> Huiling
>
> -Original Message-
> From: caret-users-boun...@brainvis.wustl.edu
> [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker
> Sent: Wednesday, November 14, 2012 10:07 AM
> To: Caret, SureFit, and SuMS software users
> Subject: Re:
___
> From: caret-users-boun...@brainvis.wustl.edu
> [caret-users-boun...@brainvis.wustl.edu] on behalf of Donna Dierker
> [donna.dier...@sbcglobal.net]
> Sent: Tuesday, November 13, 2012 5:22 PM
> To: Caret, SureFit, and SuMS software users
> Subject: Re: [caret-users] Error creating Br
mizu
>
> 2012/11/13 Matt Glasser
> I wonder if your sform has obliques in it. I agree that a screenshot
> would be helpful, together with verifying that the surfaces and T1w and
> T2w volumes are well aligned in some other screenshots.
>
> Peace,
>
> Matt.
>
> On 11/1
This could happen if your distribution didn't unzip completely, or some files
got inadvertently removed.
Suppose your caret distribution is in /usr/local/caret. Then do this:
cd /usr/local/caret/data_files/fmri_mapping_files
Then do:
ls *FLIRT*coord
If you really don't see the coord file it
x 256, 1
> mm slice
> T2w images: CUBE(XETA) TR 2500 ms, TE 80 ms, FOV = 256 x 256, 1 mm slice
>
> I obtained plausible thickness maps, but the intensity in myelin.metric are
> all zero!
> Although the scanning condition seems to be the same as the paper, the
> results are a
Matt might get to this, but here are some clues based on how I'd proceed in
your shoes:
Find a figure in one of our papers like the one I want to make, e.g.:
http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8288739&archive_name=Fig4_fsaverage_Conte-69.164k_fs_LR.spec
(I couldn't find the
I don't know of an easier way. Knowing me, I'd do:
caret_command -metric-information my.metric | grep "my column name"
# hack with cut to get just the sample deviation
caret_command -file-convert -format-convert ASCII my.metric
# hack with sed/cut to replace the upper limit here with stddev:
tag-
I think it started happening to me when I switch operating systems to ubuntu.
It might not be an issue with Mac. Haven't tried.
On Nov 2, 2012, at 1:52 PM, Colin Reveley wrote:
> does anyone know why my scene files print with the color bar, but not the
> numbers to go with it?
>
> I'm using
"all points of activation" -- all non-zero vertices? This is likely to be a
lot of vertices.
More often one is interested in the center of gravity of a supra-threshold
cluster, but let me answer your original question.
You could save the coord, metric, and paint file as ASCII and strip the hea
Have you tried leaving off the format option, letting it write in the default
format? Or specifying binary, since metric-information hints at a preference?
On Oct 29, 2012, at 7:10 AM, Colin Reveley wrote:
> Hi -
>
> I'm interested in correlating two metrics.
>
> for the sake of argument t
Certainly you can use either the caret GUI (File: Save Data File: File type
GIFTI surface file) or caret_command -file-convert to convert PALS-B12 surfaces
into GIFTI. There are closed, open, and cut topo files out there. The cut is
used only with the flat map, but you might be interested in e
David might have more squirreled away on his machine somewhere, but I couldn't
find this in sumsdb or my archives.
I'm sure some labs around here -- very likely the Snyder Lab -- have used FSL's
Brain Extraction Tool (BET) on the F99 atlas for various purposes, but I'm not
aware that they relea
Hi Gang,
>From what I can tell, you can feed TFCE any statistic (t, f, r -- whatever)
>that gets more significant as you get away from zero (positive or negative).
But as for caret_stats, we don't get much fancier than simple t- or f-stats
(and the ANOVAs are one-way).
For a stat that regresse
Don't know off-hand, but I tried this:
point your browser to sumsdb.wustl.edu
basic search archive
filename pals
filetype deform_map
search for f99 in browser results
They all look like the wrong direction to me.
