[Freesurfer] Preproc-sess failed

Hi freesurfer experts, I am practicing on the fsfast tutorial data that were given at Freesurfer website. I run the command to do the pre-processing on the sess01 <*noproc*>. *preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -fwhm 5 -per-run* it was unfinished and failed with the E

[Freesurfer] Preproc-sess failed

Hi freesurfer experts, I am practicing on the fsfast tutorial data that were given at Freesurfer website. I run the command to do the pre-processing on the sess01 <*noproc*>. *preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -fwhm 5 -per-run* it was unfinished and failed with the E

Re: [Freesurfer] Preproc-sess failed

or directory* *ERROR: 3dvolreg.afni* *Invalid null command.* 2015-06-19 16:04 GMT+07:00 Douglas Greve : > > See this thread > http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html > > > > On 6/17/15 5:59 PM, Thục Trinh wrote: > > Hi freesurfer ex

Re: [Freesurfer] Preproc-sess failed

; -Zeke > > > > > On 06/22/2015 02:40 PM, Douglas Greve wrote: > > I'm not sure what to tell you. Zeke, do you have any ideas? > > Alternatively, you can just install afni on your machine. Once you > > verify that the installation works, copy 3dvolreg from the

Re: [Freesurfer] Preproc-sess failed

hello, I am using CentOS release 6.4 ( final) 64bit and Freesurfer v.5.3.0. I think that makes the confliction. 2015-06-23 8:26 GMT+07:00 Thục Trinh : > Hello Douglas and ZK, > I set the path for shared library in my .basrch file, but it still does > not work and comes up with t

Re: [Freesurfer] Preproc-sess failed

gh.harvard.edu/fswiki/Download > > -Zeke > > > On Jun 22, 2015, at 11:29 PM, Thục Trinh wrote: > > hello, > I am using CentOS release 6.4 ( final) 64bit and Freesurfer v.5.3.0. > I think that makes the confliction. > > 2015-06-23 8:26 GMT+07:00 Thục Trinh : > >> H

Re: [Freesurfer] Preproc-sess failed

This should install the 64-bit libraries alongside the > 32-bit libraries of libXp. > > If I recall correctly, you might also need the libXpm libraries, use > > sudo yum install libXpm.x86_64 > > > > On 24 Jun 2015, at 04:49, Thục Trinh wrote: > > > >

Re: [Freesurfer] Preproc-sess failed

e files. > > > What is the output > > uname -a > > On your system? > > > On 25 Jun 2015, at 09:01, Thục Trinh wrote: > > Hi, > After complete install the suitable version of shared library as you > suggested, I cannot find any file name libXpm.x86_64 to s

Re: [Freesurfer] Preproc-sess failed

he libXp.so on your system and see if > there is a local 32-bit copy > > find / -type f -iname "libXp.so*" > > > On 25 Jun 2015, at 09:45, Thục Trinh wrote: > > the lib files are now in /usr/lib64, the ERROR still the same after I set > a new path for share

Re: [Freesurfer] Preproc-sess failed

64-bit, and > remove any 32-bit or even 64-bit version outside /usr/lib64 (BEWARE: > removing libraries is at risk of breaking functioning of other application > that depend on that particular library. If necessary, you can always run > `sudo yum install libXp.i686` to install the 32-bi

Re: [Freesurfer] Preproc-sess failed

is the directory you want to add > to your LD_LIBRARY_PATH environment variable. > > -Zeke > > > On Jun 30, 2015, at 11:39 PM, Thục Trinh wrote: > > Hi, > I did exactly what you said, and the error still remain: *3dvolreg.afni: > error while loading shared libraries: libXp.so

Re: [Freesurfer] Preproc-sess failed

eg.afni complains about > missing libXp.so.6. After installing it again with the first command, it > works again. > > On Jul 01, 2015, at 06:47 AM, Thục Trinh wrote: > > Is the command line like this: > yum install libXp.so.6.x86_64 > > because I did run yum install li

[Freesurfer] paradigm file

Hello, I'm working on fMRI analysis on flattening brain by using FSFAST tool. In our data, subjects play game: Matrix reasoning. How can I set up the paradigm file if the duration stimulus depends on the Time response of each subject following each trial. Thanks !! Trinh __

Re: [Freesurfer] paradigm file

4. Weight (usually 1) > > If each stimulus presentation has a different duration, then that would be > indicated in #3 > > doug > > > On 7/22/15 12:23 AM, Thục Trinh wrote: > > Hello, > I'm working on fMRI analysis on flattening brain by using FSFAST tool. In >

[Freesurfer] White matter Error

​ NCP140539_2_recon.rar ​Hi Freesurfer Experts, We are on the process of troubleshooting our subjects's recon and we came across with this error that we can not determine what kind of problem this is: It seems there

Re: [Freesurfer] White matter Error

ges? Your link didn't work for me. You can > check the topology of the surface computationally using mris_euler_number. > You might also try moving backwards/forwards a few slices to try to > understand what is going on. > > cheers > Bruce > >

