Re: [caret-users] pulse sequences nad handles

2003-10-02 Thread David Van Essen
On Thursday, October 2, 2003, at 10:26 AM, Carsten Poppinga wrote: hi, i've got a small question concerning surefit error correction manually: how is it possible that i've corrected handles to a total number of less than zero? The handle-counting algorithm implemented in SureFit

Re: [caret-users] talairached data

2003-10-21 Thread David Van Essen
The answer to the question is yes. Use the Map fMRI to Surface option in Caret, as described on p. 36 of Tutorial 1, to generate metric files for the human colin left and/or right hemispheres (plus the cerebellum if it is of interest). DVE On Tuesday, October 21, 2003, at 04:40 PM, Mark A.

[caret-users] Caret/SuMS Demo at SfN (Tues p.m., HBP booth)

2003-11-05 Thread David Van Essen
, or if you have questions/suggestions for John Harwell or myself. If you have colleagues who might be interested in an introduction to Caret and the atlases, please forward this email to them. David Van Essen, John Harwell

Re: [caret-users] atlas registration methods

2004-01-08 Thread David Van Essen
Mark, It is indeed a good idea to leave out the CCantToPOS landmark border on both the individual and the atlas. If you have good cingulate landmarks, the registration should be fine in this region. David On Jan 8, 2004, at 6:26 PM, Mark A. Pinsk wrote: David recommended that I do the

Re: [caret-users] surefit correcting residual errors

2004-06-02 Thread David Van Essen
Mark, DAVID or JOHN H: Although this is an occipital lobe, the cut face is further anterior than the demo volume, so there still is a substantial chunk of medial wall left (see calcarine.jpg below). Would you also cut along the medial wall, as well, in this case? I would be sure that the

Re: [caret-users] Topology clean-up for reconstruction from histological sections

2005-03-25 Thread David Van Essen
Ed, Donna's comments are (as usual) on the mark. I have several additional questions/comments. 1) What cortical layer do your contours represent? I'm guessing from your figure that they represent the pial surface, or something close to it. In that case, there is an inherent problem,

Re: [caret-users] caret 5.3 segmentation of mouse brain

2005-07-29 Thread David Van Essen
Brige, The SureFit segmentation algorithm was originally designed for segmenting T1-weighted MRI's of human cerebral cortex, plus other volume data that have similar shape and image intensity attributes. The fundamental requirements are that cortical gray matter be about 3 voxels thick and

Re: [caret-users] To all,

2005-08-23 Thread David Van Essen
Joe, If you're doing spherical registration to the PALS atlas, then the bordercolor file you want should be the following one that can be downloaded from SumsDB: ForSPHERICAL.REGISTRATION_Human.Class3.bordercolor http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=5993911 If that

Re: [caret-users] To all,

2005-08-23 Thread David Van Essen
Joe, You can have many topo files loaded at one time, and each coord file can be associated with its own topo file. If things don't look right, then use Surface: Topology: Assign Topology to Surface to make sure you have the desired matchup (e.g., cut topo for FLAT map). I'm guessing

Re: [caret-users] Re: Editing *.paint files

2005-09-04 Thread David Van Essen
Terry, On Sep 3, 2005, at 6:07 PM, Terry Sewards wrote: Hi, Is there a way in which areas can be removed from a *.paint file without converting the binary file to text and manually deleting the entries? Yes. There are two distinct options to choose from. 1) Based on border-drawing.

Re: [caret-users] Macaque atlas datasets

2005-10-14 Thread David Van Essen
from the user community helps us prioritize what aspects are most useful to concentrate on. David David Van Essen wrote: Hi Jochen, On Oct 13, 2005, at 4:58 PM, Jochen Ditterich wrote: Hi Donna and John, I was running into a strange observation when using the Surface Outline

Re: [caret-users] Misalignment between MRI and layer 4 surface model in macaque cortex datasets?