On Sep 19, 2012, at 7:01 PM, Tristan Chaplin wrote:
> Hi,
>
> I
t line so it is more specific
> than "Re: Contents of caret-users digest..."
>
>
> Today's Topics:
>
>1. Re: caret-users Digest, Vol 108, Issue 1 (Donna Dierker)
>2. Re: caret-users Digest, Vol 108, Issue 1 (Timothy Coalson)
>
>
> -
Dale,
In situations like this, I get the anatomical template image used as the atlas
target for spatial normalization. Flirt and fnirt both use the avg152T1, but
different versions. Load your atlas target in Caret, and overlay the surface
outline of the PALS mean surface used as a mapping sub
Andrew,
Assuming it's a bash script, near the top, before it starts doing anything, add
this line:
set -x
Then re-run your script, redirecting the standard output and error to a file,
e.g., script.log; then upload script.log here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Donna
On Sep 1
On Aug 31, 2012, at 3:50 AM, Lisa Ronan wrote:
> Dear List
>
> I was wondering if anyone would be able to tell me how the mean and Gaussian
> curvature values are calculated in CARET. I understand that the Gauss-Bonnet
> method is used in FreeSurfer, but when I
> compare per vertex measurements
t-users
> or, via email, send a message with subject or body 'help' to
> caret-users-requ...@brainvis.wustl.edu
>
> You can reach the person managing the list at
> caret-users-ow...@brainvis.wustl.edu
>
> When replying, please
Go here:
http://www.nitrc.org/frs/download.php/2871/GIFTI_Surface_Format.pdf
On page 36, it says: The application of a CoordinateSystemTransformMatrix,
places the coordinates into the system shown in the table below. All
coordinates are in millimeters.
So sorry: You don't get to change units
was
> a correct assumption, but I've checked by using a single ROI (for example,
> defined by the 3's in a brain of 0's) and the assigned color name came out
> to be "Unknown_name_3".
>
> Thanks for responding, Donna!
>
> On Mon, Aug 20, 2012 at 5:
ame_#" paint colors derived from the values of
> the ROIs they paint? As in, an ROI defined by the value of 4 was painted with
> the color "Unknown_name_4"?
>
> On Mon, Aug 20, 2012 at 3:19 PM, Donna Dierker
> wrote:
> First, the ifh has a lookup table, but you h
First, the ifh has a lookup table, but you have to add or subtract 2.
If you save the paint file as ASCII, there is a paint index to name lookup near
the top (and you don't have to add or subtract 2 to that one).
On Aug 20, 2012, at 1:07 PM, Megan Wang wrote:
> Hello all,
>
> I have a .4dfp f
Not in caret5, anyway. But this might be confusing, even if you could.
There is a way to channel 3 metrics into red, green, and blue channels
(Attributes: Metric).
You can threshold one of the metrics and generate areal borders around the
resulting clusters, which you can overlay on the other
It might be simpler to map a functional NIFTI volume onto your subject's
surface resampled to the F99 mesh. The functional volume must be in register,
volumetrically, with the anatomical used to segment the surface. And there
might be issues with orientation (e.g., volume is coronal, while sur
On Jul 20, 2012, at 5:06 PM, Colin Reveley wrote:
> Is it possible to inflate just part of a surface? I doubt it.
Inflate, I don't think so; smooth -- definitely. You can use paint to select
nodes, then constrain the smoothing that way.
