[caret-users] postborder script

Donna Dierker donna at brainvis.wustl.edu
Sat Nov 21 14:11:02 CST 2009


Cinematic Titanic is still five hours off, so I have time to answer your
questions.

> Thanks for sharing more scripts. So what are showing on the
> DEFORM_CHECK webpage? I saw a lateral, medial and a flat view for each
> hemisphere. Are these the deformed fiducial  and flat surface of the
> original? 

The flat map is the deformed colin right hem flat map (a common viewing
substrate for PALS_B12 data).  The surface doesn't matter; it's the depth
map displayed on it that matters.  The advantage of the flat map is that
you can see the whole hem in one view.

> Why are the medial views always cut off at the posterior
> end?  I assume as long as these surfaces look like a brain (no gross
> errors), then it's ok?  I guess I don't know what a bad result look
> like (I assume the ones you have are all good).

The occipital lobe is shorn off just to irritate me.  I didn't bother
fixing it for this purpose.

> Sorry this might be obvious, but where do I run this check_reg_output
> script?  In the atlas directory (PALS_B12.LR) or the surf directory
> in
> the subject's anatomy? I tried both but get this error:<br>
> <font face="Courier New, Courier, monospace"><br>
> ls: cannot access deformed_Human.*Fiducial.mws.*coord: No such file or
> directory

Whatever ATLAS_TARGET_DIR is set to in postborder.sh.  Probably the
fiducial is missing due to the rogue "=" preceding the filename.

> I don't have any file with names like deformed_*Fiducial*&nbsp; but I have
> other deformed surfaces. Here're the files in my atlas directory after
> I did postborder on one subject.<br>

