[Freesurfer] FW: YANQ follow-up

1 Aug 2014


      Thanks for posting back so quickly, Bruce, and for the direction.
Just to clarify, here is the command which I am using so you can see the types of files on which I am operating.
The working directory is ${FREESURFER_HOME}/subjects/bert .
I'm putting each switch on a separate line:
mri_label2label
--s Sub125
--srclabel label/rh.cortex.label
--trglabel testLabels/rh.cortext.label
--xfm mri/transforms/talairach.xfm
--xfm-invert
--regmethod volume
I plotted the output vectors for a single 1 mm slice using my tools.
This is shown in the left panel of the attached jpg.
The right panel shows the same vectors translated by hand to "fit."
The size and shape are close so this appears to be in the right direction.
I would like to find the freesurfer coords --> MRI coords transform and try it in place of talairach.xfm .
I assume that the inverse of talairach.xfm is not the correct transform to get from freesurfer --> MRI coordinates.
Is there a way to extract the correct transform?  It must have existed early in the "recon-all" run and must also be accessible to mri_convert -rl ...
I tried --nt as you suggested but my version of mri_label2label (stable5) does not recognize it.
I tried --regmethod surface --hemi rh and found that it gives identical results whether using --xfm-invert or not !
Regards,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
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-----Original Message-----
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From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-
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bounces@nmr.mgh.harvard.edumailto:bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
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Sent: Friday, August 01, 2014 9:29 AM
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To: Freesurfer support list
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Subject: Re: [Freesurfer] FW: YANQ follow-up
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Hi Don
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try mri_label2label. Also, the if you are transforming label volumes
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you need to use nearest neighbor interpolation, so include the -rt nearest switch.
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cheers
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Bruce
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On Fri, 1 Aug 2014, Krieger, Donald N. wrote:
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Hi All,
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I am still in need of finding the tool sequence to generate an ASCII
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file containing (1) voxel RAS coordinates (2) for a specific label
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(3) using the original MRI coordinates rather than freesurfer coordinates.
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  mri_convert -rl rawavg.mgz <input vol> <output vol>

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does generate a new output volume containing the "labelled" voxels
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contained in <input vol> .  I can tell because this volume shows up
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more or less correctly in freeview although the color mapping
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appears to have changed or perhaps freeview is doing some kind of "fill"
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operation differently depending on the loaded volume.  I assume
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these are in the coordinates for rawavg.mgz but cannot tell for sure.
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I need to generate  a list of these voxel coordinates from <output
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vol> to check and for my work.
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(1)    Do I need to generate a new annotation file from <output vol>
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and then use mri_annotation2label to get there?  I have not been
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able to find the tool sequence which generates the .annot files.
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(2)    An alternative appears to be mri_label2label with -xfm
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xfmfile and possibly including   --xfm-invert  .  I did get this
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command to complete successfully using mri/transforms/talaraich.xfm
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but I presume this is not the correct transform.
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Thanks and best regards,
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Don
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Don Krieger, Ph.D.
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Department of Neurological Surgery
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University of Pittsburgh
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(412)648-9654 Office
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(412)521-4431 Cell/Text
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From: Krieger, Donald N.
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Sent: Thursday, July 31, 2014 9:36 AM
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To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
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Subject: YANQ follow-up
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Thanks again for the pointer, Bruce.
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You wrote:
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...  mri_convert -rl rawavg.mgz <input vol> <output vol>
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which does produce an output volume from which I now need to extract
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RAS voxel coordinates.
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A pointer to a keyboard command would be most welcome.
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Of interest is the difference between the color mappings for the
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input and output volumes in freeview.
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When using the lookup table in freeview they are quite different
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whereas in grayscale they are almost identical.
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I wonder if this is contributing to my difficulty in finding a tool
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to extract the voxel coordinates.
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Thanks again.
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Regards,
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Don
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Don Krieger, Ph.D.
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Department of Neurological Surgery
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University of Pittsburgh
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(412)648-9654 Office
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(412)521-4431 Cell/Text
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[Freesurfer] FW: YANQ follow-up