I don't have caret handy, but look at the options under S
le medio-lateral and
> dorso-ventral position. The problem is that the highlighted voxel is
> too posterior in the volume view). Does this make sense or hint to a
> possible solution to you perhaps? Worst case scenario, I could eyeball
> how big this translation offset is, open the volume
Be aware that what AFNI/Caret calls LPI, Freesurfer calls RAS. ;-)
Can you try having mri_convert write the volume out as RAS, instead of
LPI? Freesurfer will read the header and do the right flipping/rotating
so that the surface aligns with it. Freesurfer did the right thing, as it
understands
Joern Diedrichsen played around with this years ago and found four average
neighbors iterations to work well with caret-style surfaces:
www.icn.ucl.ac.uk/motorcontrol/download/Caret_surface_statistics.pdf
But he probably smoothed the mapped fMRI before doing any sort of t- or
f-test. We typicall
Hi Pablo,
Here are some version/flavors to choose from:
caret_distribution_Linux32.v5.62.zip
caret_distribution_Linux64.v5.62.zip
caret_distribution_LinuxIntel64.v5.62.zip
caret_distribution_Linux32.v5.64.zip
caret_distribution_Linux64.v5.64.zip
caret_distribution_LinuxIntel64.v5.64.zip
caret_dis
The honest answer to most of these questions is "I don't know"; however, see
inline comments below for any hints I think are worth sharing.
On Jul 15, 2012, at 7:56 AM, Colin Reveley wrote:
> Before I begin something that's going to be tough, may I just confirm:
>
> I've got a structural and o
the same with avg152T1.nii
> from the SPM distribution.
>
>
> Atesh
>
> On Fri, Jul 13, 2012 at 12:18 AM, Donna Dierker
> wrote:
> We still don't have a SPM8 version, if that's really your question. ;-) SPM5
> is what I would use, in your shoes.
>
&g
We still don't have a SPM8 version, if that's really your question. ;-) SPM5
is what I would use, in your shoes.
If your functionals are in MNI space, as you say they are, then you're good.
When you say "hdr" I assume that's a NIFTI hdr/img pair, and not an Analyze
volume, because you're usin
What version of Caret are you running? If caret5.*, then maybe this page will
be helpful:
http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#coordFile
... and this one:
http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#metr
All of the volumes, except the inner and outer boundaries, are segmentations,
rather than structural volumes (as far as I know).
But you could find one of those intermediate volumes -- possibly named like
hindbrain* -- and subtract that volume from the anatomical volume, and then use
the volume
Leon gave me permission to pass this on to caret-users:
> "draw border update". I had great difficulty following what the FS-to-F99
> tutorial on this step, because just let many other users who have complained
> in the mailing list, nothing would happen when I tried to update borders on a
> 3D
If the t-map is across subjects (e.g., two sample t-test across groups;
paired t-test of several subjects at different time points), then there is
no reason to use one subject's cerebellum as a mapping substrate over
another's. Use the Colin cerebellar surface that already exists in some
SPM flavo
What format is this volume? If all 100 time points are distinct sub-briks
within an AFNI volume, then you should be able to use AFNI's 3daxialize to
reslice them. I'm pretty sure there is a FSL counterpart. Even if they are
separate volumes, you can loop through them via script and axialize t
On Jun 21, 2012, at 5:56 PM, Colin Reveley wrote:
> Hello folks.
>
> I need to make a marmoset surface.
>
> with macaque, my preference is to do it at full 250um resolution in
> freesurfer, so I get the ribbon, WM, pial, and import that dense mesh into
> CARET.
>
> But, it's a nightmare. So I
There are probably many ways of doing this, but one that comes to mind is
saving the existing parcellation as an ASCII paint file, and then doing this at
a command line (Linux or MacOSX):
grep ' 0$' myfile.paint
This assumes there is only one column in the paint file, which can be arranged
if
Try something along these lines:
caret_command -metric-math-postfix $OUTMETRIC $OUTMETRIC "$REGION sum"
"@$OUTMETRIC:$COLUMN_NAME@ @$OUTMETRIC:$REGION sum@ +"
From: Colin Reveley
To: caret-users@brainvis.wustl.edu
Sent: Sat, May 26, 2012 1:09:34 PM
Subject:
eding
> the number of coordinates in the coordinate file.
>
> I have checked the original rh.white, rh.pial and rh.inflated and they look
> fine in FreeSurfer. Do you know how I should solve this issue of mismatched
> topology and coordinate files?
>
> Thank you!
