[caret-users] Re: Script to streamline import of Freesurfer surfaces -- revised

2006-03-03 Thread Donna Dierker
Hi caret-users, Three things: 1. *h.white -- not *h.smoothwm: The initial version of this script averaged the Freesurfer smoothwm and pial to generate a mid-thickness fiducial. On Feb 23, 2006, Bruce Fischl wrote to David Van Essen: I also kept meaning to mention to you that the

Re: [caret-users] caret list posting query

2006-03-29 Thread Donna Dierker
Hi Jason, Which part of the five page Methods section didn't you understand? ;-) Seriously, though, was there a step or two that seemed particularly opaque? Here is my readers' digest condensed version: * Register each structural volume to wustl.edu's 711-2C space via affine transform

Re: [caret-users] caret list posting query

2006-03-29 Thread Donna Dierker
I need to qualify something I said below: On 03/29/2006 08:12 AM, Donna Dierker wrote: Hi Jason, Which part of the five page Methods section didn't you understand? ;-) Seriously, though, was there a step or two that seemed particularly opaque? Here is my readers' digest condensed version

Re: [caret-users] Macaque Segmentation

2006-03-29 Thread Donna Dierker
The only difference that comes to mind is the voxdims. Resampling your macaque structural to cubic 0.5mm rather than cubic 1.0mm tends to work best (although I've seen 0.75mm work well). You definitely do NOT want to resample to cubic 1.0mm for monkeys. On 03/29/2006 09:53 AM, Faden, Eric

Re: [caret-users] Macaque Segmentation + AC/PC Align

2006-03-29 Thread Donna Dierker
used to be. Any thoughts on what this is? or what is a good way to AC/PC align my volume? -Eric -Original Message- From: Donna Dierker [mailto:[EMAIL PROTECTED] Sent: Wed 3/29/2006 10:58 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Macaque Segmentation

Re: [caret-users] posting

2006-03-29 Thread Donna Dierker
Hi Jason, Sounds like some catastrophic problem. First, are you using the atlas target dataset cited here: http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html Second, check your landmark border polarity. Third, while handles are unlikely to cause holes in the cusrface,

Re: [caret-users] Macaque Segmentation

2006-03-31 Thread Donna Dierker
Hi Eric, Based on what you describe, you probably have some non-uniformity in your volume that bias correction may help. I use FSL's fast for this purpose (which uses BET as preprocessing), but there are many other options (e.g., MNI's nu_correct and AFNI's 3dUniformize). You can upload

Re: [caret-users] posting

2006-04-07 Thread Donna Dierker
Hi Jason, Dr. Van Essen and I just discussed your question, and we'd like more information about what you're trying to do. Often, there are easier ways to accomplish goals than posters envision. But to answer your question directly, no -- there are no published materials for adapting the

Re: [caret-users] help needed

2006-04-11 Thread Donna Dierker
Hi Shantanu, From your registration, I see you are using Windows XP. You will need Winzip or some other software that can extract zip archives. We typically extract the file caret_distribution.v5.33.windows.zip to the C: drive. When it extracts, it will create a caret folder under your C:

Re: [caret-users] help needed

2006-04-19 Thread Donna Dierker
Hi Binyam, See inline responses below. On 04/18/2006 06:28 PM, Binyam Nardos wrote: Dear Caret support, Just started using Caret and I have what might be some elementary questions for you. I have been trying to make the central sulcus landmark appear in my fiducial and inflated surfaces

Re: [caret-users] posting

2006-04-19 Thread Donna Dierker
/19/2006 08:01 AM, Donna Dierker wrote: On 04/18/2006 03:50 PM, Jason D Connolly wrote: Dear David and Donna, I re-ran the left hemisphere deformation and I noticed that the deformed flat maps look alright. It is only the fiducial, inflated and spheres that are black. Make a fordonna

Re: [caret-users] posting reply for Donna

2006-04-20 Thread Donna Dierker
Jason: See inline replies below. On 04/19/2006 04:40 PM, Jason D Connolly wrote: Dear Donna, I have uploaded the .spec file containing the black inflated, fiducial and spherical left hemisphere datasets. The file is a tar.gz format labelled fordonna. Thank you again for your help. We are

Re: [caret-users] help needed

2006-04-26 Thread Donna Dierker
Hi Shantanu, There are a couple of ways to do this. If you're lucky enough to have access to either a ROI or functional volume (e.g., AFNI +tlrc or FSL/SPM avg152 space group statistical output maps), then you can map them onto the PALS atlas using the procedure outlined in the PALS_B12