2005-10-13 Thread David Van Essen
Hi Jochen, On Oct 13, 2005, at 4:58 PM, Jochen Ditterich wrote: Hi Donna and John, I was running into a strange observation when using the Surface Outline function in Caret's MRI viewer. When applying it to your macaque cortex datasets there seems to be a relatively substantial

[caret-users] Re: Mapping regional (categorical) volume data to surfaces; average-fiducial vs multi-fiducial mapping

2005-10-26 Thread David Van Essen
-- -- *From:* David Van Essen [mailto:[EMAIL PROTECTED] *Sent:* Friday, October 21, 2005 9:36 PM *To:* Mike Fox *Cc:* Donna Hanlon; David Van Essen *Subject:* Re: visualization specs; MFM vs AFM Mike, On Oct 21, 2005, at 10:48 AM, Mike

Re: [caret-users] how to flatten a frontal lobe?

2005-11-04 Thread David Van Essen
Rishi, There is no generic 'best answer', and the choice of cuts depends on multiple factors, some related to visualization and others related to options for subsequent registration to an atlas. The first question is whether you need to make any cut at all. That depends on how large your

Re: [caret-users] Segmentation of partial hemisphere - addendum

2006-01-06 Thread David Van Essen
Roland, If your partial hemisphere does not include the anterior commissure, it will probably be important to DE-select the Disconnect Hindbrain, Disconnect Eye and Skull, Cut Corpus Callosum, and Fill Ventricles options, as these rely on stereotaxic coordinates relative to the AC. We

[caret-users] Re: log file

2006-01-08 Thread David Van Essen
:50, David Van Essen wrote: Roland, If your partial hemisphere does not include the anterior commissure, it will probably be important to DE-select the Disconnect Hindbrain, Disconnect Eye and Skull, Cut Corpus Callosum, and Fill Ventricles options, as these rely on stereotaxic coordinates relative

Re: [caret-users] Re: caret-users Digest, Vol 29, Issue 1

2006-02-06 Thread David Van Essen
Terry (et al.), Although the ECHDB is evidently defunct, the data sets you are interested in (plus much more) are available by alternate routes. The primary data sets are accessible at a website at the Zilles lab (and also one at McGill) that is indicated lower down in this message. In

Re: [caret-users] Re: caret-users Digest, Vol 29, Issue 3

2006-02-09 Thread David Van Essen
Terry, On Feb 9, 2006, at 11:37 AM, Terry Sewards wrote: In their description of the cytoarchitectonic map of area 2 Grefkes et al. (2001) show area 2 occupying the rostral bank of the postcentral sulcus, not extending into the fundus or caudal bank, but in the probabilistic maps area 2

Re: [caret-users] converting from freesurfer

2006-02-13 Thread David Van Essen
Aaron, Donna's email covers the key technical issues. I have some clarifications to add regarding the semantics of what we mean by the term 'fiducial' surface. We consider that the term 'fiducial' is applicable to ANY surface configuration that 'captures' the shape of a given

Re: [caret-users] Viewing ROIs

2006-02-14 Thread David Van Essen
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

Re: [caret-users] Re: Drawing borders on fiducial surface

2006-04-01 Thread David Van Essen
Terry, In Caret 5.3 you can draw 3-D borders on non-flat surfaces, using the Dimensions: 3D option in the Draw Borders dialog box. Instead of using the fiducial surface, a highly inflated surface works better (see below - and is easy to generate if you don't have one already). Make

Re: [caret-users] Re: caret-users Digest, Vol 31, Issue 3

2006-04-05 Thread David Van Essen
on fiducial surface (David Van Essen) --- -- - Message: 1 Date: Sat, 1 Apr 2006 22:36:15 -0700 From: Terry Sewards [EMAIL PROTECTED] Subject: [caret-users] Re: Drawing borders on fiducial surface To: caret-users@brainvis.wustl.edu

Re: [caret-users] posting - precentral sulcus as a landmark?

