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 : > 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

Re: [Freesurfer] hello freesurfer developer~

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

Re: [Freesurfer] hello freesurfer developer~

usually if the thickness is 0 that means that the vertex is not part of cortex, typically because it is on the "medial wall" (adjacent to ventricle) or in the hippocampus or some other non-neocortical structure On Fri, 4 Mar 2016, A-reum Min wrote: hello experts i have some question to you

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

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

Re: [Freesurfer] hello freesurfer developer~

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

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 : > Thank you for u r answer. > > I

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

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

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

Re: [Freesurfer] hello freesurfer developer~

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,

Re: [Freesurfer] hello freesurfer developer~

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

Re: [Freesurfer] hello freesurfer developer~

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

Re: [Freesurfer] hello freesurfer developer~

are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm images from *different* series or from the *same* series? If they are in the same series than that explains what is happening. You should only give recon-all a single file

Re: [Freesurfer] hello freesurfer developer~

Hi A-reum can you please follow the bug-reporting procedures in: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting also, don't include a snapshot of text - cutting and pasting the actual text in is far more useful, but in addition we need a lot of other information if we are to be able

Re: [Freesurfer] hello freesurfer developer~

give it the .img as input, not the .hdr. Note that using analyze is not recommended though! It doesn't store direction cosines so you will never be sure that there is no left/right flip unless you have a fiducial marker like a vitamin E tablet cheers Bruce On Wed, 16 Sep 2015, A-reum Min

Re: [Freesurfer] hello freesurfer developer~

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 How can

Re: [Freesurfer] hello freesurfer developer~

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

Re: [Freesurfer] hello freesurfer developer~

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

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

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

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

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

Re: [Freesurfer] hello freesurfer developer~

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

Re: [Freesurfer] hello freesurfer developer~

Maybe Zeke or Ruopeng know? On Jul 26, 2015, at 5:17 PM, A-reum Min naniy...@gmail.com 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: 1. No, each subject has a

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:

Re: [Freesurfer] hello freesurfer developer~

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).

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 ,

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 ,

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:

Re: [Freesurfer] hello freesurfer developer~

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

Re: [Freesurfer] hello freesurfer developer~

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

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

Re: [Freesurfer] hello freesurfer developer~

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

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

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

Re: [Freesurfer] hello freesurfer developer~

A-reum, Opening jpeg compressed dicoms is new feature so please bear with us as we try and get this working for you. Use the link below to download the libdcmjpeg.so.3.6.0 file. ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/libdcmjpeg.so.3.6 Once the download

Re: [Freesurfer] hello freesurfer developer~

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

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

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

Re: [Freesurfer] hello freesurfer developer~

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)

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

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

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

Re: [Freesurfer] hello freesurfer developer~

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

Re: [Freesurfer] hello freesurfer developer~

You're dicom file is jpeg compressed which FS version 5.3 does not handle. Get the two files from below ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/dcmdjpeg.fs ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert Copy into $FREESURFER_HOME/bin (make a