> Leon
I went to http://sumsdb.wustl.edu and selected Browse/Search: Basic Archive
Search.
I entered TEMPLATE.MedialWallSegments in the filename box and got this search
result:
Macaque.FS.R.TEMPLATE.MedialWallSegments.SPHERE.border
Selecting "Show Parent" led me here:
FS-to-F99_Aug10.zip
http://sums
Not really. Caret (and SureFit, from which the segmentation stuff came) just
wasn't designed to segment the skull. You can toggle on keep intermediate
files and look at the various intermediate volumes to see if you can use one of
them as a starting point, but I don't think any of them will wo
significance metric are there.
Note that for a two-tailed test (our norm), we use alpha of 0.025, because we
usually do both hems.
On Apr 17, 2012, at 4:12 PM, Donna Dierker wrote:
> Your trouble packing up those files will be rewarded if you execute:
>
> caret_command -file-convert -forma
Your trouble packing up those files will be rewarded if you execute:
caret_command -file-convert -format-convert XML_BASE64_GZIP *topo
On Apr 17, 2012, at 1:57 PM, gangli wrote:
> Hi Donna,
>
> I have uploaded the file 0yrVertexArea.rar, which contain all the files and
> command used for TFCE
And all four of these files exist and are colocated with the .metric:
LEFT-RIGHT.VertexArea.tmap.random.5000x.metric.data1
LEFT-RIGHT.VertexArea.tmap.random.5000x.metric.data2
LEFT-RIGHT.VertexArea.tmap.random.5000x.metric.data3
LEFT-RIGHT.VertexArea.tmap.random.5000x.metric.data4
If so, then ple
that tool will generate the
> randomized stat maps using a strategy like those in Nichols & Holmes' primer
> paper.
> But you can do a paired diff on the depth maps. Just make sure the composites
> have the columns in corresponding sequence.
> Sorry to get your hopes up on
ndomized stat maps using a strategy like those in Nichols & Holmes' primer
paper.
But you can do a paired diff on the depth maps. Just make sure the composites
have the columns in corresponding sequence.
Sorry to get your hopes up on the coords.
On Apr 5, 2012, at 4:40 PM, Donn
I put three scripts here:
http://brainmap.wustl.edu/pub/donna/US/UNC/
login pub
password download
For the coords, you'll need a different test -- coord anova:
http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation:Statistics#Coordinate_Difference_Analysis_of_Variance
One of those scripts
My versions of caret_command can read them all, and the coords/metric all have
roughly 164k nodes -- all good.
But I still don't have your command line, or inputs like I'd expect to a paired
t-test, if that's what you're doing.
For each subject, I have a metric that has a column for 3D variabil
Hi Gang,
Could you provide the full command line and/or output from running the script?
It might not work in Windows, but on Linux or MacOSX command line you would do:
paired.sh >& paired.log
Then upload paired.log here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
Depending on what informat
Hmmm. Which test are you using? What was the format of your input files, and
what is the Caret version and platform you are running? I wonder if this might
be related to a compiler bug issue that recently surfaced.
On Apr 3, 2012, at 3:44 PM, gangli wrote:
> Hi Donna,
>
> Thanks for your s
Just do areal distortion. It'll be easier to average the results.
You can average them with caret_command's math function, but I find it easier
to do it in the GUI. Load the resulting shape/metric files as metric, making
sure one column for each subject is loaded -- areal only -- and do Attrib
Enter caret_command -file-convert at the command line, and maybe redirect the
output to a file, because it is quite lengthy. It will tell you how to convert
Freesurfer surfaces.
They'll need to be on a standard mesh. And you can't do a paired test across
hemispheres, because there is no node
jacks your machine and grinds to a halt after i iterations,
then try another JRE.