Re: [caret-users] 2D Cell Coordinates

2006-04-27 Thread Donna Dierker
Hi Ed -- see inline replies below. On 04/27/2006 02:28 PM, Edward Craft wrote: Hi, I would like to extract the 2D flat-map coordinates of cells that were projected onto a 3D reference surface. Is there a way to save the 2D coordinates directly from within Caret, or will I need to compute them

Re: [caret-users] Re: MNI, Talairach, and other coordinate systems

2006-05-05 Thread Donna Dierker
specific than Re: Contents of caret-users digest... Today's Topics: 1. Re: help needed (shantanu ghosh) 2. Re: help needed (Donna Dierker) -- Message: 1 Date: Wed, 26 Apr 2006 10:35:58 +0100 (BST) From: shantanu ghosh [EMAIL

Re: Rif: Re: [caret-users] Re: MNI, Talairach, and other coordinate systems

2006-05-05 Thread Donna Dierker
Carducci PhD University of Rome La Sapienza Dept. Human Physiology and Pharmacology *Donna Dierker [EMAIL PROTECTED]* Inviato da: [EMAIL PROTECTED] 05/05/2006 08:21 EST Per favore, rispondere a Caret, SureFit, and SuMS software users Per: Caret, SureFit, and SuMS software users caret-users

Re: [caret-users] Re: Deforming borderprojection files

2006-05-12 Thread Donna Dierker
Hi Terry, You're in territory I fear to tread. I've never done a cross-species registration myself, but in theory it's doable. Like you, I'm guessing the route from PALS_B12 to F99UA1 will be through Colin. If you search http://sumsdb.wustl.edu/sums/index.jsp for filename F99UA1 and file

Re: [caret-users] Mapping foci

2006-05-22 Thread Donna Dierker
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.

Re: [caret-users] Mapping foci

2006-05-25 Thread Donna Dierker
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

Re: [caret-users] [SPAM] posting

2006-05-31 Thread Donna Dierker
Hi Jason, Not everyone knows about these handy command line utilities: /146Gb/caret_distribution/caret/bin/caret_copy_spec /146Gb/caret_distribution/caret/bin/caret_map_fmri /146Gb/caret_distribution/caret/bin/mpeg_encode /146Gb/caret_distribution/caret/bin/mpeg_play

Re: [caret-users] [SPAM] posting

2006-06-05 Thread Donna Dierker
Thank John Harwell for the handy dandy feature: caret_command -surface-deformation-apply The attached script calls this command on a bunch of files. You may need to get an updated version of caret_command, if your version doesn't have it. It's roughly April vintage (i.e., when we were

Re: [caret-users] Cortical Thickness Measurement

2006-06-13 Thread Donna Dierker
Hi Darren, Sorry to be the bearer of bad news, but no: Caret/SureFit doesn't compute cortical thickness. For a while, a student was working on it, but it never went anywhere. Occasionally, people mistake our sulcal depth measure for cortical thickness, but the two are completely different

Re: [caret-users] Cortical Thickness Measurement

2006-06-13 Thread Donna Dierker
somewhere? The only instructions seem to be fairly old and it looks like things have changed a bit since then. -Eric -Original Message- From: Donna Dierker [mailto:[EMAIL PROTECTED] Sent: Tue 6/13/2006 8:36 AM To: [EMAIL PROTECTED]; Caret, SureFit,and SuMS software users Subject: Re

Re: [caret-users] Cortical Thickness Measurement

2006-06-14 Thread Donna Dierker
? On 06/13/2006 02:09 PM, Faden, Eric (NIH/NIMH) [F] wrote: I suppose I should have been more specific. Is there any Macaque specific information? -Eric -Original Message- From: Donna Dierker [mailto:[EMAIL PROTECTED] Sent: Tue 6/13/2006 2:48 PM To: Caret, SureFit, and SuMS software users

Re: [caret-users] Questions regarding foci assignment in Caret5

2006-07-05 Thread Donna Dierker
On 07/05/2006 01:58 PM, [EMAIL PROTECTED] wrote: Hi, my name is David Kiamanesh and I am a second year medical student at WashU. I am beginning to learn Caret so that I could map fMRI data which I have collected from published papers. I have been working on learning how to use the

Re: [caret-users] Script to streamline import of Freesurfer surfaces

2006-08-01 Thread Donna Dierker
Hi Svetlana, Depending on which version of Caret you're running, you may need to download a more recent version of this script: http://brainmap.wustl.edu/pub/donna/SCRIPTS/FREESURFER/freesurfer2caret.sh login pub password download This version replaces the -hem flag in the

Re: [caret-users] SPM2 Caret

2006-08-01 Thread Donna Dierker
Hi Dr. Schlund, I interpret simple overlays of functional data as mapping functional data onto the PALS atlas. In that case, step 1 is to take the PALS tutorial, if you haven't already done so: PDF: http://sumsdb.wustl.edu/sums/download.do?id=6363278 dataset:

[caret-users] mapping SPM5 functional results onto PALS atlas

2006-08-17 Thread Donna Dierker
Hi Nicola, Your .hdr file is missing this origin information: SPM originator decodes to 40 57 26 Try writing the volume out in NIfTI format and mapping it in Caret; you'll have better luck (I hope). There are other work-arounds if this fails, but this is a classic example of why NIfTI was

Re: [caret-users] [SPAM] caret on AMD64

2006-08-29 Thread Donna Dierker
Try making sure /usr/lib64 is in your LD_LIBRARY_PATH variable, e.g.: setenv LD_LIBRARY_PATH /usr/lib64:$LD_LIBRARY_PATH ... or if your shell is bash: export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH Thanks for reporting the issue with the mailing list. It sounds like I need to check the

Re: [caret-users] [windows problem] RadialPositionMap+orig.HEAD not found

2006-08-30 Thread Donna Dierker
H Leonardo, A while back, there was a bug in the Windows version of Caret that caused some files to get written to the $CARET_HOME/bin directory instead of the current working directory. This bug has been fixed for a while, so I suggest trying the snapshot caret5.exe:

Re: [SPAM] Re: Re: [caret-users] [SPAM] caret on AMD64

2006-08-30 Thread Donna Dierker
/ -name libX11.so.6 /usr/X11R6/lib64/libX11.so.6 Thank you again, Marco */Donna Dierker [EMAIL PROTECTED]/* wrote: Hi Marco, John may have more concrete suggestions, but I want to see the output of two commands: echo $LD_LIBRARY_PATH and the other is: find / -name

Re: [caret-users] [SPAM] CARET-memory problem

2006-09-01 Thread Donna Dierker
Just a couple of things to add to John's reply: * Most users who segment using Caret, 1Gb of memory is enough, but if your volume is very high resolution or otherwise is very large (e.g., dimensions of 300x300x300 are above those of a typical Caret user; most volumes are something like

Re: [caret-users] CARET file

2006-09-13 Thread Donna Dierker
Yes, this is almost certainly Elena's issue. The AFNI file format is such that you can have multiple sub-bricks within the same file (e.g., multiple types of summary group statistics). These show up as separate columns or menu picks in the drop-down menus. But when doing segmentation, you

Re: [caret-users] ROIs

2006-09-20 Thread Donna Dierker
Hi Jason, On 09/20/2006 12:17 PM, Jason D Connolly wrote: Dear Donna, Thank you for your help in the past. We are currently trying to draw an ROI (or a mask) around activated regions on the flat map (and hopefully save these ROIs in *.cub format) to then select region-specific

Re: [caret-users] Radiological LPI conversion bug?

2006-09-21 Thread Donna Dierker
currently only have access to a Windows PC in the lab (although this is likely to change) which rules out AFNI options for now, so I may need to hold fire on this. I'll look at your other suggestion today. Thanks John Donna Dierker wrote: Hi John, On 09/19/2006 05:24 AM, [EMAIL PROTECTED

Re: [caret-users] left Hemisphere landmarks for registration with F99

2006-09-21 Thread Donna Dierker
To clarify, F6 is a six-subject macaque fascicularis atlas developed by a collaboration of wustl.edu researchers. See part 3 of the tutorial cited below for details. On 09/20/2006 08:12 PM, David Vanessen wrote: John (et al.), I guess Donna wins a six-pack, because I do indeed have a

Re: [caret-users] Assigning binary to ROI

2006-09-26 Thread Donna Dierker
On 09/25/2006 11:16 PM, DG MCLAREN wrote: Yes, this can be done. There is paper that is under review that contains this process in article format; however, I'll write the procedure below: 1) Create individual ROIs for each individual participant using their own fiducial surface (I'm assuming

Re: [caret-users] strange problem with v 5.4 and 5.5

2006-10-11 Thread Donna Dierker
Hi Roland, Try going to your home directory and doing this: rm -rf .qt See if this makes a difference. You're not the first to report something like this, but I'm not sure it's the same problem exactly. Veronica Smith reported segmentation faults when launching Caret (before trying to open

Re: [caret-users] Generate 3D coordinates list?

