Re: [Freesurfer] mri_convert error (dicom to nifti)

2016-01-12 Thread Bruce Fischl
Hi Kalli sounds like it is compressed in some way. What version of mri_convert are you using? If not dev, try that. If it is dev, try decompressing the dicoms first (e.g. run something like dcmdrle on each file first) cheers Bruce On Tue, 12 Jan 2016, Retzepi, Kallirroi wrote: Hi, I am ru

[Freesurfer] mri_convert error (dicom to nifti)

2016-01-12 Thread Retzepi, Kallirroi
Hi, I am running mri_convert (from .dcm to .nii.gz) and I get the following error: ERROR: RLL-encoded image data not supported! (Transfer Syntax UID: 1.2.840.10008.1.2.5) Any help is appreciated. Thank you! Kalli ___ Freesurfer mailing list Free

Re: [Freesurfer] (no subject)

2016-01-12 Thread Smaragdi A.
Hi Bruce, thanks for the quick reply, I am running v5.3.0 from a Linux, but more than 2/3 through my data set so don't really want to swap to 6.. Where can I get the beta and how would it help? Thanks, Areti From: freesurfer-boun...@nmr.mgh.harvard.ed

Re: [Freesurfer] error in selxavg3-sess

2016-01-12 Thread Douglas N Greve
Sorry, I've attached a matlab script. Copy it to $FREESURFER_HOME/matlab and try again doug On 01/12/2016 09:59 AM, neha hooda wrote: hii doug Thanks for the reply. But it gives the error. -- --- matlab output MATLAB is selectin

Re: [Freesurfer] (no subject)

2016-01-12 Thread Bruce Fischl
what version are you running? I believe that this is a bug that has been fixed. Hopefully we will get version 6 out soon and upgrading will fix this, but you can download a beta and try to make sure if you want cheers Bruce On Tue, 12 Jan 2016, Smaragdi A. wrote: > Hi mailing list, > > I have

Re: [Freesurfer] error in selxavg3-sess

2016-01-12 Thread neha hooda
hii doug Thanks for the reply. But it gives the error. -- --- matlab output MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc.

Re: [Freesurfer] recon-all issue

2016-01-12 Thread Bruce Fischl
Hi Susanne can you just send us the recon-all command lines that are issued by your script? And tell us what is different? Bruce On Tue, 12 Jan 2016, Schell, Susanne wrote: Dear colleagues,   as I posted before, we are recently using the freesurfer recon-all command. Here are three diff

Re: [Freesurfer] recon-all issue

2016-01-12 Thread Schell, Susanne
Dear colleagues, as I posted before, we are recently using the freesurfer recon-all command. Here are three different commands we used: 1)# Version 1: Import as DICOM #!/bin/sh -e # Segmentierung mit FreeSurfer. # Die Ergebnisse werden in dem Verzeichnis gespeichert, in dem sich # dieses Script