On Mar 29, 2012, at 7:35 PM, Donna Dierker wrote:
> Sure: If you've got a simple t-test, then caret_stats can help. But you
> won't find caret_stats in your Caret distribution. I can package
Sure: If you've got a simple t-test, then caret_stats can help. But you won't
find caret_stats in your Caret distribution. I can package it up for you
tomorrow. It runs on java. I have had problems with multiple java runtime
engines in the past. A coworker found a much improved JRE that ma
Hi Gang,
First, you need some method to generate 5000 iterations of your data,
randomized by some method like the ones in Nichols & Holmes primer paper:
http://www.fil.ion.ucl.ac.uk/spm/doc/papers/NicholsHolmes.pdf
The "Primer Paper",
TE Nichols and APHolmes.
Nonparametric Permutation Tests for F
Hmmm. Even my old "switch to an english character set" standby advice seems
unlikely to work in this case.
I don't have a Windows machine, so I doubt I can replicate your problem, but I
can have a look at your cropped anatomical volume, if could upload it here:
http://pulvinar.wustl.edu/cgi-bi
blob
> where the voxels were value 2, then they'd get a different color when you
> mapped them.
On Mar 22, 2012, at 9:05 AM, Donna Dierker wrote:
> Hi Shanti,
>
> If I understand you correctly, you mapped this ROI/paint/label volume as
> paint, so if both ROIs mapped to u
Hi Shanti,
If I understand you correctly, you mapped this ROI/paint/label volume as paint,
so if both ROIs mapped to unknown_name_1, then that means they must have had
the same intensity/integer value in the volume.
If you had one ROI where all the voxels had value 2, but then another blob
whe
Hi Carissa,
The PALS surfaces are available in several versions of stereotaxic space:
http://brainvis.wustl.edu/help/pals_volume_normalization/
Typically, functional connectivity seed regions are displayed as foci, but the
rs-fcMRI maps are often displayed as metric maps, too. It often depends
I don't have the answers at my fingertips, but here are a couple of clues that
I recall from recent experience doing this:
* Enter "caret_command -help-full > /tmp/caret_command.txt" at the command
line, and then use a text editor to read /tmp/caret_command.txt. Search for
"file-convert" and l
Regarding the connections, this is something we're working on, and I don't
think we have anything ready for public release. If you have something in
volumetric form, you could display it, and you could view surface and volume
together, varying the opacity, but I suspect you have something else
Try something like AFNI's to3d.
On Mar 9, 2012, at 11:04 AM, Timothy Coalson wrote:
> I believe .ima is an extension used for dicom data, try a dicom to nifti
> converter such as dinifti or dcm2nii (part of mricron).
>
> Tim
>
> On Fri, Mar 9, 2012 at 9:09 AM, Maestri, Matthew
> wrote:
> Hi
Yeah, several years back, we started tapering off on the flat views in favor of
the inflated or very inflated views. Internally, I think we still use flat
maps quite a bit, but for publication purposes, the inflated and very inflated
views are more easily understood for many readers.
My guess
Only the Conte69 surfaces are available for FNIRT mapping; there are no PALS
surfaces that have been registered using FNIRT -- just FLIRT and the other
methods listed here:
http://brainvis.wustl.edu/help/pals_volume_normalization/
The Conte69 surfaces are on the new fs_LR standard mesh (164k ve
line so it is more specific
> than "Re: Contents of caret-users digest..."
>
> Today's Topics:
>
> 1. Re: Interspecies comparisons - creating a new atlas for a
> different primate species (Donna Dierker)
>
>
> -- Forwarded message -
Tristan's comment triggered me to post a list of caret_command's features
(enter "caret_command -help-full" to get full usage/help):
caret_command -caret-data-file-compare
caret_command -caret-file-name-unit-test
caret_command -caret-help-create-html-index-file
caret
ia the World Wide Web, visit
>http://brainvis.wustl.edu/mailman/listinfo/caret-users
> or, via email, send a message with subject or body 'help' to
>caret-users-requ...@brainvis.wustl.edu
>
> You can reach the person managing the list at
>caret-users-
It's possible, but this isn't what preborder.sh does. First, its depth maps
are generated from a version of the midthickness that has been stereotaxically
registered to WashU's 711-2B space (because this is what the probabilistic
volumes representing the sulci are in). But also it has already
are very interested registering this atlas to the macaque monkey
> and doing analyses similar to Hill et al. (2010).
>
> Thanks,
> Tristan Chaplin
>
> On Mon, Feb 7, 2011 at 16:04, Tristan Chaplin
> wrote:
> Ok thanks for the information.
>
>
> On Fri, Feb
Not really, but if you are using a non-English character set, switching to an
English one seems to solve all sorts of seemingly unrelated problems.
It has been a very long time since I have segmented on Windows, but from what I
recall, Caret launched from a command prompt, and you could often se
Caret 5.65 is released. It contains these fixes and added features:
* WashU 711-2* PALS-B12 left hem mapping only: Fix a problem with PALS_B12
left case 03 and average fiducial surfaces
(http://brainvis.wustl.edu/help/wustl_origin/align2.2).
* Add an error check in case a file is truncated.
*
e list at
>caret-users-ow...@brainvis.wustl.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of caret-users digest..."
>
> Today's Topics:
>
> 1. Re: painting the entire GM thickness accurately fr
This ended up off-line, but was resolved by switching to an English character
set.
Begin forwarded message:
> From: Donna Dierker
> Date: December 30, 2011 1:58:51 PM CST
> To: vimr...@gmail.com
> Subject: Re: [caret-users] error in overlay
>
> You can map cubic 2mm funct
I just don't think there is an easy way to do this in Caret right now, but I
know that won't stop you. ;-)
You might try something like this:
map surf paint to vol using white, specifying outer thickness >0
map surf paint to vol using pial, specifying inner thickness >0
union these volumes and f
gt; Thank you Donna,
>
> It was specified. even I tried changing name of it. still same error.
>
>
> On Thu, Dec 29, 2011 at 6:45 PM, Donna Dierker
> wrote:
> Make sure your metric filename is not empty; see attached capture for where
> it is specified.
>
>
Make sure your metric filename is not empty; see attached capture for where it
is specified.
<>
On Dec 29, 2011, at 10:22 AM, vin . wrote:
> Dear Caret Experts,
>
> A newbie to Caret, having problem to overlay .. getting error ''
> A metric file must be provided for metric mapping ''
>
> I f
Or a twist on Rouhi's suggestion, try converting it to binary; it might be the
same as the old format, i.e.:
caret_command -file-convert -format-convert binary
deformed_deformed_Human.FS006.L.Midthickness_711-2B.mws.73730.coord
Let us know if this works.
On Dec 14, 2011, at 5:53 AM, Rouhollah
, it seems that the problem is in the way I´m saving the
> serial section file (XML format) in Neurolucida.
>
>
>
> Do you know how it´s done in Mdplot?
>
>
>
> Thanks,
>
> Andrei
>
>
>
> 2011/11/30 Donna Dierker
> Hi Andrei,
>
> B
Hi Andrei,
Because I have no Neurolucida experience, I feel pretty helpless to help you.
But my hunch is that Caret would need two different files to open/import -- the
contours and the cells. (And cellcolor, too, but I'd think you'd at least see
black dots of the cells were there.)
First th
I confess I don't follow this 100%, but if you are faced with monkey
segmentation challenges, Colin's recipe might help.
Begin forwarded message:
> From: Colin Reveley
> Date: November 20, 2011 11:20:16 AM CST
> Subject: homoeomorphic to sphere
>
>
> the problem of a minor topological defect
Without having an actual GM/WM surface to use as a mapping substrate, any
solution will be sub-optimal. If you can get a white surface, then map to it.
Otherwise, here are some ideas:
* Use either gaussian or MCWBrainfish as your mapping algorithm, instead of
enclosing/interpolated voxel:
htt
This is an older version of Caret, and it is a very minor problem.
