RE: [caret-users] Average depth maps; 3D variability maps ('DEPTHnr' corrected)
Great. Thanks for the links!
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
National Neuroscience Facility
The University of Melbourne
Levels 2 3, Alan Gilbert Building
161 Barry St
Carlton South Vic 3053 Australia
Ph:+61 3 8344 1624
Fax: +61 3 9348 0469
email: [EMAIL PROTECTED]
-Original Message-
From: [EMAIL PROTECTED] on behalf of David Van Essen
Sent: Fri 5/26/2006 11:25 AM
To: Caret, SureFit, and SuMS software users
Subject: [caret-users] Average depth maps;3D variability maps ('DEPTHnr'
corrected)
Alex et al.,
The 3-D variability maps for both left and right hemispheres are
available at:
http://sumsdb.wustl.edu:80/sums/archivelist.do?archive_id=6478157
Human.PALS_B12.LR.B_1-12.BOTH-DEPTHnr_LoContrastAVG_StdDev_3D-
Variability.73730.surface_shape
These are from a much larger data set associated with our recently
published Williams Syndrome paper (http://www.jneurosci.org/cgi/
content/full/26/20/5470).
Two aspects of these sulcal depth maps merit specific comment.
1) The intensity range for the sulcal depth maps has been adjusted to
generate a 'low contrast' (by setting the limits from -20 to +60
instead of the ususal -10 to +30), as this makes for a more muted
background when other data are superimposed. The standard contrast
can be restored by changing the limits (in Surface shape: Settings)
2) These sulcal depth maps have been corrected for a glitch in our
original depth-calculation algorithm that had led to spurious depth
values in a very restricted portion of the Sylvian Fissure. (See
Spring 2006 Sulcal Depth Algorithm Enhancement - http://
brainvis.wustl.edu/help/depthnr.html - web page. Anyone doing sulcal
depth morphometry should read this page and contact [EMAIL PROTECTED]
regarding problems and questions.) The name 'DEPTHnr' is a shorthand
for 'Depth - normals-respecting' and has been applied to our various
individual and population-average sulcal depth files that contain
this correction.
3) FYI, this file and other files of this ilk can be found in SumsDB
using its search capabilities even without knowing the full file
name. For example, searching for a 'surface_shape' file containing
the text string 'PALS' yields a list of several dozen files meeting
the search criteria, from which I selected this one based on its
descriptive name.
4) Donna is correct that the 3-D variability maps should differ only
slightly for PALS surfaces in different stereotaxic spaces. The
same goes for maps of depth variability. But if such nuances are of
interest to you, it is indeed straightforward to regenerate them if
you have the individual fiducial surfaces in the appropriate space
David VE
On May 25, 2006, at 8:29 AM, Donna Dierker wrote:
On 05/25/2006 03:27 AM, Fornito, Alexander wrote:
Never mind again!
I found the surface_shape files in the tutorial, but there only
seems to be the right hemisphere ones. I'm particularly interested
in the 3D variability maps for the PALS atlas (left and right).
3D variability -- not depth variability, right? This shape file
has both left and right hem 3D variability:
Human.PALS_B12.LR.B_1-12.BOTH-DEPTHnr_LoContrastAVG_StdDev_3D-
Variability.73730.surface_shape
http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6486399
It has these columns:
LoContrast AVERAGE B1-12 RIGHT DEPTH
3D VARIABILITY - RIGHT_HEM Human.PALS_B12
LoContrast AVG DEPTH B1-12 LEFT (Women + Men)
3D VARIABILITY - LEFT_HEM Human.PALS_B12
If you don't have the left hemispher map handy, is there anyway
that I'd be able to generate one myself?
The 3D variability is generated using Surface: Create Average
Coordinate File, and checking the Create Sample Standard
Deviation. Just make sure you choose the right coord files (e.g.,
don't mix left and right hems). If you're averaging native
coordinates, then expect much higher deviation than if you're
averaging AC-PC aligned, or better yet some scale-controlled space
(Talairach, icbm*, or 711-2*).
Also, does it matter what space the PALS atlas is in when viewing
the variability map? There seems to be only one surface_shape file
in the tutorial.
We only generated these measures on the 711-2C surfaces (the ones
we originally segmented). I wouldn't expect significant
differences using the other spaces, although the SPM ones use
nonlinear volume registration methods, so those differences might
be vary. Try it and let us know whether you think the differences
are worth worrying about.
