[caret-users] postborder script

Donna Dierker donna at brainvis.wustl.edu
Mon Nov 23 11:11:06 CST 2009


On 11/23/2009 10:44 AM, Taosheng Liu wrote:
> Donna,
>   I just re-downloaded your pre and post-border script and did this:
> $ grep Fiducial preborder.sh
> $ grep Fiducial postborder.sh
>
> Neither returned anything. I don't think there's any text string with 
> the name 'Fiducial' in it.  Maybe you have a new version of the script 
> that I'm not using? On lines 33-34 in postborder.sh, I see this:
>
>     FIDUCIAL=deformed_Human."$CASE.$HEM_FLAG".Midthickness_711-2B.coord
>     
> FIDUCIAL_MWS=deformed_Human."$CASE.$HEM_FLAG".Midthickness_711-2B.mws.coord
>
> I assume this is the actual name of the fiducial surface? 
Ah, yes -- you busted me.  The project on which I first used this script 
for production purposes was one in which the surfaces were generated 
using Caret, and they were named like *Fiducial*.  So the 
check_reg_ouptut script is tailored to that input.  The Fiducial just 
needs to be replaced with Midthickness.

Sorry that did not occur to me sooner.
> I'm attaching a spec file 
> (deformed_Human.FS006.L.73730.register.73730.spec). There's a bunch of 
> coord files.  The first one, 
> deformed_deformed_Human.FS006.L.Midthickness_711-2B.mws.73730.coord 
> looks like the one that's needed for check_reg_output? (why are there 
> two 'deformed',
The first (actually inner) deformed_ is from the downsampling step in 
preborder.sh (resample subroutine).  The second (outer) is the true 
registration step.
> I couldn't figure out from the postborder script. Also what is 
> mws?--medial wall smoothed?).
Good guess!
>
> Thanks for the pointer about borders being aligned. So I'd like to run 
> your check_reg_out script. Here's a listing from my PALS.B12.LR 
> directory (I've run postborder on two subjects). Thank you for your help.
>
> --ts
>
> tsliu at photon:/oldfmri/anat2/PALS_B12.LR$ ls -ltr
> total 41908
> -rw-r--r-- 1 tsliu tsliu 16777568 2009-11-04 14:52 TEMPLATE.LPI.nii
> -rwxr-xr-x 1 tsliu tsliu   557688 2009-11-05 15:07 TEMPLATE.check.RH.scene
> -rwxr-xr-x 1 tsliu tsliu   661921 2009-11-05 15:07 TEMPLATE.check.LH.scene
> -rwxr-xr-x 1 tsliu tsliu    14958 2009-11-05 15:07 TEMPLATE.areacolor
> -rwxr-xr-x 1 tsliu tsliu    12178 2009-11-05 15:12 border_color_key.jpg
> -rwxr-xr-x 1 tsliu tsliu     7316 2009-11-05 15:12 
> Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.RIGHT.FIDUCIAL.var1.border
> -rwxr-xr-x 1 tsliu tsliu     8139 2009-11-05 15:12 
> Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.RIGHT.FIDUCIAL.border
> -rwxr-xr-x 1 tsliu tsliu     7810 2009-11-05 15:12 
> Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.LEFT.FIDUCIAL.var1.border
> -rwxr-xr-x 1 tsliu tsliu     8673 2009-11-05 15:12 
> Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.LEFT.FIDUCIAL.border
> -rw-r--r-- 1 tsliu tsliu     3532 2009-11-05 16:51 
> ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor
> -rw-r--r-- 1 tsliu tsliu  2587758 2009-11-09 12:29 
> Human.sphere_6.73730.topo
> -rw-r--r-- 1 tsliu tsliu     1961 2009-11-09 12:29 
> TEMPLATE_REG-with-POP-AVG_4K_NoFid.deform_map