2006-10-24 Thread Donna Dierker
You may need to use File: Convert Data File Formats (or command line tool caret_file_convert) to convert the coord file to ASCII. On 10/23/2006 04:18 PM, John Harwell wrote: Try this, * Select the nodes in your ROI. * Change Normal Selection to Not Selection and then press the Select Nodes

Re: [caret-users] Fishy brainfish sampling

2006-10-30 Thread Donna Dierker
Graham, 1. You're right: BrainFish isn't mapping negative activity as intended. I just mapped CARET_TUTORIAL_SEPT06/BURTON_04_VibroTactile_EARLY_BLIND+orig.HEAD onto PALS_B12 711-2C using BrainFish, and although this volume has big regions of negative activity, the metric file gets

Re: [caret-users] caret docs; Display Control especially

2006-10-31 Thread Donna Dierker
Hi Graham, Burying your head in David's PALS paper is indeed the best way to get your head around this stuff. It took me three careful reads before I really digested it. (And you can't whip through in a short plane ride.) To get a more hands-on feel for Caret/SureFit surfaces, consider

Re: [caret-users] Voxel Size for Macaque Anatomicals

2006-11-03 Thread Donna Dierker
Donald, I hope Madison is treating you well. Check out part 3 of this tutorial (PDF and zip file in this directory): CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu/sums/directory.do?id=6585200 On 11/03/2006 12:22 PM, DG MCLAREN wrote: David, Awhile ago you mentioned that there were three

Re: [caret-users] Mapping Macaque SPM Functionals to a Caret Surface

2006-11-07 Thread Donna Dierker
editor) to match your volume file, or write your volume out with an orientation and origin that matches your surface. But first you need to get the magic numbers that specify the affine transform from your surface to your volume. On 11/07/2006 10:27 AM, Simone Kamphuis wrote: Donna Dierker schrieb

Re: [caret-users] Mapping Macaque SPM Functionals to a Caret Surface

2006-11-08 Thread Donna Dierker
for the functional volume. I changed this back to 0 and that was all! The activation I find in SPM matches very nicely with the activation I see in Caret, so I am very happy about that. Thanks a lot! Simone Donna Dierker schrieb: Hi Simone, Actually, when I look at it in Caret, the functional

Re: [caret-users] registration landmarks

2006-11-08 Thread Donna Dierker
On 11/08/2006 01:39 PM, Veronica S Smith wrote: Hi, I have attached a screen capture of the flat map, inflated map and spherical map with the 3 additional registration landmarks drawn. Yeah, there are a lot of crossovers in the flat map near the sylvian, but they don't seem to have interfered

Re: [caret-users] registration landmarks

2006-11-08 Thread Donna Dierker
On 11/08/2006 02:12 PM, Donna Dierker wrote: Your anterior termination looks too far superior and posterior -- roughly 15-30 degrees too far clockwise. I should have specified when looking at the lateral inflated view.

Re: [caret-users] nifti images

2006-11-14 Thread Donna Dierker
Hi Mateus, I can't address your original problem with the NIfTI orientation/rotation, but I did have a look at your volumes, and this statement confuses me: The histogram of my images (3D_original.nii and 3D_resliced.nii) shows several noisy sharp peaks. The attached captures show the

Re: [caret-users] nifti images

2006-11-15 Thread Donna Dierker
Hi Mateus, See inline replies below. On 11/14/2006 09:45 AM, Mateus Joffily wrote: Hi Donna, Thanks for your help. I am sending you two histograms of 3D_resliced.nii: (1) histogram_resliced_1.jpg is the same histogram you already sent to me; (2) histogram_resliced_2.jpg is the histogram of

Re: [caret-users] nifti images

2006-11-17 Thread Donna Dierker
and non-integer bin size. What do you think? Thanks, Mateus Donna Dierker wrote: Hi Mateus, See inline replies below. On 11/14/2006 09:45 AM, Mateus Joffily wrote: Hi Donna, Thanks for your help. I am sending you two histograms of 3D_resliced.nii: (1) histogram_resliced_1.jpg is the same

Re: [caret-users] Spherical registration

2006-11-28 Thread Donna Dierker
On 11/28/2006 11:48 AM, Mateus Joffily wrote: Hi, I am a little bit confused on how to proceed to register an individual surface into an Atlas. The 'Caret5 Tutorial: Segmentation, Flattening, and Registration' explains how to perform a spherical registration using the