Sorry about all the emails anhd thanks again,
Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
National Neuroscience Facility
The University of Melbourne
Levels 2 3, Alan Gilbert Building
161 Barry St
Carlton South Vic 3053 Australia
Ph:+61 3 8344 1624
Fax: +61 3
RE: [caret-users] Mapping foci
Ok, let me see if I got this right... 1 - I loaded the Human.PALS_B12.LR.MULTI-FIDUCIAL_SPM2_fMRI-MAPPER.B1-12.LEFT.73730.spec file from the caret/data_files/fmri_mapping directory and loaded all the coord files 2 - I created the average using Surface Average coord file and requested the standard deviation surface_shape file. 3 - I exited and reloaded the average coord file and surface_shape file. Compared to the 711-2C map, there seems to be a fair amount more variability with SPM2 (I tried to attach pics, but the messgae was to big for the list). Just wandering why this would be the case. From what I understand, the SPM2 normalization routine begins with an affine transformation, followed by a linear combination of basis functions to model nonlinear shape differences. In contrast, it seems the 711-2C stops at the affine registration. Could the greater variability in the SPM2 image result from the greater warping involved through the use of the additional basis functions? One other thing I'd like to clarify; are the surfaces for the SPM2 and 711-2C PALS atlases created after the volumes were initially registered to their repsective templates, or was some transform applied directly to the surfaces after they were reconstructed in native space? Therefore, do the maps correspond to the SD of distance each voxel moves during normalization, mapped onto the corresponding surface node, or the distance moved at some other stage? Thanks again for your help! Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] on behalf of Donna Dierker Sent: Thu 5/25/2006 11:29 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Mapping foci On 05/25/2006 03:27 AM, Fornito, Alexander wrote: Never mind again! I found the surface_shape files in the tutorial, but there only seems to be the right hemisphere ones. I'm particularly interested in the 3D variability maps for the PALS atlas (left and right). 3D variability -- not depth variability, right? This shape file has both left and right hem 3D variability: Human.PALS_B12.LR.B_1-12.BOTH-DEPTHnr_LoContrastAVG_StdDev_3D-Variability.73730.surface_shape http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6486399 It has these columns: LoContrast AVERAGE B1-12 RIGHT DEPTH 3D VARIABILITY - RIGHT_HEM Human.PALS_B12 LoContrast AVG DEPTH B1-12 LEFT (Women + Men) 3D VARIABILITY - LEFT_HEM Human.PALS_B12 If you don't have the left hemispher map handy, is there anyway that I'd be able to generate one myself? The 3D variability is generated using Surface: Create Average Coordinate File, and checking the Create Sample Standard Deviation. Just make sure you choose the right coord files (e.g., don't mix left and right hems). If you're averaging native coordinates, then expect much higher deviation than if you're averaging AC-PC aligned, or better yet some scale-controlled space (Talairach, icbm*, or 711-2*). Also, does it matter what space the PALS atlas is in when viewing the variability map? There seems to be only one surface_shape file in the tutorial. We only generated these measures on the 711-2C surfaces (the ones we originally segmented). I wouldn't expect significant differences using the other spaces, although the SPM ones use nonlinear volume registration methods, so those differences might be vary. Try it and let us know whether you think the differences are worth worrying about. Sorry about all the emails anhd thanks again, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Fornito, Alexander Sent: Thu 5/25/2006 1:10 PM To: Caret, SureFit, and SuMS software users; Caret, SureFit, and SuMS software users Subject: RE: [caret-users] Mapping foci Never mind, I found it. Its a separate coord file - right? Are there any surface-shape files for depth hidden anywhere, or do I generate that myself? Thanks again, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] on behalf of Donna Dierker Sent: Tue 5/23/2006 12:45 AM To: Caret, SureFit
RE: [caret-users] Mapping foci
Never mind, I found it. Its a separate coord file - right? Are there any surface-shape files for depth hidden anywhere, or do I generate that myself? Thanks again, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] on behalf of Donna Dierker Sent: Tue 5/23/2006 12:45 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Mapping foci Hi Alex, Just a few things to add to John's replies: * Why are you using Colin instead of PALS? Unless you have a very specific reason to use Colin, I would use the PALS_B12 atlas for this purpose. In this case, you would use the average fiducial corresponding to the stereotaxic space. You will find several of them in your $CARET_HOME/data_files/fmri_mapping_files subdirectory. This page describes the methods used for normalizing the 12 Buckner brains to the various spaces: http://brainvis.wustl.edu/help/pals_volume_normalization/ * The above link also explains how FLIRT, SPM2, and SPM99 use the same template/target, but the methods produce