGR/1/I0071579.dcm /tmp/root.tmp.decompressed.dcm.kBIYHL /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj01 exited with ERRORS at Fri Apr 3 10:39:27 PDT 2015 For more details, see the log file /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ++ I copy the libdcmjpeg.so.3.6 and paste in FREESURFER_HOME/lib after that type the setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib but.. didn't working .. same error occured -- dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6: cannot open shared object file: No such file or directory and i click the root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out then show up these dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6: cannot open shared object file: No such file or directory how can i to do ㅜㅜ help me doug ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail
Re: [Freesurfer] hello freesurfer developer~
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 to me a url( ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/dcmdjpeg.fs ) and then, replace my existing $FREESURFER_HOME/bin/dcmdjpeg.fs file. Also, make sure it is set to executable by typing the following in a terminal window: $ chmod a+x $FREESURFER_HOME/bin/dcmdjpeg.fs 2015-04-05 2:30 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi A-reum sorry, I'm coming into this late. Can you summarize what the problem is? Are you trying to read compressed dicom? If so, can you try running dcmdjpeg on it to create a new (uncompressed) series and give that to recon-all? cheers Bruec On Sat, 4 Apr 2015, A-reum Min wrote: Hello developers.. i type the recon-all -i~then show up theses ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory + error is occured (a little differntly..) then, i click the root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, show up these dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory i'm so sorry..to bother you.. 2015-04-04 9:21 GMT+09:00 A-reum Min naniy...@gmail.com: hello i type the recon-all -i~ then show up theses +++ +++ ERROR: 32256, see /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux +++ +++ the error is occured (a little differntly..) then, i click the /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out, show iuo these sh: /usr/local/freesurfer/bin/dcmdjpeg.fs: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory plz help me 2015-04-04 4:12 GMT+09:00 zkauf...@nmr.mgh.harvard.edu: A-reum, Please download the following file: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_ binaries/centos6_ x86_64/dcmdjpeg.fs And replace your existing $FREESURFER_HOME/bin/dcmdjpeg.fs file with the one from the link above. Also, make sure it is set to executable by typing the following in a terminal window: $ chmod a+x $FREESURFER_HOME/bin/dcmdjpeg.fs And then try again. -Zeke Hi doug... recon-all dosen't working.. If i type the recon-all -i~ then, error occured... +++ ++ JPEG compressed, decompressing cd /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01 dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_FSPGR/1/I0071579.dcm /tmp/root.tmp.decompressed.dcm.kBIYHL /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj01 exited with ERRORS at Fri Apr 3 10:39:27 PDT 2015 For more details, see the log file
Re: [Freesurfer] hello freesurfer developer~
Hi doug... recon-all dosen't working.. If i type the recon-all -i~ then, error occured... + JPEG compressed, decompressing cd /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01 dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_FSPGR/1/I0071579.dcm /tmp/root.tmp.decompressed.dcm.kBIYHL /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj01 exited with ERRORS at Fri Apr 3 10:39:27 PDT 2015 For more details, see the log file /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ++ I copy the libdcmjpeg.so.3.6 and paste in FREESURFER_HOME/lib after that type the setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib but.. didn't working .. same error occured -- dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6: cannot open shared object file: No such file or directory and i click the root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out then show up these dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6: cannot open shared object file: No such file or directory how can i to do ㅜㅜ help me doug ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] hello freesurfer developer~
Hello developers.. i type the recon-all -i~ then show up theses ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory + error is occured (a little differntly..) then, i click the root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, show up these dcmdjpeg.fs: error while loading shared libraries: libijg8.so.3.6: cannot open shared object file: No such file or directory i'm so sorry..to bother you.. 2015-04-04 9:21 GMT+09:00 A-reum Min naniy...@gmail.com: hello i type the recon-all -i~ then show up theses ++ ERROR: 32256, see /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux ++ the error is occured (a little differntly..) then, i click the /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out, show iuo these sh: /usr/local/freesurfer/bin/dcmdjpeg.fs: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory plz help me 2015-04-04 4:12 GMT+09:00 zkauf...