Re: [caret-users] Spherical registration

2006-11-28 Thread Donna Dierker
database from http://sumsdb.wustl.edu/. Could you, please, confirm me if this is the atlas that I need to download: 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730'? Thanks, Mateus Donna Dierker wrote: On 11/28/2006 11:48 AM, Mateus Joffily wrote: Hi, I am a little bit confused on how

Re: [caret-users] Caret Tutorial

2006-11-28 Thread Donna Dierker
On 11/28/2006 02:02 PM, Veronica S Smith wrote: Hi, I was just checking out the latest Caret Tutorial and wanted to clarify that the PDF file, Caret_Tutorial_Oct6, is a companion to the archive, CARET_TUTORIAL_SEPT06. It appears that the latter consists of data files only. Is that correct?

Re: [caret-users] Spherical registration

2006-11-29 Thread Donna Dierker
I did remove the port numbers from the list, which seemed to have no ill effect on my end. Perhaps it resolved the problem on your end. On 11/29/2006 03:15 AM, Mateus Joffily wrote: Hi Donna, I don't know what happened, but now all the links work. Thanks, Mateus Donna Dierker wrote

Re: [caret-users] distance from a node

2006-11-29 Thread Donna Dierker
If you were talking about geodesic distance (i.e., running along the contour of the fiducial surface -- not as the crow flies through the CSF/WM), then you could use the Surface: ROI feature for this purpose. (First operation Geodesic Distance, and then threshold the resulting metric at the

Re: [caret-users] crash of X KDE session

2006-11-29 Thread Donna Dierker
Hi Marco, Although your problem is a bit different, another possible culprit is the .caret5_preferences file: http://brainvis.wustl.edu/pipermail/caret-users/2006-November/000931.html We're still struggling with this problem at University of Washington. Today I asked Veronica to try the

Re: [caret-users] distance from a node

2006-11-30 Thread Donna Dierker
On Nov 29, 2006, at 11:28 AM, Donna Dierker wrote: If you were talking about geodesic distance (i.e., running along the contour of the fiducial surface -- not as the crow flies through the CSF/WM), then you could use the Surface: ROI feature for this purpose. (First operation Geodesic

Re: [caret-users] crash of X KDE session

2006-11-30 Thread Donna Dierker
Marco, Does the problem occur when you use File: Open Volume Anatomy (or functional) File to open the same file? If so, does it occur if you convert the file to NIfTI and/or AFNI? I'm guessing it will (e.g., suggesting a display issue, rather than a file I/O issue), but it helps to be

Re: [caret-users] projecting PALS-B12 atlas into individual brain

2006-11-30 Thread Donna Dierker
On 11/30/2006 08:34 AM, Mateus Joffily wrote: Hi, I have concluded the spherical registration of one individual surface into PALS-B12. Three spec files have been created: (1) Human.Isa.R.spec (original spec file); (2) deformed_Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec; (3)

Re: [caret-users] Spherical registration

2006-11-30 Thread Donna Dierker
using 'Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730' atlas, which procedure should I follow? Thanks, Mateus Donna Dierker wrote: I did remove the port numbers from the list, which seemed to have no ill effect on my end. Perhaps it resolved the problem on your end. On 11/29/2006 03:15 AM

Re: [caret-users] distance from a node

2006-11-30 Thread Donna Dierker
will be using this for and whether this is a pressing need, it will help us to prioritize the request. Also, if other Caret users would like to see this functionality, let us know. Best regards, David On Nov 29, 2006, at 11:28 AM, Donna Dierker wrote: If you were talking about geodesic distance

Re: [caret-users] segmentation fails w/ uniformized data

2006-12-07 Thread Donna Dierker
Hi Rebecca, As John said, uploading your volume is the quickest way for us to help, but here are some additional thoughts/factors: * For very non-uniform volumes, 3dUniformize may not be enough. You might need a bigger gun like FSL's FAST (http://www.fmrib.ox.ac.uk/fsl/fast/index.html),

Re: [caret-users] tailarach coordinate

2006-12-07 Thread Donna Dierker
Hi Mateus, Your question throws me a little bit, but I'll try to provide a helpful answer. When you register your surface to PALS_B12.LR, one of the resulting files in the atlas target directory is a file named like def*Fiducial*coord -- what David calls the resampled fiducial. (He

Re: [caret-users] using caret for a meta-analysis

2006-12-08 Thread Donna Dierker
Hi Leon, Shawn has done exactly what you want to do, so if anyone knows the pitfalls, he does. ;-) Besides Shawn's useful notes, make sure you read sections 1.2.3 and 5.2 of this tutorial, if you haven't done so already: CARET_TUTORIAL_SEPT-06