subtle differences (http://brainvis.wustl.edu/help/mni305_diffs/arch_diffs_mni305.html) -- enough so that David felt it was worth having separate surfaces. I tried to talk him out of it, mostly because I'm lazy.;-) (Notice there is no SPM5 version yet.;-) * The AFNI coords are the only ones we have in true Talairach space, so yes -- these are the ones to use for mni2tal'd coordinates. * I know nothing about SPM96, but the spm_templates.man file in my SPM2 distribution contains this helpful excerpt: % In SPM96, we released a single subject brain for use as a % template. Although the MNI gave us this data, they never % recommended that this brain should be used as a stereotaxic % standard. This is something that we at the FIL chose to do. % The official standard for the ICBM stereotactic space is % the MNI305 brain - which this was not. This brain has many % merits for simulation but it suffers from all the single % brain criticisms that apply to Talairach. In this release, the % single subject T1 has been replaced by a 152 subject average. We % (in the SPM group) chose to use the 152 subject T1-weighted % average rather than the 305 brain average because there are also % T2-, and PD-weighted images of the same subjects. This should % allow much more flexibility in the range of different MR % contrasts that can be spatially normalized to the same % stereotaxic space (by registering to a linear combination of % template images). On 05/22/2006 08:55 AM, John Harwell wrote: Alex, When mapping foci using the Map Stereotaxic Focus Dialog, the focus entered is projected using the fiducial surface displayed in the main window. So, the main window surface must be in the same stereotaxic space as the focus that is being mapped. The stereotaxic space entry on the Map Stereotaxic Focus dialog is a meta-data entry for now. Map foci as follows: 1) As needed, change the fiducial surface in the main window so that it is in the appropriate stereotaxic space for the focus currently being mapped. It is okay to load multiple fiducial surfaces in Caret. 2) Save the foci projection file. 3) Exit Caret. 4) Start Caret. 5) Reopen the spec file and choose the foci projection file just saved and choose only one of the fiducial surfaces. Since the foci projection file stores the foci relative to a triangle in the surface, the foci will be approximately transformed from the other stereotaxic spaces. Good Luck. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On May 22, 2006, at 12:36 AM, Fornito, Alexander wrote: Hi, I'd like to map some foci from past studies onto the Colin surface. I've noticed that there seems to be 2 options for selecting co- ordinate type during this process; 1 - when loading the Colin spec file, there is the option of choosing the SPM99, SPM2, etc fidcucial surface. 2 - in the 'studies' tab of the 'map stereotaxic focus' dialog, it is possible to choose the stereotaxic space used in the study. Just want to check that I've got this right: If I chose the Colin fiducial to be SPM2, then that means the surface has been registered to SPM2 template space. If I want to map the focus of a study that used SPM99 space, will choosing SPM99 in the 'map stereotaxic focus' dialog automatically convert the coords so
RE: [caret-users] Viewing ROIs
That did the trick. Thanks John. I've noticed that caret_file_convert can be used to convert functional files to metric files. Can it be used for converting Caret paint files into freesurfer label files? I couldn't see if any flags that might indicate so. Also, are there any command line utilites for inflating a surface? Thanks again, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] on behalf of John Harwell Sent: Thu 16/02/2006 1:36 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Viewing ROIs Alex, Yes, it is possible to export paint data into free surfer label files. Choose Export File from the File Menu. On the Export Data File dialog, set the File Type to Free Surfer Ascii Label File as Paint (*.label). At the bottom of the dialog is a section titled Export Selections that allows selection of a surface. For an unknown reason, Free Surfer also stores coordinates in the label file. Enter a name for the file name but be aware that this file name is not used. After pressing the OK button, you will be asked to choose the Paint File Column that is to be exported. Select the column and press the OK button. For each name in the paint column, a label file will be created. For instance if the paint column contains nodes identified as SULCAL and GYRAL, two label files will be created, SULCAL.label and GYRAL.label. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Feb 14, 2006, at 11:34 PM, Fornito, Alexander wrote: Thanks for the tip. On another issue; I've noticed its possible to import freesurfer label files into Caret. Is it possible to do the reverse, i.e., export a paint file as a freesurfer label file? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users winmail.dat
RE: [caret-users] Viewing ROIs
