Dear Freesurfer experts,
I have a question about qdec...as it is supposed to be doing whole brain
cortical analyses, how come one first has to generate statistical tables,
and chose thicknesses of different regions from these tables? Is this just
an option, rather than being necessary for qdec?
Hi Doug,
Thanks for your quick response - that all makes sense now.
Best wishes,
Clare
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Message: 13
Date: Fri, 10 Aug 2012 10:19:43 +
From: Gibbard, Clare c.gibb...@ucl.ac.uk
Subject: [Freesurfer] QDEC results
To: freesurfer@nmr.mgh.harvard.edu
Hi Nick,
I just upgraded to the new version --
freesurfer-Darwin-tiger-i686-stable-pub-v4.0.5, and it seems now that I
can't start qdec at all. The only error returned is Bus error.
I ran the ldd command again and there were still the links to files in
/pubsw/... BTW, I'm running this on a Mac
Ming,
Can you send me the output of:
uname -a
and then do this:
setenv DYLD_PRINT_LIBRARIES 1
qdec
and send me that output?
The /pubsw's in the otool output (ldd doesnt exist on the mac, you're
probably using a wrapper supplied in matlab) do not indicate which
library is actually loading.
Jim,
I haven't used SPM so I can't comment on what SPM likes, but the
utilities asegstats2table and aparcstats2table will create text-file
tables of the aseg and aparc data for one or more subjects, which I
would think could be easily imported into SPM.
If you use mri_glmfit directly, there is a
You can try running mri_surf2vol to put into a volume, but you're better
off with mri_glmfit
Nick Schmansky wrote:
Jim,
I haven't used SPM so I can't comment on what SPM likes, but the
utilities asegstats2table and aparcstats2table will create text-file
tables of the aseg and aparc data
I see that group.levels has four levels. Unfortunately, right now qdec
only supports two levels for a discrete factor. One the features in the
works is to increase this.
On Wed, 2008-02-27 at 14:04 -0500, Cameron B. Ellis wrote:
Hi,
I pasted an error that I am receiving in qdec below.
Hi Nick-
I've run into the same problem recently and am looking at piping my FreeSurfer data out to another stats program. There is all sorts of info on the list about sending FS data out to Matlab, but are there any tips for getting it into a format that SPM will agree with? My other option is
Jim,
Can you send me the file?
Nick
On Tue, 2007-12-04 at 22:10 -0600, James N. Porter wrote:
Actually, scratch that. I had a hunch that I should change my header
from subj to fsid like the wiki guide has, and now the table loads.
However, qdec immediately crashes afterwards.
Now my
Jim,
I looked at the qdec.table.dat file that you sent me. The problem was
that it was in 'Mac' text format, which uses the LF char to indicate
end-of-line, whereas the 'Unix' text format was expected, which uses the
'CR' char to indicate end-of-line (and fyi, 'DOS' text file use two
chars: CR
Yep, that does it. I had hoped my use of Kate and Open Office would
have corrected this type of thing, but I guess not. Thanks for the new
command to add to my repertoire.
Jim Porter
Graduate Student
Clinical Science Psychopathology Research
University of Minnesota
Nick Schmansky
Jim,
I've updated qdec such that it will automatically handle qdec.table.dat
files originating on either Mac, Windows or Unix. This will appear in
the next public release.
Also, to correct an inaccuracy on my part, Mac's use CR as end-of-line,
Unix uses LF, while Windows (DOS) uses CR LF.
Nick
Actually, scratch that. I had a hunch that I should change my header
from subj to fsid like the wiki guide has, and now the table loads.
However, qdec immediately crashes afterwards.
Now my error is qdec.bin: QdecDataTable.cpp:438: void
QdecDataTable::Dump(FILE*): Assertion 'nInputs' failed.
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