> -rw-r--r-- 1 tsliu tsliu 16777568 2009-11-04 14:52 TEMPLATE.LPI.nii<br>
> -rwxr-xr-x 1 tsliu tsliu&nbsp;&nbsp; 557688 2009-11-05 15:07
> TEMPLATE.check.RH.scene<br>
> -rwxr-xr-x 1 tsliu tsliu&nbsp;&nbsp; 661921 2009-11-05 15:07
> TEMPLATE.check.LH.scene<br>
> -rwxr-xr-x 1 tsliu tsliu&nbsp;&nbsp;&nbsp; 14958 2009-11-05 15:07
> TEMPLATE.areacolor<br>
> -rwxr-xr-x 1 tsliu tsliu&nbsp;&nbsp;&nbsp; 12178 2009-11-05 15:12
> border_color_key.jpg<br>
> -rwxr-xr-x 1 tsliu tsliu&nbsp;&nbsp;&nbsp;&nbsp; 7316 2009-11-05 15:12
> Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.RIGHT.FIDUCIAL.var1.border<br>
> -rwxr-xr-x 1 tsliu tsliu&nbsp;&nbsp;&nbsp;&nbsp; 8139 2009-11-05 15:12
> Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.RIGHT.FIDUCIAL.border<br>
> -rwxr-xr-x 1 tsliu tsliu&nbsp;&nbsp;&nbsp;&nbsp; 7810 2009-11-05 15:12
> Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.LEFT.FIDUCIAL.var1.border<br>
> -rwxr-xr-x 1 tsliu tsliu&nbsp;&nbsp;&nbsp;&nbsp; 8673 2009-11-05 15:12
> Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.LEFT.FIDUCIAL.border<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp;&nbsp;&nbsp; 3532 2009-11-05 16:51
> ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp; 2587758 2009-11-09 12:29
> Human.sphere_6.73730.topo<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp;&nbsp;&nbsp; 1961 2009-11-09 12:29
> TEMPLATE_REG-with-POP-AVG_4K_NoFid.deform_map<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp; 884991 2009-11-09 12:29
> Human.sphere_6_forFIDUCIAL.73730.coord<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp; 884981 2009-11-09 12:29
> Human.sphere_6.73730.coord<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 501 2009-11-09
> 12:29
> Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp;&nbsp; 10253 2009-11-09 12:29
> Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.borderproj<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp;&nbsp; 25902 2009-11-11 11:22
> Zeroes_711-2B.nii.gz<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp;&nbsp; 79321 2009-11-20 17:00
> sanity.scene<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp;&nbsp; 20237 2009-11-20 17:34
> deformed_Human.FS003.L.LANDMARKS.73730.borderproj<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp; 1476643 2009-11-20 17:34
> deformed_Human.FS003.L.Initial.73730.surface_shape<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp; 1771641 2009-11-20 17:34
> deformed_Human.FS003.L.73730.register.73730.deform_map<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp; 885299 2009-11-20 17:34
> deformed_deformed_Human.FS003.L.Midthickness_711-2B.mws.73730.coord<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp; 886443 2009-11-20 17:34
> deformed_Human.FS003.L.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.73730.coord<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 894 2009-11-20
> 17:34
> deformed_Human.FS003.L.73730.register.73730.spec<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp;&nbsp; 23055 2009-11-20 17:36
> deformed_Human.FS003.R.LANDMARKS.73730.borderproj<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp; 1476643 2009-11-20 17:36
> deformed_Human.FS003.R.Initial.73730.surface_shape<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp; 1771641 2009-11-20 17:36
> deformed_Human.FS003.R.73730.register.73730.deform_map<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp; 885300 2009-11-20 17:36
> deformed_deformed_Human.FS003.R.Midthickness_711-2B.mws.73730.coord<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp; 886444 2009-11-20 17:36
> deformed_Human.FS003.R.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.73730.coord<br>
> -rw-r--r-- 1 tsliu tsliu&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 894 2009-11-20
> 17:36
> deformed_Human.FS003.R.73730.register.73730.spec<br>
> -rwxr-xr-x 1 tsliu tsliu&nbsp;&nbsp;&nbsp;&nbsp; 2181 2009-11-20 17:38
> check_reg_output.sh<br>
> </font><br>