Thanks for the tip. On another issue; I've noticed its possible to import freesurfer label files into Caret. Is it possible to do the reverse, i.e., export a paint file as a freesurfer label file? Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] on behalf of David Van Essen Sent: Wed 15/02/2006 2:25 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Viewing ROIs Alex, One more tidbit: It occasionally happens that a coordinate file has an incorrect hemisphere assignment. The easiest way to fix this is to re-save the coord file and reassign the hemisphere at the time of re-saving. You can also text-edit the spec file. David Also, how and when do I run the script for adding the hem flag to the spec file? I created my surfaces using the command line utlity.Maybe I've done something wrong? My commands are below. I've also noticed that alothough my left surface comes up in the correct orientation, Caret confuses the medial and lateral surfaces for my right hemispheres; when I press L it takes me to the medial view, and when I press M it takes me to the lateral view. All other viewing conrtols seem to be correct. ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
RE: [caret-users] Viewing ROIs
Ok, I had a look under attributes and I saw the ROI I created, so I assume this is correct. I tried to create a new ROi under the attributes area color tab named ???. This got rid of the WARNING: Paint names with no corresponding area colors:??? in the shell but it highlighted the rest of the brain (outside the ROI).I could still not visualize my ROI. I've also noticed that in cases where I can visualize the ROI, only exposed nodes are highlihted; nodes in the sulcal depths are not highlighted. I created my surfaces using the command line utlity.Maybe I've done something wrong? My commands are below. I've also noticed that alothough my left surface comes up in the correct orientation, Caret confuses the medial and lateral surfaces for my right hemispheres; when I press L it takes me to the medial view, and when I press M it takes me to the lateral view. All other viewing conrtols seem to be correct. LEFT: /usr/local/caret/bin/caret_file_convert -sc -is FSS lh.white.asc -os CARET 101.lh.white.coord 101.lh.closed.topo RAW CLOSED -spec 101.lh.spec -hem LEFT /usr/local/caret/bin/caret_file_convert -sc -is FSS lh.pial.asc -os CARET 101.lh.pial.coord 101.lh.closed.topo RAW CLOSED -spec 101.lh.spec -hem LEFT /usr/local/caret/bin/caret_command -surface-average 101.lh.FIDUCIAL.coord 101.lh.white.coord 101.lh.pial.coord /usr/local/caret/bin/caret_command -volume-create 256 256 256 -128 -128 -128 1 1 1 RIA 101_segvol.hdr /usr/local/caret/bin/caret_command -surface-to-segmentation-volume 101.lh.FIDUCIAL.coord 101.lh.closed.topo 101_segvol.hdr /usr/local/caret/bin/caret_command -surface-identify-sulci 101.lh.spec left 101_segvol.hdr 101.lh.closed.topo 101.lh.FIDUCIAL.coord 101.lh.FIDUCIAL.coord RIGHT: /usr/local/caret/bin/caret_file_convert -sc -is FSS rh.white.asc -os CARET 101.rh.white.coord 101.rh.closed.topo RAW CLOSED -spec 101.rh.spec -hem RIGHT /usr/local/caret/bin/caret_file_convert -sc -is FSS rh.pial.asc -os CARET 101.rh.pial.coord 101.rh.closed.topo RAW CLOSED -spec 101.rh.spec -hem RIGHT /usr/local/caret/bin/caret_command -surface-average 101.rh.FIDUCIAL.coord 101.rh.white.coord 101.rh.pial.coord /usr/local/caret/bin/caret_command -volume-create 256 256 256 -128 -128 -128 1 1 1 RIA 101_segvol.hdr /usr/local/caret/bin/caret_command -surface-to-segmentation-volume 101.rh.FIDUCIAL.coord 101.rh.closed.topo 101_segvol.hdr /usr/local/caret/bin/caret_command -surface-identify-sulci 101.rh.spec right 101_segvol.hdr 101.rh.closed.topo 101.rh.FIDUCIAL.coord 101.rh.FIDUCIAL.coord Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] on behalf of John Harwell Sent: Tue 14/02/2006 5:43 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Viewing ROIs On Feb 13, 2006, at 1:13 AM, Fornito, Alexander wrote: Hi, I seem to be able to view manually drawn ROIs with variable consistency, and its causing me a bit of confusion. For example, in the right hemisphere of one of my subjects, I draw the ROI using LayersBordersDraw Border. I then save the area color file and paint file, and when I check the paint row in the D/C, I can see the ROI I drew. If I repeat this process in the left hemisphere, I can't see it and the shell I'm running Caret from returns the message: WARNING: Paint names with no corresponding area colors: ??? I'm not sure why the same process would work for one hemisphere and not the other. Note this also happens if I exit Caret and try to re- load the area color and paint files. Any help is much appreciated. Thanks, Alex Alex, When you assign a paint area, nodes that have not been identified by the user are given the name ??? which implies that the nodes' identities are unknown. The WARNING message is produced because there is no color available for nodes with identity ???. You can eliminate this message by adding a color for ??? by selecting Edit from the Attributes:Area Colors menu. The lack of a color for ??? should not affect the drawing of ROIs. On the Surface:Region of Interest Dialog, make sure that you see nodes appear in green after pressing the Select Nodes pushbutton to select your region. When assigning the paint identifier, be sure to provide a name for the nodes before pressing the Assign pushbutton. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman
