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
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
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
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
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
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
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
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
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
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
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
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:
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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:
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
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
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
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
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
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)
>
>
> -
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
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
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
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
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
"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
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
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-
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
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
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
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
___
> 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
> 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:
roblem.
>
> Thank you,
>
> Yuichiro Shimizu
>
> 2012/11/15 Donna Dierker
>>
>> Hi Yuichiro,
>>
>> I think the most efficient thing is for you to upload your T1 & T2 NIFTI
>> volumes here:
>>
>> http://pulvinar.wustl.edu/cgi-bin
h/Template). Is there any script to add path for
> each file since I think these files may be saved under different directories,
> not only /usr/local/caret/data_files/fmri_mapping_files/.
>
> Thanks,
> Huiling
>
> From: caret-us
Hi Nimit,
Have you read the tutorials here:
http://sumsdb.wustl.edu/sums/stereotaxictocaretfoci.do;jsessionid=pygt0bden1
Donna
On Nov 17, 2012, at 1:47 PM, Nimit Sohoni wrote:
> Here is the excel file layout:
>
> Coordinates in MNI space
> ROI# XY Z
> 1 "some coordinat
with any particular study. Can one do this?
>>
>> On Mon, Nov 19, 2012 at 10:25 AM, Donna Dierker
>> wrote:
>> Hi Nimit,
>>
>> Have you read the tutorials here:
>>
>> http://sumsdb.wustl.edu/sums/stereotaxictocaretfoci.do;jsessionid=pygt0bden1
&
To my knowledge, there is no "flipLR.sh" script that x-flips the volumes and
surfaces; updates the specs and scenes; etc.
It is possible, but not simple, in my opinion. Fast is in the eye of the
beholder, but I'm guessing you could pull it off under a week, QA included.
Reliable -- this is the
Hi Fried,
I don't think you need install-caret anymore. It just added read and execute
permissions to some of the subdirectories, but I assume those already have the
needed permissions now. Otherwise, if you do run into permissions problems, a
simple chmod -R 757 /usr/local/caret might do the
Passing on Colin's thoughts on matlab.
Begin forwarded message:
> From: Colin Reveley
> Subject: Forward to list
> Date: December 7, 2012 12:34:38 PM CST
>
> I can't figure out how to use my iPad to send to the list. Could you pleas
> forward:
>
> Tim: thanks. That sounds like a confusing pro
thank you for your responses.
>
> Do you know where I could find the MNI coordinates
> of the PALS B12 surface ?
>
> Best, Frederic
>
>
> Frédéric Roux
> Postdoctoral Researcher
> www.bcbl.eu
>
> - Original Message -
> From: "Donna Dierker&qu
Hi Isabelle,
I haven't answered, because I don't know the answer. I searched the archives
and couldn't find that error. Googling it doesn't enlighten me much either.
Maybe one of the programmers will have a better idea. Meanwhile, it might help
to provide the exact name of the zip file you
On Dec 16, 2012, at 3:03 PM, Colin Reveley wrote:
> Hi -
>
> I want to make a figure like the attached, which is from lewis + van essen
> 2000.
>
> the difference is that my data is all MRI (it's FSL diffusion tracking), but
> I want to present it exactly like this.
>
> clearly producing th
Besides the focus number and x,y,z, you need some other fields (e.g., name,
comment-number, section-number, class-name). See this page:
http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#cellFile
Foci and cell files are identical in format. Try also just call
ot;None" as the name for all foci. I changed the name
> first to .foci, then back to .foci.csv, but it still froze both times I tried
> loading.
>
> On Wed, Dec 19, 2012 at 8:55 AM, Donna Dierker
> wrote:
> Besides the focus number and x,y,z, you need some other fie
ject the foci and send
you the fociproj.
>
> On Thu, Dec 20, 2012 at 12:36 PM, Nimit Sohoni wrote:
> Hmm, I don't believe so. At least, I am using the default English character
> set; I am using a Mac so there might be others installed, but they aren't in
> use.