> <br>
> Donna Dierker wrote:
> <blockquote cite="mid:4B070BE9.3020500 at brainvis.wustl.edu" type="cite">
>   <pre wrap="">On 11/20/2009 02:01 PM, Taosheng Liu wrote:
>   </pre>
>   <blockquote type="cite">
>     <pre wrap="">Hi Donna,
>   Thank you for the tip. The spec file generated by the preborder file
> is all fine (I think one of the errors is caused by me). I'm
> continuing to postborder now! I can't believe this is happening ;)
>     </pre>
>   </blockquote>
>   <pre wrap=""><!---->And you could be drawing all those borders by hand
> right now....
>   </pre>
>   <blockquote type="cite">
>     <pre wrap="">(I'm also changing the subject line, to end one of my
> longest email
> threads--again, thanks very much).
>   After manual tweaking those borders, I saved the borderproj file as
> something like "Human.FS003.L.LANDMARKS.borderproj". This causes
> overwriting the same file, which I assume contains borders generated
> by the automated procedure. I'm overwriting this because I think the
> postboder script uses this file (line 41), correct? I assume the bvo
> version is for the QA purpose.  I ran it and it finished Ok. My
> question now is how do I check the result? There's a warning message:
> WARNING: coordinate file
> deformed_Human.FS003.L.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.73730.coord
> has 73730 crossovers after deformation.
>
> which sounds pretty bad (the R hemisphere didn't have this warning).
>     </pre>
>   </blockquote>
>   <pre wrap=""><!---->You'll always get this on left hemispheres.  Ignore
> it.  (If you ran the
> crossover check with the same coord but a different, LEFT topo file,
> you'd get zero.  But this crossover check is being done by the
> registration process, and it's using the same topo used for
> registration.  So you'll always get crossovers for all nodes on the
> left, 0 on the right (or hopefully no more than a few for the right).
>   </pre>
>   <blockquote type="cite">
>     <pre wrap="">FYI, here's a list of files in the surf/ directory that
> were
> changed/generated when I ran the script. Sorry to bother you with this
> screen output, but I want to make sure they look ok and understand
> what these things are (for the purpose of reading the spherical
> registration into Matlab). There's an extra "=" at the beginning of
> one file, which is caused by an extra "=" on line 34.
>     </pre>
>   </blockquote>
>   <pre wrap=""><!---->Good catch.  I fixed it on my end, too.
>
> Your atlas target directory will have the deformed output.  How you
> check it depends on what you're deforming.  I do shape studies, so I
> check both the deformed fiducial and depth map, to make sure they look
> sane.  I have a check_reg_output.sh file in my atlas target directory
> for just that purpose.  It produces a sanity checking page like this
> (hot off the press from yesterday):
>
> <a class="moz-txt-link-freetext"
> href="http://brainmap.wustl.edu/pub/donna/TODD/ADHD/CHECK_SCENES/DEFORM_SANITY_CHECK/views.html">http://brainmap.wustl.edu/pub/donna/TODD/ADHD/CHECK_SCENES/DEFORM_SANITY_CHECK/views.html</a>
> login pub
> password download
>
> I put both the script and the sanity.scene file it uses here:
>
> <a class="moz-txt-link-freetext"
> href="http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2009_10">http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2009_10</a>
>
> If you are deforming fMRI (i.e., metric) files, then you might adapt the
> scene to overlay the deformed metric.  Depending on how the columns are
> named, that could be tricky.  And deforming it could be a two-part
> process, if the fMRI is mapped to the Freesurfer native mesh, rather
> than the 73730 surface.
>   </pre>
>   <blockquote type="cite">
>     <pre wrap="">--ts
>
> -rw-r--r-- 1 tsliu tsliu    30340 2009-11-20 14:11
> Human.FS003.L.LANDMARKS.borderproj.bak
> -rw-r--r-- 1 tsliu tsliu    20058 2009-11-20 14:11
> Human.FS003.L.LANDMARKS.borderproj