Re: [caret-users] using caret for a meta-analysis

2006-12-08 Thread Donna Dierker
, Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 08, 2006 6:34 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] using caret for a meta-analysis Hi Leon, Shawn has done exactly what you

Re: [caret-users] (no subject)

2006-12-11 Thread Donna Dierker
Hi Dr. Ghosh, I think you want the login and password for the download page: http://brainmap.wustl.edu/pub/caret/index.html login: Rabbit password: Carrot If you're talking about your caret-users mailing list options, you can get a password reminder here:

Re: [caret-users] Flat surface crossovers

2006-12-11 Thread Donna Dierker
It means start on the outside and end on the inside, as shown in the attached capture, which shows an exaggeratedly thick red cut near some crossovers. Both Erin and I would have left these minor, peripheral crossovers alone (i.e., no cuts), because we know from experience they tend to cause

Re: [caret-users] using caret for a meta-analysis

2006-12-22 Thread Donna Dierker
before projection. Any idea what I may be doing wrong, or not interpreting correctly? Thanks, Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 08, 2006 7:49 PM To: Caret, SureFit, and SuMS software users

Re: [caret-users] using caret for a meta-analysis

2007-01-08 Thread Donna Dierker
. Leon -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Friday, December 22, 2006 4:19 PM To: Leon Deouell Cc: 'Caret, SureFit,and SuMS software users' Subject: Re: [caret-users] using caret for a meta-analysis Hi Leon, This looks

Re: [caret-users] metric file stats

2007-01-10 Thread Donna Dierker
Hi Clayton, 1. A reasonable question, but I'm afraid this document is both incomplete and obsolete: http://brainvis.wustl.edu/courses/Caret_5_332_Tutorial_Analysis.doc For example, Find Significant Clusters is now called Two-Sample T-test. But maybe it will still prove helpful. This submenu

Re: [caret-users] metric file stats

2007-01-11 Thread Donna Dierker
, COG-[XYZ], lat-lon, and p-value) as we currently do for our Find Significant Cluster feature. Clayton Curtis On Jan 10, 2007, at 4:23 PM, Donna Dierker wrote: Hi Clayton, 1. A reasonable question, but I'm afraid this document is both incomplete and obsolete: http://brainvis.wustl.edu

Re: [caret-users] [SPAM] finding a local maximum

2007-01-12 Thread Donna Dierker
Hi Akiko, Try this: Copy your metric file to a surface_shape file and load it as a surface shape. (The formats are identical.) Then, try Surface: Region of Interest: Surface Shape cluster analysis. You'll need to do this for each tail (i.e., once at thresh=3.0 and once at thresh=-3, or

Re: [caret-users] metric file stats

2007-01-12 Thread Donna Dierker
Curtis [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *Date: *January 10, 2007 7:38:51 PM EST *To: *Adam C. Riggall [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *Subject: **Fwd: Re: [caret-users] metric file stats* *From: *Donna Dierker [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] *Date: *January 10

Re: [caret-users] finding a local maximum

2007-01-12 Thread Donna Dierker
- Original Message - From: Donna Dierker [EMAIL PROTECTED] Date: Friday, January 12, 2007 9:11 am Subject: Re: [caret-users] [SPAM] finding a local maximum Hi Akiko, Try this: Copy your metric file to a surface_shape file and load it as a surface shape. (The formats are identical

Re: [caret-users] import and registration questions

2007-01-16 Thread Donna Dierker
Hi Remya, See inline replies below. On 01/15/2007 01:36 PM, Remya Nair wrote: Hi Donna I am new to Caret, so any help would be greatly appreciated. There are a number of things that I intend to do. 1. View macaque data sets in Caret. These are in Dicom format and so I understand that they

Re: [caret-users] Brodmann areas in transaxial slices

2007-01-22 Thread Donna Dierker
Hi Lena, I think there may be multiple atlases that serve this purpose, but it sounds like you're looking for something more volume than surface-based. You might try the SPM Anatomy toolbox: http://www.fz-juelich.de/ime/spm_anatomy_toolbox Dr. Van Essen has the Brodmann areas mapped onto

Re: [caret-users] ROI - borders around clusters

2007-01-24 Thread Donna Dierker
The only thing I can think to try is to restart Caret and repeat your selection of all nodes within threshold 1.0 to 5.0. I can see from your capture that you did this and your green nodes include clusters for which it didn't draw borders. My only guess is that perhaps somehow the create