>
&g
If you import a Freesurfer surface into Caret, it won't align with the volume
in mri/orig.mgz until you apply an offset transformation defined by something
like mri_info -cras (I forget the exact command). Depending on which surface
you apply that transformation -- before or after cras offset -
-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: transform surf and vol (Donna Dierker)
>
>
> -- Forwarded
Toolbar: D/C: Metric Settings, near the bottom
On Dec 27, 2012, at 8:52 PM, Dawei Li wrote:
> Hi all,
>
> I would like to map several functional images on a single PALS-B12
> atlas to directly compare activations. I was able to go through all
> the steps except that I couldn't find an option
I don't know why it is failing, but I would try mapping to just one surface at
a time (left or right), and see if it works that way (i.e., aiming for a
work-around).
On Jan 3, 2013, at 9:49 PM, Jack Grinband wrote:
> Hi,
> I'm new to caret. I am trying to get my activation map to show up on
>
The one thing that comes to mind is to make sure D/C: Foci Main: Show Foci is
toggled on.
On Jan 3, 2013, at 9:21 PM, Roy Smith wrote:
> Can one walk me through how to project foci to a surface step by step and
> display them? I was given foci, focicolor and fociproj files (they are
> errorle
right sides of a brain?) I tried it but one goes away when I do that,
> even though I selected the "Keep Loaded Spec" option.
>
>
> On Fri, Jan 4, 2013 at 7:18 AM, Erin Reid wrote:
> Also make sure you have a Fiducial surface loaded.
>
> On 1/3/13 10:19 PM, Donna
Also, Eva (we've traded off-list messages), your volume seems to load okay --
overlays avg152T1 reasonably well, but it's patchy and I ran into trouble
mapping it on my end (the dreaded "you need a metric file for metric mapping"
message, even though I specified one).
You said it failed -- how?
Hi Ana,
I'm not sure Caret (caret5, at least) does what you want. There is this:
caret_command -surface-geodesic
[-node node-number]
Generate the geodesic distance from all nodes to all other nodes
unless a nod
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..."
>>
>>
>> Today's Topics:
>>
>>1.
As I indicated off-list, you can project the PALS lobar parcellation from
surface-land to volume-land, specifying a thickness below the surface, but this
will miss white matter beyond that thickness.
You probably need a proper volumetric parcellation of the lobes (frontal,
parietal, occipital,
Hi Isabelle,
Have you tried projecting the cells (something like Layers: Cells: Project
Fiducial Cells -- or the foci equivalent of cells)?
I'm not sure caret5 has the opacity feature you seek, but look under D/C: Page
Selection: Surface Miscellaneous. You can select Hide Surface from the Draw
Sorry to several of you who posted over the last several weeks. We swapped
servers in February and thought we had things working. And most things are
working, but the list moderators were not getting notified of new posts, so
they weren't getting through. (We screen them, because spammers spo
I haven't noticed this particular problem. Using Toolbar: Spec and opening the
desired area color, choosing Replace when prompted, might be easier (or might
not).
But what I have noticed is that even after I open the right area color file and
replace, and save a scene with that area color file
Erin might know more, since she has actually done this, but I'm giving my
guesses below -- worth every bit you paid for them.
On May 2, 2013, at 8:24 AM, Colin Reveley wrote:
> a) Is it possible to make a surface from saggital or horizontal sections,
> rather than coronal sections?
I have ne
Hi Luke,
You can definitely analyze your data in surface-land, though many people put
their metric/surface_shape files into matlab or some third-party package to do
this.
There is a caret_stats package that does a few basic stats tests (e.g., two
sample and paired t-tests; one-way ANOVA). See
I believe Eva and I troubleshooted this issue off-list.
On Apr 5, 2013, at 5:24 AM, Eva Hilland wrote:
>
>
>
>
>
> Hi Caret-users,
>
> I have used Caret lately for visualization of group-level fmri results, and
> it works very well. Yesterday I encountered a problem that I never
> exper
Hi Alex,
Yes: You can write out Caret coord files as ASCII text:
http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#coordFile
You can use caret_command -file-convert -format-convert to batch convert a
bunch of coord files, or you can use the File: Save Data F
I should have been more clear: "I doubt it" was in response to this:
> is it required that the contours be midthickness
I would think you could at least fool it into working.
On May 7, 2013, at 1:28 PM, Colin Reveley wrote:
> thanks
>
> re: saggital and horizontal: forget that then.
>
>
This can be tricky/weird. The surfaces need to be in the same view, in the
sense of Surface: View: Adjust View (scale, rotation, translation, etc.) -- in
the main window.
