Thanks Zeke. I tried upgrading to the latest FS version, 5.2.0, but I see that the available download ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0/freesurfer-Linux-centos4-stable-pub-v5.2.0.tar.gzis only in .tar.fz format rather than in .VDI format, as v5.1.0ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdiwas (and the .TAR archive does not contain a .VDI file inside it). Virtualbox seems to only accept the VDI format. Apologies if there's something obvious here that I"m not seeing..
And yes, it's true that I eventually did get mri_concat to work in QDEC, however that was only after repeatedly trying the same thing, I hadn't really changed anything. My guess is that, when I used to get that error from QDEC/mri_concat in the past, it was another case of mri_concat not responding to the command line. This could be, as Doug says, a problem with my Virtualbox, but unfortunately I don't know what else to do with it, and I've been wanting to complete this analysis for weeks now... :(
On 1 April 2013 15:24, zkaufman@nmr.mgh.harvard.edu wrote:
Hi Tudor,
That is unfortunate. You mention in the email below dated (Feb 1) that you got mri_concat working for you. If it worked for you then, but doesnt now, and nothing changed in the meantime, Im not sure there's much we can do to diagnose the issue. The mri_concat binary I sent you works in our CentOS4 environment and as well as the countless others who have downloaded freesurfer 5.1 for CentOS4. Are you required to use 5.1 for your analysis? Freesurfer 5.2 was released earlier this month and can be downloaded here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Download
-Zeke
Hi Zeke,
Thanks very much for this, I replaced the file with the one you sent, but now after typing a test command: mri_concat -i C01.nii.gz -i C02.nii.gz -o test.nii.gz or indeed after typing mri_concat on its own, I always get the message "Killed" at the command line!
Tudor
---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] Error from mri_concat while using QDEC From: "Tudor Popescu" tudor3@gmail.com Date: Fri, February 1, 2013 12:12 pm To: "Douglas N Greve" greve@nmr.mgh.harvard.edu Cc: "free surfer" freesurfer@nmr.mgh.harvard.edu
Hi Doug
Strangely, the basic mri_concat command now worked, and so did the full one. I think I initially had a "" at the end of my command, just after the file name, which should not have been there; although having tried again with the backslash reinstated at the end, the command still worked. Also, the Analyze in the QDEC GUI now completes without error as well.
It's quite frustrating that I still don't know why it hasn't been working all this time, especially since I didn't really do anything different now (that I was aware of!) and the files were located on the same partition (Virtualbox's shared folder).
Anyhow, thanks again for your kind help!
Tudor
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