@nmr.mgh.harvard.edu: A-reum, Please download the following file: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/dcmdjpeg.fs And replace your existing $FREESURFER_HOME/bin/dcmdjpeg.fs file with the one from the link above. Also, make sure it is set to executable by typing the following in a terminal window: $ chmod a+x $FREESURFER_HOME/bin/dcmdjpeg.fs And then try again. -Zeke Hi doug... recon-all dosen't working.. If i type the recon-all -i~ then, error occured... + JPEG compressed, decompressing cd /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01 dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_FSPGR/1/I0071579.dcm /tmp/root.tmp.decompressed.dcm.kBIYHL /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj01 exited with ERRORS at Fri Apr 3 10:39:27 PDT 2015 For more details, see the log file /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ++ I copy the libdcmjpeg.so.3.6 and paste in FREESURFER_HOME/lib after that type the setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib but.. didn't working .. same error occured -- dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6: cannot open shared object file: No such file or directory and i click the root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out then show up these dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6: cannot open shared object file: No such file or directory how can i to do ㅜㅜ help me doug ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hello freesurfer developer~
hello i type the recon-all -i~ then show up theses ++ ERROR: 32256, see /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux ++ the error is occured (a little differntly..) then, i click the /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out, show iuo these sh: /usr/local/freesurfer/bin/dcmdjpeg.fs: /lib/ld-linux.so.2: bad ELF interpreter: No such file or directory plz help me 2015-04-04 4:12 GMT+09:00 zkauf...@nmr.mgh.harvard.edu: A-reum, Please download the following file: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/dcmdjpeg.fs And replace your existing $FREESURFER_HOME/bin/dcmdjpeg.fs file with the one from the link above. Also, make sure it is set to executable by typing the following in a terminal window: $ chmod a+x $FREESURFER_HOME/bin/dcmdjpeg.fs And then try again. -Zeke Hi doug... recon-all dosen't working.. If i type the recon-all -i~ then, error occured... + JPEG compressed, decompressing cd /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01 dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_FSPGR/1/I0071579.dcm /tmp/root.tmp.decompressed.dcm.kBIYHL /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out for more details Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj01 exited with ERRORS at Fri Apr 3 10:39:27 PDT 2015 For more details, see the log file /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ++ I copy the libdcmjpeg.so.3.6 and paste in FREESURFER_HOME/lib after that type the setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib but.. didn't working .. same error occured -- dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6: cannot open shared object file: No such file or directory and i click the root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out then show up these dcmdjpeg.fs: error while loading shared libraries: libdcmjpeg.so.3.6: cannot open shared object file: No such file or directory how can i to do ㅜㅜ help me doug ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] hello freesurfer developer~
I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and 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 dcmdjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin) and my subjects path(own data) /usr/local/freesurfer/subjects/PISA_SPGR/1 --SUBJECTS_DIR 2015-04-03 10:50 GMT+09:00 A-reum Min naniy...@gmail.com: I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and 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 dcmjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin) and my subjects path(own data) /usr/local/freesurfer/subjects/PISA_SPGR/1 --SUBJECTS_DIR 2015-04-03 7:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: Is dcmdjpeg.fs in your path? What are the contents of the file /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ? On 04/02/2015 04:53 PM, A-reum Min wrote: Hi doug. I try this as a test. (here is a my terminal) *** [areum@localhost ~]$ su Password: [root@localhost areum]# tcsh [areum@localhost areum]# setenv FREESURFER_HOME /usr/local/freesurfer [areum@localhost areum]# source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni [areum@localhost areum]# setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/PISA_SPGR/1 [areum@localhost areum]# setenv FS_LOAD_DWI 0 [areum@localhost areum]# mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh $Id: mri_convert.c,v 1.219 2015/03/24 17:25:41 greve Exp $ reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1 Ref Series No = 3 Found 246 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 IsDWI = 0 PE Dir = ROW (dicom read) Loading pixel data JPEG compressed, decompressing cd /home/areum dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm /tmp/root.tmp.decompressed.dcm.QGcfri /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out for more details ** error occured again.. ㅜㅜ when i type the source $FREESURFER_HOME/SetUpFreeSurfer.csh, then show up these freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni But... my own data directory is /usr/local/freesurfer/subjects/PISA_SPGR/1 so my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR/1 is it okay...? and i will send my dicom file to u... plz help me as soon as possible ㅜㅜ 2015-04-03 5:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Can you send me /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ? I might not be able to get to it until after the 13th. Also, try this as a test: setenv FS_LOAD_DWI 0 mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh If that works, you can set that environment variable and run recon-all. But if you can send me the dicom above I'd appreciate it. doug On 04/02/2015 01:40 AM, A-reum Min wrote: hi doug recon is still not working... if i type the recon-all -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all -s subj001 then error occured ++ ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ERROR
