Re: [Freesurfer] FW: YANQ follow-up

6 Aug 2014

      Thanks a million for all of the answers about cor2label+ in the other post - very helpful.
I produced the figure using a csh script which reads in the vectors and creates a display list which xfig understands.
The display list is in the attached xfig file which needs to be gunzip'd before displaying it with:
   xfig   126_free_p5.fig
The attached gif is the background cut in the figure.
I got it by  using ImageJ to read in the DICOM images and create the axial slices 1 mm apart.
The registration of those images is slightly off.
I generated the vectors by applying the transform extracted from aseg.mgz  with mri_info --tkr2scanner to the vectors in rh.cortex.label and rh.V2.label .
I used one of my fortran routines to do the matrix x vector multiplication.
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-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-
bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Wednesday, August 06, 2014 6:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: YANQ follow-up
How did you create that image? You can use mri_cor2label to extract the
labels from aparc+aseg (it will take values > 255) doug
On 08/04/2014 01:16 PM, Krieger, Donald N. wrote:
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Thanks Doug,
Got it.
I've attached a sample image on which I've drawn transformed vectors
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1.rh.cortex.label (red)
2.rh.V2.label_orig (blue)
3.rh.V2.label_white (yellow)
4.rh.V2.label_pial (aqua)
I used mri_annotation2label to extract vectors from the aparc and BA
annotation files.
I used mri_info to extract the tkr2scanner transform from aparc+aseg.mgz .
You can see that the cut through the mri volume on which the dots are
drawn is slightly off.
It would be helpful to hear if you think there is something else I
should check.
The registration of dots with the white/gray matter boundary is
comparable for axial slices 2 cm apart top to bottom.
For each label, I now need to extract vectors which fill the specified
volume, gray or white.
It looks like this information is present in mri/filled.mgz but I have
not found a way which I understand to extract vectors from a .mgz volume.
mri_cor2label appears to work but it uses -id labelid which I haven't
been able to puzzle out.
The documentation states that labelid ranges from 0-255 so it's not
the same as that present in FreeSurferColorLUT.txt .
Can you please explain this or put me out of my misery by telling me
mri_cor2label is not the tool to use.
Finally, when I load aparc+aseg.mgz in freeview, subcortical
structures are clearly segmented including the cerebellum, basal
ganglia, etc.
How do I extract these vectors into .label files?
There is no aseg.annot in the label directory and none of the .annot
files yield .label files for these structures.
Do I need to run something else which is not included by default in
recon-all to generate this file or is there some other route to get there?
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.edu [mailto:freesurfer-
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bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
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Sent: Friday, August 01, 2014 4:05 PM
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To: freesurfer@nmr.mgh.harvard.edu
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Subject: Re: [Freesurfer] FW: YANQ follow-up
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Hi Don, try looking at this page for more info on our coordinate systems
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https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
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On 08/01/2014 10:47 AM, Bruce Fischl wrote:
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Hi Don
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the -rt nearest switch is for mri_convert. I'll leave the rest of the
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questions for Doug :) Bruce On Fri, 1 Aug 2014, Krieger, Donald N.
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Thanks for posting back so quickly, Bruce, and for the direction.
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Just to clarify, here is the command which I am using so you can see
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the types of files on which I am operating.
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The working directory is ${FREESURFER_HOME}/subjects/bert .
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I'm putting each switch on a separate line:
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mri_label2label
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--s Sub125
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--srclabel label/rh.cortex.label
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I plotted the output vectors for a single 1 mm slice using my tools.
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This is shown in the left panel of the attached jpg.
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The right panel shows the same vectors translated by hand to "fit."
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The size and shape are close so this appears to be in the right
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direction.
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I would like to find the freesurfer coords --> MRI coords transform
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and try it in place of talairach.xfm .
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I assume that the inverse of talairach.xfm is not the correct
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transform to get from freesurfer --> MRI coordinates.
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Is there a way to extract the correct transform? It must have existed
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early in the "recon-all" run and must also be accessible to
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mri_convert -rl ...
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I tried --nt as you suggested but my version of mri_label2label
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(stable5)
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does not recognize it.
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I tried --regmethod surface --hemi rh and found that it gives
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results whether using --xfm-invert or not !
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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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-----Original Message-----
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From: freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-
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bounces@nmr.mgh.harvard.edu
mailto: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
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you need to use nearest neighbor interpolation, so include the -rt
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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
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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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> (2) An alternative appears to be mri_label2label with -xfm
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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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> University of Pittsburgh
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> (412)648-9654 Office
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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.edu
mailto: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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> which does produce an output volume from which I now need to
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extract
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> A pointer to a keyboard command would be most welcome.
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> Thanks again.
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> Regards,
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--
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Douglas N. Greve, Ph.D.
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MGH-NMR Center
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greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
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Phone Number: 617-724-2358
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Fax: 617-726-7422
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] FW: YANQ follow-up