Hi,
I am running bedpostx within Freesurfer Tracula with default settings.
I got the following error message:
Queuing post processing stage
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_post: unexpected operator
[: 486: x: unexpected operator
[: 486: -le:
Hi Judit - Hard to tell what could've gone wrong but you can try running
the postprocessing yourself as follows:
bedpostx_postproc.sh /path/to/subject/dmri
Hope this helps,
a.y
On Thu, 8 Sep 2011, Judit Haasz wrote:
Hi,
I am running bedpostx within Freesurfer Tracula with default
Hello,
I am using mri_convert to convert dicom image into analyze format using:
mri_convert -i PATH_TO_DICOM_HERE --out_type analyze -o analyze.img
The problem is:
The hdr.hist.orient in the output file is set to 0, but the pixels in
the analyze image are saggital.
Does anybody have any
I have no idea. That's pretty old code that we are not really
maintaining anymore. Why are you using analyze?
doug
Mohana Ramaratnam wrote:
Hello,
I am using mri_convert to convert dicom image into analyze format using:
mri_convert -i PATH_TO_DICOM_HERE --out_type analyze -o analyze.img
Ben Deen wrote:
Hi,
I have an update to this query. I tried using mkanalysis-sess instead
of the .new version, and now I do seem to be able to get rid of
intensity normalization and prewhitening (or at least, adding these
flags now has an effect on betas/t-stats, and in the expected
Hi Doug,
Thanks for your response. The comments below all regard question #2,
is this is the only one that still concerns me.
I actually was using the nowhiten flag in the last analysis I
described, which was run in version 4.5. From looking at the ces,
cesvar, and t images in the contrast
So, which version did you find that ces/sqrt(cesvar) did not equal t?
doug
Ben Deen wrote:
Hi Doug,
Thanks for your response. The comments below all regard question #2,
is this is the only one that still concerns me.
I actually was using the nowhiten flag in the last analysis I
4.5, but only for my results, not others from my lab.
On Thu, Sep 8, 2011 at 3:37 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
So, which version did you find that ces/sqrt(cesvar) did not equal t?
doug
Ben Deen wrote:
Hi Doug,
Thanks for your response. The comments below all
Hi,
I am making an analysis in freesurfer 5.1 using mkanalysis-sess and I am a
bit confused about the flag refeventdur. In the help it is said that it
should be set to the event duration if the events have similar durations. I
have four conditions that last for 16 second each in a block design
Hi Maryam, yes, I admit, that is a confusing option. The events that
the help refers to only apply to task events (not the fixation). In your
case, you would just set it to 16 sec.
doug
On 9/8/11 10:55 PM, Maryam Vaziri Pashkam wrote:
Hi,
I am making an analysis in freesurfer 5.1 using
Hi,
After running dti_recon and recon_all, I noticed that they produce different
volumes of structures for the same brain. Just trying to understand why that
is?
best,
AJ
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