2006-04-09 Thread David Van Essen
Hi Jason, Donna's email nicely laid out our lab's perspective on several important issues regarding cortical landmarks and registration. I will amplify on a few aspects here. The issues that arise in considering whether the precentral sulcus may be a useful landmark are linked to the

Re: [caret-users] caret users group posting

2006-04-17 Thread David Van Essen
Jason, I suspect that somewhere along the line, the deformed left hemisphere surfaces got linked to an inappropriate topology file. However, the atlas spec file you used should be valid - It is a left-right hybrid target that is viewed with a right hemisphere topology. We have done

Re: [caret-users] Re: Deforming borderprojection files - macaque to PALS registration

2006-05-16 Thread David Van Essen
Terry et al., Donna's evaluations and recommendations regarding registration of the macaque to the PALS atlas are on track - it can indeed be done by a two-step procedure using existing deformation_map files. However, this brings home the point that it makes more sense to do a direct

[caret-users] Average depth maps; 3D variability maps ('DEPTHnr' corrected)

2006-05-25 Thread David Van Essen
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

Re: [caret-users] Reversing the polarity of the functional color scale bar in Caret

2007-03-03 Thread David Van Essen
Reza, There are several options to deal with your issue. 1) The easiest is probably to reverse the polarity of one of the datasets (metric file columns) using Attributes: Metric: Metric File Mathematical Operations: Multiply Column A by scalar. Choose the relevant column, multiply by

[caret-users] Stereotaxic foci meta-analyses

2007-07-31 Thread David Van Essen
Antonio et al., As Donna's email noted, we have substantially revamped the process of mapping stereotaxic foci onto the PALS atlas. The revised mapping methods are best accessed at http://sumsdb.wustl.edu/sums/stereotaxictocaretfoci.do or, equivalently, from: Tutorials: Converting

Re: [caret-users] CARET: MFM ?

2007-10-10 Thread David Van Essen
Brian, Your question gets at the heart of the differences between AFM (average fiducial mapping) and MFM (multi-fiducial mapping), which is discussed in my 2005 Neuroimage paper. In essence, the MFM value at a given node is the average of the value for the corresponding nodes in the 12

Re: [caret-users] Viewing multiple functional maps

2007-10-21 Thread David Van Essen
Alex, Stephanie, et al., 1) Stephanie's RGB suggestion provides one excellent option for you to check out. 2) Another set of options is to use the Surface: ROI window, which allows you flexibility in selecting various regions using data in a metric column. Then use the Surface ROI:

Re: [caret-users] Rhesus Macaque Cortical Partitioning

2007-11-20 Thread David Van Essen
Hamied, Donna is correct that Romanski et al is not one in our F99 atlas dataset. There are various other schemes that include auditory cortex and are available on our macaque F99 atlas (see Macaque.F99.RIGHT.DEMO.73730.spec in http://sumsdb.wustl.edu/sums/directory.do?

Re: [caret-users] listing clusters

2008-01-10 Thread David Van Essen
Christa-Lynn, Two comments. 1) Working from the menu options, you can use the Surface: Region of Interest window to do something that I think is close to what you want. Select your overall ROI. If, for example, you want everything except the medial wall, choose Selection Method: Nodes

Re: [caret-users] beginner question

2008-01-20 Thread David Van Essen
Jessica, On Jan 20, 2008, at 7:18 PM, jessica f cantlon wrote: I have a beginner's question about using caret to project foci to the PALS atlas. When I go to do that I get the message These foci do not have associated stereotaxic spaces: and it lists all of them, even though I have gone

[caret-users] Foci uncertainty limits using RGB paint files; changing foci colors

2008-01-21 Thread David Van Essen
Jessica, Answers to both questions: On Jan 21, 2008, at 10:04 AM, jessica f cantlon wrote: Thank you David...I started over and everything looks to be working now. Good! I was wondering if there is any info about how to estimate peaks as spheres and then flatten them. I saw an article

Re: [caret-users] data set

2008-01-21 Thread David Van Essen
Sofia, The link you showed worked for me this morning, so I am puzzled as to why you had a problem. Try the following link instead: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6588227 It is identical to the one you used except that it doesn't include the ':8081' port, and it

Re: [caret-users] Foci uncertainty limits using RGB paint files; changing foci colors