Re: [Freesurfer] tilted head

They are fine. Thank you. 2015-10-08 10:06 GMT+07:00 Bruce Fischl : > I think it should be fine. Do the segmentations and surfaces look accurate? > > On Oct 7, 2015, at 10:54 PM, Thục Trinh wrote: > > Hi Freesurfer Experts, > > We are on the process of troubleshooting on al

Re: [Freesurfer] White matter Error

for all ?h.pial, ?h.white and ?h.inflated. Can you help me with this problem. Thank, Trinh 2015-10-05 23:09 GMT+07:00 Bruce Fischl : > Hi Trinh > > the inflated.nofix files are the ones before the topology fixer so they > will always have defects in them > > cheers > Bruce >

[Freesurfer] wrong segmentation

Hi Freesurfer experts, I ran recon-all for our subjects and there is a problem with the wrong segmentation between the white/gray matter. this error appears in couples continued slices. Picture are attached. Do you have any suggestion to fix this error. Thank you, Trinh __

Re: [Freesurfer] wrong segmentation

heers > Bruce > > On Thu, 29 Oct 2015, Thục Trinh wrote: > > Hi Freesurfer experts, >> I ran recon-all for our subjects and there is a problem with the wrong >> segmentation between the white/gray matter. this error appears in couples >> continued slices. Picture ar

[Freesurfer] FS v.6.0

Hello Freesurfer experts, I used recon-all command for all my subject by FS v.5.3. But now I decide to upgrade to FS v.6 to eliminate some segmentation errors. The pial errors still appear on the new output of FS v.6 Can I replace the braimask.mgz of FS v.6 by the brainmask.mgz of FS v.5.3 (that b

[Freesurfer] missing 3volreg.afni

Hi FS experts, I'm working on my fMRI data using FSFAST v.6 tool. But the first step of Preproc-sess was failed with an error :" *ERROR: cannot find AFNI command 3dvolreg.afni ". * I found a thread that had the same error with mine (in FS v.5.3) : http://www.mail-archive.com/freesurfer%40nmr.mgh.h

Re: [Freesurfer] missing 3volreg.afni

Hi Douglas, It still does not work. 2015-12-21 23:29 GMT+07:00 Douglas N Greve : > that link works for me. Can you try again? > > On 12/20/2015 02:17 AM, Thục Trinh wrote: > > Hi FS experts, > > > > I'm working on my fMRI data using FSFAST v.6 tool. But the fi

Re: [Freesurfer] missing 3volreg.afni

The link is fine. But when I click on the 3dvolreg file to get the download, it failed with the error: "this webpage is not available" 2015-12-22 23:12 GMT+07:00 Douglas Greve : > what happens when you click on it? > > > On 12/22/15 9:28 AM, Thục Trinh wrote: > > Hi

Re: [Freesurfer] missing 3volreg.afni

gt; On 12/22/15 7:56 PM, Thục Trinh wrote: > > The link is fine. But when I click on the 3dvolreg file to get the > download, it failed with the error: "this webpage is not available" > > 2015-12-22 23:12 GMT+07:00 Douglas Greve : > >> what happens when you click o

Re: [Freesurfer] missing 3volreg.afni

reg to 3dvolreg.afni and it should work. > > > On 12/23/15 1:22 AM, Thục Trinh wrote: > > Hi, > It comes up with this error: > /freesurfer/bin/3dvolreg.afni: Exec format error. Wrong Architecture. > ERROR: 3dvolreg.afni > Invalid null command. > > 2015-12-23 7:59 GMT+

[Freesurfer] visualize fsaverage

Hello freesurfer experts, I'm having a trouble with visualize the first level analysis output of FSFAST on brain surface (fsaverage). When I open tksurfer tool to look at the contrast for the analysis on Right hemisphere space, the result display the contrast on left hemisphere and vice versa whe

Re: [Freesurfer] visualize fsaverage

e down. Is there another computer you can test it > on? What platform are you using? > > On 01/19/2016 09:20 AM, Thục Trinh wrote: > > Hi Bruce, > > I worked on my functional data, the command lines below, > > > > * preproc-sess -s NCP140008_1 -fsd raw -stc down

[Freesurfer] mkanalysis-sess

Hello, I am using mkanalysis-sess command to configure analysis and I have some questions. 1, After run preproc-sess on raw data, why would we want to repeat all the flag using for preprocessing at mkanalysis-sess (-stc up -fwhm 5). Is it gonna effect to our f.nii if I input different value from

[Freesurfer] Paired analysis FSFAST

Hello, I'm working on group analysis in fMRI activation using FSFAST. I tend to test whether any significant changed in fMRI activation within group across two time points ( pre-training vs post). I ran first level already. I still confuse about the concat data and the mri_glmfit command. Here ar

Re: [Freesurfer] Cortical Segmentation

he 3 subject dirs we can take a look. > > cheers > Bruce > > > > On Sun, 14 Dec 2014, Thục Trinh wrote: > > Hello Freesurfer Experts, >> Here is my procedure that I have a small problem on: >> >> I took MRI structure images on one subject, but used di