> -rw-r--r-- 1 tsliu tsliu   884991 2009-11-09 12:29 
> Human.sphere_6_forFIDUCIAL.73730.coord
> -rw-r--r-- 1 tsliu tsliu   884981 2009-11-09 12:29 
> Human.sphere_6.73730.coord
> -rw-r--r-- 1 tsliu tsliu      501 2009-11-09 12:29 
> Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec
> -rw-r--r-- 1 tsliu tsliu    10253 2009-11-09 12:29 
> Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.borderproj
> -rw-r--r-- 1 tsliu tsliu    25902 2009-11-11 11:22 Zeroes_711-2B.nii.gz
> -rw-r--r-- 1 tsliu tsliu    79321 2009-11-20 17:00 sanity.scene
> -rw-r--r-- 1 tsliu tsliu    20237 2009-11-20 17:34 
> deformed_Human.FS003.L.LANDMARKS.73730.borderproj
> -rw-r--r-- 1 tsliu tsliu  1476643 2009-11-20 17:34 
> deformed_Human.FS003.L.Initial.73730.surface_shape
> -rw-r--r-- 1 tsliu tsliu  1771641 2009-11-20 17:34 
> deformed_Human.FS003.L.73730.register.73730.deform_map
> -rw-r--r-- 1 tsliu tsliu   885299 2009-11-20 17:34 
> deformed_deformed_Human.FS003.L.Midthickness_711-2B.mws.73730.coord
> -rw-r--r-- 1 tsliu tsliu   886443 2009-11-20 17:34 
> deformed_Human.FS003.L.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.73730.coord
> -rw-r--r-- 1 tsliu tsliu    23055 2009-11-20 17:36 
> deformed_Human.FS003.R.LANDMARKS.73730.borderproj
> -rw-r--r-- 1 tsliu tsliu  1476643 2009-11-20 17:36 
> deformed_Human.FS003.R.Initial.73730.surface_shape
> -rw-r--r-- 1 tsliu tsliu  1771641 2009-11-20 17:36 
> deformed_Human.FS003.R.73730.register.73730.deform_map
> -rw-r--r-- 1 tsliu tsliu   885300 2009-11-20 17:36 
> deformed_deformed_Human.FS003.R.Midthickness_711-2B.mws.73730.coord
> -rw-r--r-- 1 tsliu tsliu   886444 2009-11-20 17:36 
> deformed_Human.FS003.R.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.73730.coord
> -rw-r--r-- 1 tsliu tsliu      894 2009-11-20 17:36 
> deformed_Human.FS003.R.73730.register.73730.spec
> -rwxr-xr-x 1 tsliu tsliu     2181 2009-11-20 17:38 check_reg_output.sh
> -rw-r--r-- 1 tsliu tsliu      915 2009-11-21 13:32 
> deformed_Human.FS003.L.73730.register.73730.spec
> -rw-r--r-- 1 tsliu tsliu    17875 2009-11-21 16:00 
> deformed_Human.FS006.L.LANDMARKS.73730.borderproj
> -rw-r--r-- 1 tsliu tsliu  1476643 2009-11-21 16:00 
> deformed_Human.FS006.L.Initial.73730.surface_shape
> -rw-r--r-- 1 tsliu tsliu  1771641 2009-11-21 16:00 
> deformed_Human.FS006.L.73730.register.73730.deform_map
> -rw-r--r-- 1 tsliu tsliu   885299 2009-11-21 16:00 
> deformed_deformed_Human.FS006.L.Midthickness_711-2B.mws.73730.coord
> -rw-r--r-- 1 tsliu tsliu   886443 2009-11-21 16:00 
> deformed_Human.FS006.L.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.73730.coord
> -rw-r--r-- 1 tsliu tsliu  1771641 2009-11-21 16:02 
> deformed_Human.FS006.R.73730.register.73730.deform_map
> -rw-r--r-- 1 tsliu tsliu    21447 2009-11-21 16:02 
> deformed_Human.FS006.R.LANDMARKS.73730.borderproj
> -rw-r--r-- 1 tsliu tsliu  1476643 2009-11-21 16:02 
> deformed_Human.FS006.R.Initial.73730.surface_shape
> -rw-r--r-- 1 tsliu tsliu   885300 2009-11-21 16:02 
> deformed_deformed_Human.FS006.R.Midthickness_711-2B.mws.73730.coord
> -rw-r--r-- 1 tsliu tsliu   886444 2009-11-21 16:02 
> deformed_Human.FS006.R.SPHERICAL.73730.MWS.SPHERE_CYCLE4.ALIGNED.73730.coord