2008-01-23 Thread David Van Essen
be easier, and in any event it allows for post hoc adjustment of the colors. David thanks, jessica David Van Essen wrote: Jessica, Answers to both questions: On Jan 21, 2008, at 10:04 AM, jessica f cantlon wrote: Thank you David...I started over and everything looks to be working now

Re: [caret-users] constantly getting either Error in hind brain segmentation or segmentation fault

2008-02-24 Thread David Van Essen
Krishna, Caret's segmentation algorithm was originally generated for humans and has not yet been fully customized for the macaque. However, i would not expect the behavior you describe. Try uploading your dataset to http://pulvinar.wustl.edu/cgi-bin/upload.cgi Then let Donna Dierker

Re: [caret-users] Brodmann's areas 12 and 34

2008-03-10 Thread David Van Essen
Paul, On Mar 10, 2008, at 5:04 PM, Paul Rasser wrote: Could you please let me know why Brodmann's areas 12 and 34 were not included in the subdivision of the Human.colin atlas? Thanks, Paul Rasser Area 34 is in the medial hippocampal region (just anterior and medial to area 28) and is

Re: [caret-users] Communicating with AFNI

2008-03-15 Thread David Van Essen
Rishi, John's matrix-related comments appear to be on track, based on my superficial reading. But I wanted in particular to follow up on his comment about future support for Caret-AFNI communication. We set this up quite a few years ago when Caret didn't handle volume visualization.

Re: [caret-users] Question about paint regions modalities?

2008-04-24 Thread David Van Essen
Antoine et al., John's comments are on the mark. Subdividing cortex into different functional modalities is challenging to do in macaques, where there is a lot of experimental data, and even more difficult in humans. Nonetheless, because the issue is of obvious importance, I stuck my

Re: [caret-users] Translucent fiducial surface?

2008-06-29 Thread David Van Essen
Leeland, You can get translucency by converting to a vtk model using the Save option for the Caret coordinate file. This can also preserve surface coloration. I don't have a lot of experience with this, but John may be able to provide additional tips now that he is back from Australia.

Re: [caret-users] Translucent fiducial surface?

2008-06-29 Thread David Van Essen
not find it satisfactory. David VE On Jun 29, 2008, at 10:18 PM, David Van Essen wrote: Leeland, You can get translucency by converting to a vtk model using the Save option for the Caret coordinate file. This can also preserve surface coloration. I don't have a lot of experience

Re: [caret-users] Caret keeps crashing on mac os

2008-07-25 Thread David Van Essen
Joe, I don't know if you saw John Harwell's follow-up email, appended below, suggesting that Manish's problem was with an older version of OSX. Since yours is more recent, there is evidently a different problem. Unless other users have experienced this and found a solution, this will

Re: [caret-users] help mapping an SPM5 activation volume to a surface

2008-08-06 Thread David Van Essen
Amit, The answer to your question does depend a lot on whether you need the left and right hemisphere surfaces truly side-by-side in the same Caret window. If that is the case, then the links Donna pointed to are the preferred way to go. However, for many purposes, it is advantageous to

Re: [caret-users] Resampling a surface

2008-08-07 Thread David Van Essen
Andrew, To amplify on what Donna said about the Caret process. The closest that Caret software and atlases come to providing uniform resampling is through the use of our 'standard-mesh', 73,730-node spherical mesh:

Re: [caret-users] RGB paint option

2008-09-30 Thread David Van Essen
Hi Alireza, One more option to add to Donna's good summary. You can use Attributes: Metric: Convert Metric to RGB Paint. This brings up a reasonably self-explanatory popup window that allows you to assign one metric columns to the 'R' channel, another to the 'G' channel, and a third to

Re: [caret-users] MNI coordinate - additional information on stereotaxic foci

2008-10-27 Thread David Van Essen
Alireza, To expand on what Donna said, The foci and foci projection (fociproj) file types in Caret are likely to be useful for the needs that you describe. For example, if you enter the center of your ROI as a stereotaxic focus in an identified stereotaxic space, you can then project it

Re: [caret-users] too many crossovers

2008-11-19 Thread David Van Essen
Bela, Donna's comments are on the mark. Two additional points: 1) As you evaluate landmarks, use the 'Show First Link Red' option to make sure that landmarks are not only in a reasonable location relative to other landmarks but also are oriented consistently in the source and target

Re: [caret-users] Quick projection of foci?

