Hi Doug,
when I run the following: mri_vol2vol.mac --targ rawavg.mgz --mov orig.mgz --reg reg.dat --o originraw.mgz
I get this error message:
dyld: Library not loaded: libvnl_algo.dylib Referenced from: /Applications/freesurfer/bin//mri_vol2vol.mac Reason: image not found Trace/BPT trap
I don't know if the reason is that the library is not found or that it doesn't find the image file, which would be strange because all files in in the correct path. I couldn't find libvnl_algo.dylib. (I use the latest FS version)
Frederick
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
Ah, yes, that one was for linux. I've copied a mac version there now (has .mac extension).
doug
Frederick Klauschen wrote:
Hi Doug,
I am running Freesurfer on MacOsX Darwin. The
command
as you suggested: mri_vol2vol --targ rawavg.mgz --mov orig.mgz --reg reg.dat --o orig-in-rawavg.mgz
using the mri_vol2vol version that came with FS I
get
the message: ERROR: Option --targ unknown
using the mri_vol2vol from the link you provided results in: Exec format error. Binary file not executable. Probably, that is a version compiled for x86 and
not
Mac?
Thanks for your help, Frederick
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
This should do it:
tkregister2 --targ rawavg.mgz --mov orig.mgz
--reg
reg.dat --noedit mri_vol2vol --targ rawavg.mgz --mov orig.mgz --reg reg.dat --o orig-in-rawavg.mgz
If this does not work with your version of
vol2vol,
then use the one here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
Frederick Klauschen wrote:
Hi,
I have to bring up an issue again which we had
some
discussion about before, but which we haven't yet found a satisfying solution. I would like pose my
question a
little more precisely again:
- I have a dataset that is in 181x217x181
coordinates. 2) I am processing it as follows:
mri_convert name.img name/mri/orig/001.mgz recon-all -motioncor -subjid name
- after step 2, the resulting dataset is somehow
transformed to a 256x256x256 dataset, i. e. the 181x217x181 is embedded into the 256^3 array: it is rotated and the origin in 181x217x181 is
not
the
origin in the 256x256x256 array. 4) Since I would like to do a voxelwise
comparison
between the recon-all result and my initial
dataset
1), I need to backtransform the result into the 181x217x181 coordinates (and of course, the backtransformation should be the exact inverse of
the
transformation in 2). I haven't found any info
about
how this transformation is done by FS, mri_info
does
not provide it.
Thanks, Frederick
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam
protection around
http://mail.yahoo.com _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam
protection around
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
__________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com