> -rw-r--r-- 1 tsliu tsliu      894 2009-11-21 16:02 
> deformed_Human.FS006.R.73730.register.73730.spec
> -rw-r--r-- 1 tsliu tsliu      915 2009-11-21 16:13 
> deformed_Human.FS006.L.73730.register.73730.spec
>
> Donna Dierker wrote:
>> On 11/21/2009 03:26 PM, Taosheng Liu wrote:
>>   
>>> Thanks! It happens to be a working day for me. So I'll keep asking 
>>> questions :)
>>>
>>> I don't think my inability to run the check_reg_output is due to the 
>>> extra '=' issue, because I did that after fixing it. Anyway I just did 
>>> another brain from fresh (preborder, fix them by hand, and 
>>> postborder). I still don't see any file named like 
>>> deformed_Human.*Fiducial.mws.*coord anywhere. Maybe there's additional 
>>> processing that I'm not doing?
>>>     
>> Hmmm.  Perplexing.  The registration spec file fed to caret_command 
>> -surface-register-sphere-spec-only had to have a *Fiducial*coord, or 
>> else registration would have failed.  But the presence of 
>> deformed_Human.FS003.L.73730.register.73730.spec noted below suggests 
>> registration succeeded.  The deformed Fiducial coord is a standard 
>> output of registration, so that file should be somewhere.  And I do like 
>> to look at it as a sanity check of the registration results.
>>   
>>> In any case, I just want to know how to assess the results. So I 
>>> assume the following is reasonable too? I went to the ATLAS_DIR, which 
>>> is the PALS_B12.LR directory downloaded from your server.  I start the 
>>> GUI and open a spec file, say: 
>>> deformed_Human.FS003.L.73730.register.73730.spec
>>>
>>> There're two borderproj files: 
>>> deformed_Human.FS003.L.LANDMARKS.73730.borderproj and 
>>> Human_PALS_B12.LR.MEN_WOMEN.AVG-LANDMARKS_Core6.borderproj
>>>
>>> So the latter must be the border in the atlas space and I assume the 
>>> former is the deformed borders from my subject? They look pretty much 
>>> aligned on a surface. Does that mean it's ok then? I'm inserting a 
>>> screen shot here (with two sets of borders loaded):
>>>
>>>
>>>
>>>
>>>     
>> Yes, this is good, but it is also virtually guaranteed by the 
>> registration process:  It aligns the landmarks and lets what is in 
>> between flow to reduce distortion.  I prefer examining both the fiducial 
>> and depth map as a means of sanity checking registration results, but as 
>> I said earlier, if you're interested in fMRI, then examing the deformed 
>> metrics is a good idea, too.
>>
>> Could you send a listing of the PALS_B12.LR, post-registration?
>>   
>>> --ts
>>>
>>>
>>>
>>> Donna Dierker wrote:
>>>     
>>>> 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=""><!---->
>>>>> _______________________________________________
>>>>> caret-users mailing list
>>>>> <a class="moz-txt-link-abbreviated"
>>>>> href="mailto:caret-users at brainvis.wustl.edu">caret-users at brainvis.wustl.edu</a>
>>>>> <a class="moz-txt-link-freetext"
>>>>> href="http://brainvis.wustl.edu/mailman/listinfo/caret-users">http://brainvis.wustl.edu/mailman/listinfo/caret-users</a>
>>>>>
>>>>>   </pre>
>>>>>           




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