2009-04-01 Thread David Van Essen
Alex, LayersFociEdit Foci Colors is one option for generating colors, but it is indeed tedious if you have more than a few to assign. A better way is to capitalize on a color-creation option that John recently implemented in Window - Caret Command Executor. Select COLOR FILE CREATE MISSING

Re: [caret-users] question for caret aka mapping AAL to PALS/colin

2009-04-01 Thread David Van Essen
Jinhui, The 73730-node (standard-mesh) colin surfaces are accessible in SumsDB. If you want just the coordinate files, select: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6154943 (archive_name=Human.colin.R.RegToPALS_B12.LR.FIDUCIAL.TLRC.711-2B. 71723.coord)

Re: [caret-users] Quick projection of foci?

2009-04-01 Thread David Van Essen
Not sure if this is because I might not have correctly-projected foci. Thanks again for your help, Alex On 01/04/2009 13:03, David Van Essen vanes...@brainvis.wustl.edu wrote: Alex, LayersFociEdit Foci Colors is one option for generating colors, but it is indeed tedious if you have more

Re: [caret-users] Quick projection of foci?

2009-04-01 Thread David Van Essen
/2009 14:00, David Van Essen vanes...@brainvis.wustl.edu wrote: Alex, 1) Did you turn on the foci view in Display Control - Foci Main? 2) What version of Caret are you using? I think it needs to be Caret 5.61. If this doesn't solve it, John will need to chime in as I'm off to a meeting

Re: [caret-users] Q) fiducial surface in '711-2C' space?

2009-04-07 Thread David Van Essen
Yune, I suggest you read the following for an explanation. On navigating the human cerebral cortex: response to 'in praise of tedious anatomy'. Van Essen DC, Dierker D. Neuroimage. 2007 Oct 1;37(4):1050-4; discussion 1066-8. Epub 2007 Sep 4. PMID: 17766148 David On Apr 7, 2009, at 8:26 AM,

Re: [caret-users] Q) why are some foci located out of the brain?

2009-04-08 Thread David Van Essen
YSL, Most of the foci at issue are in the cerebellum, which is not in view in your main window. If you project all foci to the 'PC-CC' (PALS- Cerebral, Colin-Cerebellar) atlas, then you will be able to see the cerebellar foci in relation to the cerebellar cortical surface. One focus does

Re: [caret-users] Does ? mean a broken font in the identify window?

2009-04-12 Thread David Van Essen
YSL, Basically, '???' means that there was no specific assignment for that node in that column of the paint file. Use Display Control: Page Selection: Paint Selection to see what was mapped for that particular column (e.g., the 4th column is probably visuotopic areas, which only cover a

Re: [caret-users] A question when mapping a functional volume to brain surface

2009-05-27 Thread David Van Essen
Dr. Wang, Donna's suggestions are good ones. Two other possibilities spring to mind. 1) Are you looking at the results of multi-fiducial mapping (chosen in the 'mapping atlas' window once you have selected the PALS_B12 atlas left or right hemiephere)? This gives substantially different

Re: [caret-users] MedialWall and BA40

2009-06-12 Thread David Van Essen
Traci, An addendum (actually an intercalation) to John's suggestion: On Jun 11, 2009, at 11:33 AM, John Harwell wrote: Traci, Select Attributes Menu-Paint-Assign Paint Names and Properties. Select the appropriate column in the Column Selection pulldown. This is a nice feature that lets