Re: [caret-users] ROI - borders around clusters

2007-01-25 Thread Donna Dierker
have any other idea about what can be the problem... Thank you very much, Mateus Donna Dierker wrote: The only thing I can think to try is to restart Caret and repeat your selection of all nodes within threshold 1.0 to 5.0. I can see from your capture that you did this and your green nodes

Re: [caret-users] ROI - borders around clusters

2007-01-26 Thread Donna Dierker
) with the two metrics included ('metric1': problematic one; and 'metric2': with smaller clusters that works fine). If you have any other idea about what can be the problem... Thank you very much, Mateus Donna Dierker wrote: The only thing I can think to try is to restart Caret and repeat your selection

Re: [caret-users] caret question

2007-01-26 Thread Donna Dierker
Hi Gene, It sounds like you've actually created a new coord file -- an inflated version of a the colin SPM2 fiducial. So if you wanted to use this later, you'd need to save it as a separate coord file. Then you could use D/C: Scene to append a scene using this coord file, and then save the

Re: [caret-users] A Question about Spherical Registration

2007-02-21 Thread Donna Dierker
Hi Reza, The atlas target dataset you used was the right one, but it is a stripped down version that minimizes the number of files that get deformed from the atlas to the individual's directory. (Some people want to look at the atlas paint or border files on their individual's surface, so

Re: [caret-users] installation problems

2007-02-23 Thread Donna Dierker
Hi Erik, When John comes in, he'll probably be more help, but until then here are some thoughts: * On my new 64-bit Linux workstation, find /usr -name libGLU.so.1 returns this output: /usr/X11R6/lib/libGLU.so.1 /usr/X11R6/lib64/libGLU.so.1 /usr/lib/libGLU.so.1 /usr/lib64/libGLU.so.1 * The

Re: [caret-users] lesions

2007-02-26 Thread Donna Dierker
On 02/23/2007 10:16 PM, Joan Fisher wrote: Dear Caret users: I have a group of MRIs of children with unilateral brain injury that I would like to get morphometric measurements on. Specifically, I would like to know how the gray and white matter in each hemisphere compare overall (for the

Re: [caret-users] Flattening and Spherical Registration of the Monkey Brain

2007-02-26 Thread Donna Dierker
On 02/23/2007 02:05 PM, Reza Rajimehr wrote: Dear Donna and David, Thank you for the helpful comments and suggestions. I successfully finished flattening of an individual human brain and its spherical registration to the human PALS atlas, and the registration is perfect. Now I want to start

Re: [caret-users] A Problem with .borderproj files

2007-03-02 Thread Donna Dierker
Reza, The only thing I'd add to John's advice is that the text editor part is for identifying which borders are dups -- not for deleting them. You can delete them from the border file, but then you'll need to tweak other lines. For example, the number of borders is in a line by itself

Re: [caret-users] Map SPM volume

2007-03-07 Thread Donna Dierker
Hi Julian, When mapping to atlas, are you selecting a spec file created from this dataset: CARET_TUTORIAL_SEPT-06 http://sumsdb.wustl.edu/sums/directory.do?id=6585200 ... using steps as described in Section 5.1 of this tutorial: Caret_Tutorial_Oct06.pdf

Re: [caret-users] Map SPM volume

2007-03-07 Thread Donna Dierker
Of Donna Dierker Sent: Wednesday, March 07, 2007 4:05 PM To: Caret, SureFit, and SuMS software users Subject: [BULK] Re: [caret-users] Map SPM volume Importance: Low Hi Julian, When mapping to atlas, are you selecting a spec file created from this dataset: CARET_TUTORIAL_SEPT-06 http

Re: [BULK] Re: [caret-users] Map SPM volume

2007-03-08 Thread Donna Dierker
Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: Wednesday, March 07, 2007 4:05 PM To: Caret, SureFit, and SuMS software users Subject: [BULK] Re: [caret-users] Map SPM volume Importance: Low Hi Julian, When mapping to atlas, are you selecting a spec

Re: [caret-users] resizeunderlayvolume

2007-03-09 Thread Donna Dierker
Hi Florian, To my surprise, no -- I don't think there is. Seems like a useful option, but currently John is working on other things. You might download AFNI (http://afni.nimh.nih.gov/afni) and try 3dZeropad. Even if you don't use AFNI for analysis, it has some really handy command line

Re: [caret-users] Registering Individual Macaque to F99 template

2007-03-12 Thread Donna Dierker
See inline replies below (both in Donald's and Hamied's messages). On 03/12/2007 12:00 PM, DG MCLAREN wrote: Sterling Johnson's lab here at UW-Madison is working on creating a group averaged macaque atlas for volume registration. However, we aren't quite ready to make them public as there are a