Re: [Freesurfer] hello freesurfer developer~
I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and 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 dcmjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin) and my subjects path(own data) /usr/local/freesurfer/subjects/PISA_SPGR/1 --SUBJECTS_DIR 2015-04-03 7:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: Is dcmdjpeg.fs in your path? What are the contents of the file /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ? On 04/02/2015 04:53 PM, A-reum Min wrote: Hi doug. I try this as a test. (here is a my terminal) *** [areum@localhost ~]$ su Password: [root@localhost areum]# tcsh [areum@localhost areum]# setenv FREESURFER_HOME /usr/local/freesurfer [areum@localhost areum]# source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni [areum@localhost areum]# setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/PISA_SPGR/1 [areum@localhost areum]# setenv FS_LOAD_DWI 0 [areum@localhost areum]# mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh $Id: mri_convert.c,v 1.219 2015/03/24 17:25:41 greve Exp $ reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1 Ref Series No = 3 Found 246 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 IsDWI = 0 PE Dir = ROW (dicom read) Loading pixel data JPEG compressed, decompressing cd /home/areum dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm /tmp/root.tmp.decompressed.dcm.QGcfri /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out for more details ** error occured again.. ㅜㅜ when i type the source $FREESURFER_HOME/SetUpFreeSurfer.csh, then show up these freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni But... my own data directory is /usr/local/freesurfer/subjects/PISA_SPGR/1 so my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR/1 is it okay...? and i will send my dicom file to u... plz help me as soon as possible ㅜㅜ 2015-04-03 5:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Can you send me /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ? I might not be able to get to it until after the 13th. Also, try this as a test: setenv FS_LOAD_DWI 0 mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh If that works, you can set that environment variable and run recon-all. But if you can send me the dicom above I'd appreciate it. doug On 04/02/2015 01:40 AM, A-reum Min wrote: hi doug recon is still not working... if i type the recon-all -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all -s subj001 then error occured ++ ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071581.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071582.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071583.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer
Re: [Freesurfer] hello freesurfer developer~
Hi doug dcmdjpeg.fs path is /usr/local/freesurfer/bin (FREESURFER_HOME/bin) I click the /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out file. and 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 always error in tmp file(x signed root.tmp.decompressed.dcm.000). so, fix the x signed root.tmp.decompressed files... and i have no libdcmjpeg.so.3.6.. i need it. 2015-04-03 7:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: Is dcmdjpeg.fs in your path? What are the contents of the file /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ? On 04/02/2015 04:53 PM, A-reum Min wrote: Hi doug. I try this as a test. (here is a my terminal) *** [areum@localhost ~]$ su Password: [root@localhost areum]# tcsh [areum@localhost areum]# setenv FREESURFER_HOME /usr/local/freesurfer [areum@localhost areum]# source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni [areum@localhost areum]# setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/PISA_SPGR/1 [areum@localhost areum]# setenv FS_LOAD_DWI 0 [areum@localhost areum]# mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm junk.mgh $Id: mri_convert.c,v 1.219 2015/03/24 17:25:41 greve Exp $ reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1 Ref Series No = 3 Found 246 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 IsDWI = 0 PE Dir = ROW (dicom read) Loading pixel data JPEG compressed, decompressing cd /home/areum dcmdjpeg.fs +te /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm /tmp/root.tmp.decompressed.dcm.QGcfri /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out ERROR: 32512, see /tmp/root.tmp.decompressed.dcm.QGcfri.dcmdjpeg.out for more details ** error occured again.. ㅜㅜ when i type the source $FREESURFER_HOME/SetUpFreeSurfer.csh, then show up these freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni But... my own data directory is /usr/local/freesurfer/subjects/PISA_SPGR/1 so my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR/1 is it okay...? and i will send my dicom file to u... plz help me as soon as possible ㅜㅜ 2015-04-03 5:02 GMT+09:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Can you send me /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ? I might not be able to get to it until after the 13th. Also, try this as a test: setenv FS_LOAD_DWI 0 mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm junk.mgh If that works, you can set that environment variable and run recon-all. But if you can send me the dicom above I'd appreciate it. doug On 04/02/2015 01:40 AM, A-reum Min wrote: hi doug recon is still not working... if i type the recon-all -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all -s subj001 then error occured ++ ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071581.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071582.dcm ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOM File: /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071583.dcm ERROR