Re: [caret-users] PALS atlas labels to Freesurfer fsaverage

2009-10-19 Thread David Van Essen
and mapping algorithms. Ideally, these would be covered in a specific tutorial, but we won't have a chance to generate that for a while. I hope this helps. David From: David Van Essen vanes...@brainvis.wustl.edu Date: May 27, 2009 10:59:12 PM CDT To: Brad Dickerson br...@nmr.mgh.harvard.edu Cc

Re: [caret-users] way to go back to the original surface space after spherical registration

2009-12-28 Thread David Van Essen
Jidan, Here are additions to Donna's comments. On Dec 28, 2009, at 8:22 AM, Donna Dierker wrote: That is way too hard of a question on the Monday morning following a long weekend. ;-) Agreed - but your questions raise important issues. See further inline comments On 12/28/2009 02:55 AM,

Re: [caret-users] registering a deformed to an undeformed fiducial surface

2009-12-29 Thread David Van Essen
Jidan, On Dec 29, 2009, at 6:16 AM, z丹丹 wrote: Your asumption is right. Here is the analysis I wan t to do. I have a 3D fiducial surface , based on this fiducial surface ,let's say, template, I generated some simulated fiducial surface with some deformation, let's say subject. So

Re: [caret-users] strange coloring

2010-01-04 Thread David Van Essen
YSL, Two other options to try: 1) Select the palette PSYCH rather than PSYCH-NO-NONE, which differs only in how near-zero is handled. 2) Click on a node in the blue patch in question, and use the ID Window to determine what the actual metric value(s) are for those nodes in the metric column

Re: [caret-users] Problem segmenting macaque brain

2010-04-06 Thread David Van Essen
Jochen, Loading the segmentation volume plus the original MR volume should allow you to select: Volume: Segmentation: Edit Voxels. This lets you add missing parts to your heart's content. David On Apr 5, 2010, at 4:28 PM, Jochen Ditterich wrote: Thank you, Donna! I am apparently

Re: [caret-users] Question concerning contour drawing

2010-05-17 Thread David Van Essen
Matt, I found this previous posting: http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00203.html explaining you should not cross over cortical contours and not jump widely from one section to the next. Are these the only issues one should be worried about? Yes, basically.

Re: [caret-users] sulcal depth question

2010-07-05 Thread David Van Essen
Joost, In addition to Donna's pointers, check out: Van Essen, D.C., Dierker, D., Snyder, A., Raichle, M.E., Reiss, A., and Korenberg, J. (2006) Symmetry of cortical folding abnormalities in Williams syndrome revealed by surface-based analyses. J. Neuroscience 26:5470-5483 It shows how

Re: [caret-users] Calculating mid-thickness and accurately drawing borders

2011-01-18 Thread David Van Essen
Tristan, On Jan 17, 2011, at 6:56 AM, Tristan Chaplin wrote: Hi, I'm working on constructing brain models from histological sections with cortical areas demarcated. Until now we've been writing our own progrms to achieve this. I'd like to start to use Caret for more of this work so

Re: [caret-users] macaque F99 atlas and freesurfer

2011-01-18 Thread David Van Essen
Yang et al, A tutorial document and associated dataset for registering Freesurfer macaque datasets to F99 are available at the following URL: http://sumsdb.wustl.edu/sums/directory.do?id=8285961dir_name=FREESURFER-to-F99 For future reference, FREESURFER-to-F99 is a subdirectory of the TUTORIALS

Re: [caret-users] QT issue + tracer metric to regional area

2011-02-12 Thread David Van Essen
Hi Colin, Regarding (1), we will have a new Caret release this coming week. I'm not sure whether it's likely to help with your ubuntu problem, but Jon Schindler and/or Jon Harwell might have a clue. Regarding (2) you can use Surface: Region of Interest Operations, then select all nodes;

Re: [caret-users] Caret 5.616 Excel Sheets

2011-02-16 Thread David Van Essen
Also, if you have not yet projected the foci, they will not be visible unless a 'fiducial' surface is displayed in the main window. David VE On Feb 16, 2011, at 3:04 PM, Erin Reid wrote: David, First check to make sure you have Show Foci checked in the D/C menu: Foci Main page. If that is