For some reason, the first of the 12 Buckner subjects that went into the
PALS_B12 atlas had a deformed fiducial surface with some spikiness -- a problem
that is fixed by a small number of smoothing iterations after registration.
No cropping is needed, but the "paint volume" (aka label/ROI/parcellation
volume) needs to be in register, volumetrically, with the anatomical volume
used
to generate the fiducial surface. The voxdims need not match, but the origin
and rotation must match. Headers must correctly identify the
istinfo/caret-users
> or, via email, send a message with subject or body 'help' to
>caret-users-requ...@brainvis.wustl.edu
>
> You can reach the person managing the list at
>caret-users-ow...@brainvis.wustl.edu
>
> When repl
caret-users-requ...@brainvis.wustl.edu
>
> You can reach the person managing the list at
>caret-users-ow...@brainvis.wustl.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of caret-users digest..."
>
> Toda
with subject or body 'help' to
>caret-users-requ...@brainvis.wustl.edu
>
> You can reach the person managing the list at
>caret-users-ow...@brainvis.wustl.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re:
"this is now where our development effort is focused these days" should have
read "this is NOT where our development effort is focused these days"
On Oct 25, 2011, at 9:33 AM, Donna Dierker wrote:
> Sorry I don't have time to read this more carefully, but I'm s
ith a high resolution monkey file (do you use the 64
> bit version of caret?).
>
> However, Donna Dierker gave me some pointers, why it would be problematic to
> use a voxel size different from 0.5 mm. I am not sure, if this is still true,
> but that might be a reason for you
This can wait a week or so to be addressed, but I wondered whether others had
noticed this behavior.
When the user loaded a STANDARD-SCENES spec (both or left), and selected
Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_711-2C.clean.align.73730.coord, the PALS
inflated, and very inflated surfaces, the
specific box specifying that I want to use my own palette file, it is
> not ticked by default just as the .coord and .topo files.
>
> I think I am missing something to mention at the beginning to specify to
> caret to get the correct palette file.
>
> Thanks,
>
> Best w
There probably is more than one way to do this. The way I'm used to batching
images is using caret_command -show-scene with some TEMPLATE.scene file that
has variable names like FIDUCIAL_FNAME for any files that vary. The palette
file will probably remain constant across your subjects, so stor
There are probably many from which to choose, but here is one:
PALS_VE05_FIG-2F-O.LANDMARKS_INDIVIDUAL_POP-AVG.73730.spec
http://sumsdb.wustl.edu/sums/downloadspecfile.do?archive_id=6259845
Scene Fig-2N, for example.
You can also download the registration target dataset and view it that way:
ht
I'm afraid that's because disconnecting the hindbrain really isn't optional,
the way the checkbox suggests. You pretty much have to crop to a hemisphere;
center the volume near the anterior commissure; and be happy with a hemispheric
segmentation/surface. (At least this is how it was last time
Size" either by min nb of nodes or min
> >surface area.
> It is those values that I've tried modifying without any luck: I create a new
> metric column with my cluster min size, change the column name in my
> visualization, but all my clusters remain.
>
>
>
Hmmm. I don't know that Caret can do this. There are several cluster-based
tests that find the minimum area required to correct for multiple comparisons,
given an input cluster-forming threshold (say, t=+/-3.0):
caret_command.txt: caret_command -metric-statistics-anova-one-way
caret_com
Have a look at the documents and datasets available here:
http://sumsdb.wustl.edu/sums/stereotaxictocaretfoci.do
Also, these colin cerebellar surfaces are included in the caret distribution,
for mapping and foci projection purposes:
caret/data_files/fmri_mapping_files/Human.colin.cerebellum.LR.
See inline replies.
On Aug 17, 2011, at 2:24 PM, Colin Reveley wrote:
> There's a pipeline from freesurfer to caret and ve has put in summs db a doc
> and data sets about to register a freesurfer surface to f99.
>
> Im interested in using afni suma and freesurfer more.
>
> But what I need is t
201 - 300 of 852 matches
Mail list logo