Re: [caret-users] the name

2007-03-13 Thread Donna Dierker
Hi Ervin, I think the confusion stemmed from receiving a caret-users mailing list confirmation with a more personalized login and password around the same time you receive the download information. To download Caret, use this access information: To obtain the Caret software, use this

Re: [caret-users] About Monkey to Human Deformation

2007-03-14 Thread Donna Dierker
Hi Reza, Hmmm. I can almost replicate this behavior. When I load CARET_TUTORIAL_SEPT06/COMPARE_MACAQUE_HUMAN/RegF99toPALS_23-LDMK-VE_Macaque.F99UA1.RIGHT.Register-with-PALS_23-LDMK-VE.73730.spec.deform_map, both the individual and atlas directory buttons are disabled, but Data File and

Re: [caret-users] Announcement: open access MR data (OASIS)

2007-03-14 Thread Donna Dierker
OAS1_0163_MR1 Human_Buckner_Case03 OAS1_0350_MR1 Human_Buckner_Case08 OAS1_0361_MR1 Human_Buckner_Case10 OAS1_0368_MR2 Human_Buckner_Case12 OAS1_0448_MR1 Human_Buckner_Case02 OAS1_0450_MR1 Human_Buckner_Case09 Donna Dierker http://brainmap.wustl.edu/ On 03/14/2007 12:37 PM, Daniel Marcus wrote

Re: [caret-users] Monkey Atlas and stereotaxic

2007-03-14 Thread Donna Dierker
Hi Remya, Glad to hear you got your hands on a T1 scan. There's no documentation I know of that covers what you want to do, but it's not that hard (if I understand it correctly). I think you'll just need two versions of your volumes (one AC-centered, one inter-aural) and two versions of

Re: [caret-users] About Monkey to Human Deformation

2007-03-14 Thread Donna Dierker
Hi Reza, See inline reply below. Donna On 03/14/2007 03:40 PM, Reza Rajimehr wrote: Hi Donna, The Data File button is disabled in my Caret, so I think I have to use the caret commands. Just a question: what are source and target paths in the first caret command. I assume that the source path

Re: [caret-users] Surface Flattening

2007-03-19 Thread Donna Dierker
Hi Rishi, You can safely ignore this warning. You only need the area color if you actually want to view the paint file. In your case, you're just humoring the flattening algorithm. But if you want to view the paint file, a generic area color file is attached. Donna On 03/19/2007 09:51

Re: [caret-users] Identifying Medial Wall for Flattening

2007-03-21 Thread Donna Dierker
On 03/21/2007 08:08 AM, Rishi Kalwani wrote: hi, after flattening i get a compressed medial wall surface with an orange border(along with blue borders) how well does this orange border demark the medial wall? is it necessary to make corrections? We ALWAYS redraw the medial wall and

Re: [caret-users] Calcarine Sulcus and Border Drawing

2007-03-22 Thread Donna Dierker
Rishi, See inline replies below. Donna On 03/22/2007 10:45 AM, Rishi Kalwani wrote: hi, in the core6 landmark website it says not to draw the calcarine sulcus if it makes a hard ventral turn. This means as it extends from the medial wall toward the occipital pole. the CaSu on my

[Fwd: Re: [caret-users] Macaque Neuroanatomy]

2007-03-23 Thread Donna Dierker
Passing on Jim Lewis' reply about Hamied's query, which DVE and Rolf Kotter also covered. Original Message Subject:Re: [caret-users] Macaque Neuroanatomy Date: Fri, 23 Mar 2007 15:49:10 -0400 From: James Lewis [EMAIL PROTECTED] To: Donna Dierker [EMAIL

Re: [caret-users] mapping SPM5 volumes in Caret

2007-03-26 Thread Donna Dierker
Hi Tobias, I don't recognize this problem. Hmmm. How about if I give it a try on my end. Can you upload one or more of your volumes here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi From the 'QEventDispatcherUNIX::unregisterTimer error, I guess you're running Linux. We'll see if my

Re: [caret-users] mapping SPM5 volumes in Caret

2007-03-26 Thread Donna Dierker
help: I've uploaded a couple of volumes ('Tobias_feature.hdr', etc) and the metric files (note that in the metric files, my volumes are referred to by different names). I'm actually using Windows though, not Linux. Many thanks and best wishes, Tobias. On 3/26/07, Donna Dierker [EMAIL PROTECTED

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