Re: [caret-users] 73730 mesh

2011-04-09 Thread David Van Essen
Colin, Segmentation produces a 'native mesh' whose exact node number cannot be prespecified in Caret (or in other segmentation algorithms I know about). The 73,730-node mesh ('74k' in our latest lingo) arises from surface-based registration to an atlas - either the macaque F99 atlas (a 74k_f99

Re: [caret-users] Mirroring hemispheres and Landmark Vector Difference registration

2012-03-23 Thread David Van Essen
Tristan, Registering from a left hem source to a right hem target (or vice versa) should work for the LVD as well as the LPR algorithm. I've done it myself on multiple occasions. Importantly, your source and target spec files must have the correct hemisphere assignment. Check that

Re: [caret-users] 164k to fsaverage

2012-05-04 Thread David Van Essen
Sam, It is possible to carry out the conversion you desire in a single step. First, some clarifying comments. 1) What you call 'Caret 164k mesh' is what we call the '164k_fs_LR' mesh, to signify that it is derived from registering the fsaverage left hem (164k_fs_L mesh) and right hem

Re: [caret-users] paxinos reg

2012-05-09 Thread David Van Essen
Colin., http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293370archive_name=Macaque.PHT00.R.REGISTER-with-F99.41218.spec is a newly uploaded archive that contains the PHT00 with its native mesh. The paint colors are very different from those on the F99 atlas, and there may be some

Re: [caret-users] A question about FS-to-F99 tutorial

2012-05-22 Thread David Van Essen
Hello Nik, Here is the solution to the mystery: The tutorial as it currently runs expects the user to start with the right hemisphere (stated near bottom of p. 2). The file that you need for stage 1 of the left hemisphere is created during Stage 3 for the right hemisphere (see below). This

Re: [caret-users] stuck in FS-to-F99 tutorial Update Borders step

2012-07-18 Thread David Van Essen
Pablo, On a Mac, use 'Shift-click' to complete whatever edits you have started in border update. (It may be ctrl-click or something else on linux or a PC). This appiies to the erase, extend, or replace options. The 'Apply' button is what you need to press in order to get started in the

Re: [caret-users] Freesurfer Surface and Volume are not in register when shown in Caret

2012-07-20 Thread David Van Essen
Pablo, Registration to F99 should not be impacted by issues of scaling. (For example, it doesn't affect our monkey-to-human registration despite large scale differences.) But if you want to rescale just for the sake of veridical representation, you can use caret_command

Re: [caret-users] caret-users Digest, Vol 106, Issue 18

2012-07-21 Thread David Van Essen
. Re: part of a surface (David Van Essen) 3. Re: Freesurfer Surface and Volume are not in register when shown in Caret (Pablo Polosecki) 4. Re: Freesurfer Surface and Volume are not in register when shown in Caret (David Van Essen) -- Forwarded message

Re: [caret-users] A precuneus cluster disappeared after surface projection

2012-09-16 Thread David Van Essen
Hello Dale, If Donna's explanation is correct (as I suspect is the case), you may have better results using the Conte69 atlas surface that is registered to the FNIRT MNI152 volume, In general, we are encouraging investigators to migrate to this atlas for a number of reasons, including the

Re: [caret-users] Human to Macaque registrations

2012-09-22 Thread David Van Essen
Tristan, I have uploaded to SumsDB a file that should be what you want. However, it is caveat emptor, as I do not have time at the moment to validate it. Please let me know if it works properly for you. David VE

Re: [caret-users] Customized colormaps

2012-12-19 Thread David Van Essen
Hi Arman, Use Attributes: Palette: Edit to modify an existing palette (and rename it) or to generate a completely new palette. If you like it, be sure to save the palette file, and to include it when saving scenes of datasets you want to quickly reload. David On Dec 18, 2012, at 11:45 AM,

Re: [caret-users] contours

2013-05-07 Thread David Van Essen
Colin You can reconstruct contours from any sectioning plane into a surface. But I believe the z axis will be that between sections, so you will need to rotate appropriately at the end. A white matter surface sill be fine as long as the topology doesn't get messed up by thin gyral blades.