> -rw-r--r-- 1 tsliu tsliu   295251 2009-11-20 14:11 Human.FS003.L.MWS.roi
> -rw-r--r-- 1 tsliu tsliu   885167 2009-11-20 14:11
> =deformed_Human.FS003.L.Midthickness_711-2B.mws.coord
> -rw-r--r-- 1 tsliu tsliu   885409 2009-11-20 14:12
> Human.FS003.L.VeryInflated.73730.coord
> -rw-r--r-- 1 tsliu tsliu   885528 2009-11-20 14:12
> Human.FS003.L.SPHERICAL.73730.MWS.coord
> -rw-r--r-- 1 tsliu tsliu   885325 2009-11-20 14:12
> Human.FS003.L.Inflated.73730.coord
> -rw-r--r-- 1 tsliu tsliu   885486 2009-11-20 14:12
> Human.FS003.L.Ellipsoid.73730.coord
> -rw-r--r-- 1 tsliu tsliu   886301 2009-11-20 14:12
> Human.FS003.L.SPHERICAL.73730.MWS.SPHERE_CYCLE1.coord
> -rw-r--r-- 1 tsliu tsliu   886301 2009-11-20 14:13
> Human.FS003.L.SPHERICAL.73730.MWS.SPHERE_CYCLE2.coord
> -rw-r--r-- 1 tsliu tsliu   886301 2009-11-20 14:13
> Human.FS003.L.SPHERICAL.73730.MWS.SPHERE_CYCLE3.coord
> -rw-r--r-- 1 tsliu tsliu   886301 2009-11-20 14:13
> Human.FS003.L.SPHERICAL.73730.MWS.SPHERE_CYCLE4.coord
> -rw-r--r-- 1 tsliu tsliu   886302 2009-11-20 14:13
> Human.FS003.L.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.coord
> -rw-r--r-- 1 tsliu tsliu      315 2009-11-20 14:13
> Human.FS003.L.73730.register.spec
> -rw-r--r-- 1 tsliu tsliu   886533 2009-11-20 14:14
> deformed_Human.FS003.L.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.coord
> -rw-r--r-- 1 tsliu tsliu  3717645 2009-11-20 14:14
> deformed_Human.FS003.L.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.deform_field
> -rw-r--r-- 1 tsliu tsliu    29934 2009-11-20 14:14
> Human.FS003.R.LANDMARKS.borderproj.bak
> -rw-r--r-- 1 tsliu tsliu    22875 2009-11-20 14:14
> Human.FS003.R.LANDMARKS.borderproj
> -rw-r--r-- 1 tsliu tsliu    20094 2009-11-20 14:14
> medial_wall_merged.borderproj
> -rw-r--r-- 1 tsliu tsliu   295251 2009-11-20 14:14 Human.FS003.R.MWS.roi
> -rw-r--r-- 1 tsliu tsliu   885168 2009-11-20 14:14
> =deformed_Human.FS003.R.Midthickness_711-2B.mws.coord
> -rw-r--r-- 1 tsliu tsliu   885410 2009-11-20 14:14
> Human.FS003.R.VeryInflated.73730.coord
> -rw-r--r-- 1 tsliu tsliu   885529 2009-11-20 14:14
> Human.FS003.R.SPHERICAL.73730.MWS.coord
> -rw-r--r-- 1 tsliu tsliu   885326 2009-11-20 14:14
> Human.FS003.R.Inflated.73730.coord
> -rw-r--r-- 1 tsliu tsliu   885487 2009-11-20 14:14
> Human.FS003.R.Ellipsoid.73730.coord
> -rw-r--r-- 1 tsliu tsliu   886302 2009-11-20 14:14
> Human.FS003.R.SPHERICAL.73730.MWS.SPHERE_CYCLE1.coord
> -rw-r--r-- 1 tsliu tsliu   886302 2009-11-20 14:15
> Human.FS003.R.SPHERICAL.73730.MWS.SPHERE_CYCLE2.coord
> -rw-r--r-- 1 tsliu tsliu   886302 2009-11-20 14:15
> Human.FS003.R.SPHERICAL.73730.MWS.SPHERE_CYCLE3.coord
> -rw-r--r-- 1 tsliu tsliu  2952909 2009-11-20 14:15
> spherical_morph_distortion.surface_shape
> -rw-r--r-- 1 tsliu tsliu   886302 2009-11-20 14:15
> Human.FS003.R.SPHERICAL.73730.MWS.SPHERE_CYCLE4.coord
> -rw-r--r-- 1 tsliu tsliu     1522 2009-11-20 14:15
> Human.FS003.R.73730.spec
> -rw-r--r-- 1 tsliu tsliu   886303 2009-11-20 14:15
> Human.FS003.R.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.coord
> -rw-r--r-- 1 tsliu tsliu      315 2009-11-20 14:15
> Human.FS003.R.73730.register.spec
> -rw-r--r-- 1 tsliu tsliu   886380 2009-11-20 14:15
> deformed__sphere_cycle_1.coord
> -rw-r--r-- 1 tsliu tsliu   886457 2009-11-20 14:15
> deformed__sphere_cycle_2.coord
> -rw-r--r-- 1 tsliu tsliu   886534 2009-11-20 14:16
> deformed_Human.FS003.R.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.coord
> -rw-r--r-- 1 tsliu tsliu  3716510 2009-11-20 14:16
> deformed_Human.FS003.R.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.deform_field
> -rw-r--r-- 1 tsliu tsliu     1527 2009-11-20 14:21
> Human.FS003.L.73730.spec
>
> Fax: 517.353.1652
>     </pre>
>   </blockquote>
>   <pre wrap=""><!---->
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>   </pre>
> </blockquote>
> <br>
> <pre class="moz-signature" cols="72">
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