For example, say you have mean midthickness surfaces for group A in Window 1,
group B in Window 2. Both are dorsal view.
If you need more info, would you like me to post your query on
hcp-us...@humanconnectome.org? This list tends to be more caret5 inquiries,
although I suppose it also supports Caret workbench. Questions about the HCP
dataset and pipeline clearly fall under the hcp-us...@humanconnectome.org scop
This post, along with Matt's earlier one triggered the important point that the
CIFTI file format is coming along very fast -- progressing quickly from "nice
idea in theory" to "David and Matt are using this all the time." It's covers a
lot of data types:
http://www.nitrc.org/plugins/mwiki/ind
I think the most efficient way to help is for you to put the volume you are
mapping (a label/ROI volume) along with the surface files together in a single
directory, then zip it up and put the zip file here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
If there is an anatomical volume that alig
The .bash_profile and/or .bashrc files are appropriate for bash users, but for
tcsh, modify like so:
1. If you didn't install caret in /usr/local, then replace /usr/local below
with the parent dir where you unzipped caret.
2. Use a text editor, vi, or other editor to append this line to your ~
On Jul 2, 2013, at 12:24 PM, Colin Reveley wrote:
> When one saves a paint volume in caret as a nifti, there are two header
> extensions that reflect the value<->name mapping.
>
> One of these is an afni header extension. It is marked as deprecated.
Is this the LUT_NAMES, where the ordinal pos
I'm pretty sure you're the first person to ask that question. Or at least the
first I've heard it.
Obviously the macaque and human brains have different scales, but it might, in
principle, be possible. Computing a volumetric transform from the F99
individual monkey volume to either MNI305 or
uman
> MNI.
> thanks a lot
> Pablo
>
>
> 2013/7/8 Donna Dierker
> I'm pretty sure you're the first person to ask that question. Or at least
> the first I've heard it.
>
> Obviously the macaque and human brains have different scales, but it might,
> i
Hi Nicky,
Sorry I can't help. I doubt there are many Windows users who edit
segmentations out there. (Could be wrong.)
The only suggestion I have is that if you have some other program (e.g.,
MRIcron) that can edit voxels, you can do your editing there; save the
resulting NIFTI volume; and t
Hi Nan,
1. Identifying a focus or two among a forest of foci: If you know the name of
the focus, you use D/C: page dropdown = Foci Name to toggle all off, then
toggle on just the ones you want. If you don't know their names, then you can
save the foci file as a csv file and use a spreadsheet
ng you to do your analysis on the surface, rather than on
the volume. Matt does very fine-grained work for which he finds volumetric
analysis/display inadequate. As a complement to surface-based display and
analysis, he uses volumes all the time.
> --Michael
>
>
>
> On Sat,
Hi Zhuangming,
The orientation issue needs sorting, because downstream things will fail if
that's not right. Upload the volume to which your surface is aligned here:
http://brainvis.wustl.edu/cgi-bin/upload.cgi
I may not be able to look at it until tomorrow, but someone else might get a
chanc
Make good friends with these features:
* Surface: View: Adust View
* Surface: View: Save View
* D/C: Scenes: Append Scene / Save New Scene
The first two features are pretty much what you want and not a lot of
power/complexity you don't want.
But the fact that you're crea
Sounds like you have a segmentation already, so don't use -volume-segment.
Try something like this instead:
caret_command -surface-identify-sulci $SPECFNAME $HEM $SEGVOL $TOPO $FIDUCIAL
$FIDUCIAL
---
caret_command -surface-identify-sulci
ntation -> Reconstruct into surface.
>
> On Fri, Jul 26, 2013 at 2:00 AM, Donna Dierker
> wrote:
> Sounds like you have a segmentation already, so don't use -volume-segment.
>
> Try something like this instead:
>
> caret_command -surface-identify-sulci $SPECFNA
Hi Daniel,
Can you send a listing of the directory containing the surfaces you're using?
This will tell us not only whether you're using PALS or fs_LR, but also whether
you are using caret5-style files or workbench (GIFTI) style files.
This file, for example, will work if you've got fs_LR me
soon. Thanks a lot for your help!
>
> Best,
> Daniel
>
> --
> Yung-Jui "Daniel" Yang, PhD
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> (203) 737-5454
>
> On 7/29/13 10:08 AM, "Donna Dierker" wrote:
>
>
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