Re: [caret-users] plot arrows on caret ROIs?

2013-07-10 Thread David Van Essen
Hi Nan, To view multiple surfaces and surface views in one window, I suggest you switch from Caret5 to Connectome Workbench, which has many features not available in Caret. Start by downloading Workbench: http://www.humanconnectome.org/connectome/get-connectome-workbench.html Import your

Re: [caret-users] mapping fMRI maps generated in freesurfer - accessing interatlas deformation maps

2013-11-08 Thread David Van Essen
Shahin et al., In the SumsDB database you can go to http://sumsdb.wustl.edu/sums/directory.do?id=8291757dir_name=Inter-atlas_deformation_maps and download http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293223archive_name=inter-atlas_deformation_maps.zip The

Re: [caret-users] Surface paint displays on the opposite surface side

2014-05-09 Thread David Van Essen
To all, I think the key distinction may be whether the 'foreground' and 'background' surfaces are on opposite sides of the origin. (John Harwell can correct me if I'm wrong.) A surface can be translated so that its center of gravity is at the origin in order to achieve that end. David On

Re: [caret-users] Brodmann areas 13-16 - Insular cortex

2014-06-18 Thread David Van Essen
Hello Milan, Years ago, I generated the Brodmann surface-based maps in Caret by manually estimating areal boundaries on a surface-based atlas using as a reference the classical Brodmann drawing of a right hemisphere (reprinted in Polyak, 1947). Because this illustration did not include

Re: [caret-users] Hi res recon

2014-10-14 Thread David Van Essen
Alternatively, you may find that FreeSurfer will work better for your current needs. Matt Glasser and others have gotten it to work reasonably well on macaque structural images. David On Oct 15, 2014, at 2:38 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Aditya, On monkeys, yes.

[caret-users] Registration remains open (but time is short!) for the 2015 HCP Course!

2015-05-14 Thread David Van Essen
Organizers David Van Essen PI, Human Connectome Project Jennifer Elam, Ph.D. Outreach Coordinator, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 el...@pcg.wustl.edu

[caret-users] Register for the 2015 HCP Course: Exploring the Human Connectome

2015-04-01 Thread David Van Essen
and existing users of HCP data, methods, and tools, and will cover both basic and advanced topics. Faculty listings and the full schedule of covered topics, more info, and register on the HCP Course website. We hope to see you in Hawaii! Best, 2015 HCP Course Organizers David Van Essen, Jenn Elam

[caret-users] Minor addendum to: Unable to reach http://sumsdb.wustl.edu/sums/

2017-02-07 Thread David Van Essen
/zip_targz_tgzCARET.QUICK-START.03-06.tar.gz/568256_info.html but the correct URL can be achieved by inserting a single ‘/‘ between ‘tgz’ and 'CARET’ : http://brainvis.wustl.edu/sumsdb/zip_targz_tgz/CARET.QUICK-START.03-06.tar.gz/568256_info.html > On Feb 7, 2017, at 6:47 PM, David Van Essen <

Re: [caret-users] How to transform freesurfer frmi maps to caret version?

2016-09-22 Thread David Van Essen
To all, 1) For mapping FreeSurfer data to ‘fs_LR’ (Conte69) space we now recommend using a streamlined process described in: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP? and the Resampling-FreeSurfer-HCP.pdf

Re: [caret-users] CARET Tutorial problem

2017-03-01 Thread David Van Essen
e CARET_TUTORIAL_SEPT06.zip dataset at > http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030 > <http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030> > Could I download the dataset from other link? > Thank you! > > Muchen On Feb 7, 2017, at 6:47 PM, Dav

Re: [caret-users] info in the deformation maps

2017-10-20 Thread David Van Essen
Hi Tony et al. John’s explanation regarding deformation map files is correct. Here, I’m drawing to your attention the fact that Connectome Workbench (and wb_command) provides improved methods for mapping from one surface mesh that has been registered to another (see below). Depending on your