[Freesurfer] invalid=96777 in recon-all

Hello, I am using FreeSurfer version 5.3.0 in 64bit desktop, I got these errors at the begining of recon-all but the reconstruction is not stop, keep on going with lots of invalid=96777. pass 1 of 1 setting smoothness coefficient to 0.039 blurring input

Re: [Freesurfer] recon-all stopped with error

> output? > > Are the folders in fsavg symlinks also? > > > On Mon, 29 Jul 2013, Pom Sailasuta wrote: > > So now I got the following in /home/pom/Software/freesurfer/**subjects >> dir and still no lh.BA1.label >> per your first email. >> >> [pom@PomLinux /

Re: [Freesurfer] recon-all stopped with error

Sorry, now I understand, will try to do recon-all again. Hopefully it starts from where it left off before the errors. thanks so much. Pom On Mon, Jul 29, 2013 at 1:45 PM, Pom Sailasuta wrote: > So now I got the following in /home/pom/Software/freesurfer/subjects dir > and still no

Re: [Freesurfer] recon-all stopped with error

subjects dir (/home/pom/Software/**freesurfer/subjects) > > i.e. > cd /home/pom/Software/freesurfer/**subjects > ln -s ./fsavg/fsaverage . > > > -Louis > > On Mon, 29 Jul 2013, Pom Sailasuta wrote: > > fsavg dir contains several directories. >> >> [

Re: [Freesurfer] recon-all stopped with error

nk. A few lines up in your error log it prints "Too > many levels of symbolic links". > -Louis > > > On Mon, 29 Jul 2013, Pom Sailasuta wrote: > > Hi, >> >> I am wondering the errors I got from recon-all is from my FreeSurfer >> installation, please c

[Freesurfer] recon-all stopped with error

Hi, I am wondering the errors I got from recon-all is from my FreeSurfer installation, please comments. Here is my error: Reporting on 70 segmentations /home/pom/Software/freesurfer/subjects/S009002A/label # #@# BA Labels lh Mo

Re: [Freesurfer] MRI_Convert error

NIFTI, like MRIcron, then pass them to us? > > cheers > Bruce > > > On Thu, 25 Jul 2013, Pom Sailasuta wrote: > > >> Hello, >> >> I am resending this post since there is no reply for 2 days, I really >> appreciate your help. >> >> thanks

[Freesurfer] MRI_Convert error

Hello, I am resending this post since there is no reply for 2 days, I really appreciate your help. thanks so much. I have several errors using mri_convert to convert 3T Philips T1-wt, DTI and fMRI images. The last one on T1-wt images tells me to send email to freesurfer, so here is the error mes

[Freesurfer] mri_convert errors

Hello, I have several errors using mri_convert to convert 3T Philips T1-wt, DTI and fMRI images. The last one on T1-wt images tells me to send email to freesurfer, so here is the error messages: [pom@PomLinux /home/pom]% !mri mri_convert -it dicom -i IM_0001 -ot mgz -o 001.mgz mri_convert -it dic

[Freesurfer] tkmedit error

Hi, I got an error with tkmedit command "freeglut (/home/pom/freesurfer/freesurfer/bin/tkmedit.bin): Unable to create direct context rendering for window 'Medit: ' This may hurt performance. Xlib: extension "XFree86-DRI" missing on display ":0.0". The only DRI related file I have is called /us

[Freesurfer] tutorial course

Hello, Is it too late to register for the April tutorial course at MGH? thanks -- Pom ___ 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

Re: [Freesurfer] mni is already installed

7;t have perl, then it will fail. I don't know which version > of perl you need. I run with v5.8.8, but the mni tools are pretty old, so I > bet an older version of perl will work. > > doug > > Pom Sailasuta wrote: > >> [Pom@pom-PC bin]$ which nu_correct >> /u

Re: [Freesurfer] mni is already installed

N Greve wrote: > what happens when you type 'which nu_correct' ? > doug > > Pom Sailasuta wrote: > >> Hi Dr. Greve, >> >> mni is already installed, (came with freesurfer software) in >> /usr/l

[Freesurfer] mni is already installed

Hi Dr. Greve, mni is already installed, (came with freesurfer software) in /usr/local/freesurfer/mni. thank you -- Pom ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informa

[Freesurfer] more errors

Hi Bruce, Thank you so much. I got new error as follow // Pom@pom-PC subjects]$ recon-all -s 211-1029-MKA_elan -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /usr/local/fre

[Freesurfer] mri_convert error

Hello, I got an error below using mri_convert, please help /// [Pom@pom-PC mri]$ mri_convert -it dicom -ot mgz /orig/i399386.MRDC.1 001.mgz mri_convert -it dicom -ot mgz /orig/i399386.MRDC.1 001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve E

Re: [Freesurfer] error in test run

thank you Pom On Thu, Feb 17, 2011 at 5:30 PM, Douglas N Greve wrote: > Where did you get the 0.8 manual from? That must be 10 years old by now. > But to answer your question, we have an entire wiki dedicated to > documentation at surfer.nmr.mgh.harvard.edu/fswiki > > doug

[Freesurfer] manual

Is there a later FreeSurfer manual other than version 0.8? The instruction in this version called file that does not exist (FreeSurferDefs.csh). -- Pom ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

[Freesurfer] license error

Hello, I just installed freesurfer on my new Fedora 14 desktop following the instruction from the website. Howver when testing for installation, there are errors as follows: [root@pom-PC stable5]# tkmedit bert orig.mgz -- ERR