Hi Marco,
Very cool. I'll try running these new libraries on our Linux test
clients here. If I run into no problems, I'll incorporate this change
(i.e., undefining HAVE_FTRUNCATE when building netcdf libs) into our
next Linux distribution, so other users of *fat* file systems won't run
not aware of anyone who has done so.
Other posts to this thread also would be of interest to the SureFit
mailing list ([EMAIL PROTECTED]).
Thanks,
Donna Hanlon
Van Essen Lab
Washington University School of Medicine
http://brainmap.wustl.edu
Bruce Fischl wrote:
Hi Johannes,
sorry, we don't
Hi Marco,
I confess you have piqued my curiosity. Would you mind uploading your
dataset (gzipped tar file containing the directory with the structural
volume, as well as SURFACES subdirectory) to our upload site:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
If you'd rather not,
Hi Marco,
Let's make sure you're doing what we are expecting you to do, since
there is no tutorial yet for Map to Individual:
* On the Map fMRI to Surface dialog, select the volume as you specified
below.
* Select Map to Individual.
* Press the Parameters button.
* Press the Params button
Hi Carsten,
Odds are you didn't select a checkbox in the cut faces section of
SureFit's Volume Preparation, Define VOI and Identify Cut Faces tab.
Are you really segmenting a partial hemisphere? If so, what part did
you crop out? If you cropped out the frontal lobe (i.e., you segmented
an
Hi Luke,
I'm hoping your problem is the one documented here, because there is a
quick and easy fix for it:
http://brainmap.wustl.edu/SureFit/RELEASE_NOTES.html#mesa3dnow
Let me know either way whether setting MESA_NO_3DNOW fixes it.
Donna Hanlon
PS: I like your hostname.
Luke Bloy wrote
Hi Mark,
I think David is probably the best person to respond to your questions,
but he's out of town today; he should be back tomorrow. He may have had
a good reason for making the left hem cut the way he did, and I don't
know how redoing the calcarine cut would impact registration.
This is Donna Hanlon forwarding a message from Mark Pinsk, with the
attached screen capture removed and put here:
http://pub:[EMAIL PROTECTED]/pub/donna/v_RH_fiducial.jpg
login pub
password download
Mark -- the only attachment that made it through to the caret-users
moderator approval
Hi Dr. Hinkley,
You can write your SPM normalized functional volumes out in 2x2x2 and
map them to the colin atlas. Just make sure you select the right
bounding box.
Could you give me the URL where it states the default spm2 voxel size is
at 1x1x1? I need to clarify/correct it.
Donna
On
Hi Veronica,
Do which caret at the command line. It's possible you have multiple
versions installed, and it's finding the old version due to the way the
PATH variable is set in your .cshrc or .bash_profile.
Donna
On 05/06/2004 01:53 PM, Veronica S. Smith wrote:
Hi,
I just installed Caret
Hi Marc,
After you run Prepare for Flattening in SureFit, then you can open the
resulting spec file in caret and do Surface: Measurements: Crossover
Check.
It's not all that uncommon to have a few (e.g., 3) errors left, yet not
be able to see them on the inflated surface. If, after
- Original Message -
From: Donna Hanlon [EMAIL PROTECTED]
To: Caret, SureFit, and SuMS software users
[EMAIL PROTECTED]
Sent: Thursday, May 20, 2004 11:35 AM
Subject: Re: [caret-users] surefit correcting residual errors
Hi Marc,
Your first error object (16-22,71-78,3-9) was a tiny
-
From: Donna Hanlon [EMAIL PROTECTED]
To: Caret, SureFit, and SuMS software users
[EMAIL PROTECTED]
Sent: Tuesday, June 01, 2004 9:53 AM
Subject: Re: [caret-users] surefit correcting residual errors
Hi Marc,
Sorry for the belated response; Monday was a US holiday, so none of us
were
crossovers are along the perimeter.
thanks,
marc
I was not able to find errors in the places you mentioned
- Original Message -
From: Donna Hanlon [EMAIL PROTECTED]
To: Caret, SureFit, and SuMS software users
[EMAIL PROTECTED]
Sent: Tuesday, June 01, 2004 12:16 PM
Subject: Re: [caret-users
recommended.
Donna
On 06/03/2004 08:15 AM, Marc Malloy wrote:
I have uploaded my latest segmentation.
When making the cut, you want to cut along the sulcus to the perimeter of
the brain, correct?
- Original Message -
From: Donna Hanlon [EMAIL PROTECTED]
To: Caret, SureFit, and SuMS software
Marc Malloy and I carried on a series of exchanges off-list, which
eventually produced a decent segmentation of his partial hemisphere.
But I learned something in the process that I wanted to pass on to the
list: When you have a partial hemisphere that includes substantial
portions of the
Hi Mellanie,
I had a look at the segmentation you uploaded, and I checked your peaks.
I would have selected exactly the same peaks you did, so they were not
the problem in this case.
It's tough to see where the connecting strands are in the surface
windows, because the skull obstructs the
Sophie,
First, I want to clarify what you did. I think you mean this:
* you generated a *segment_vent_corr*mnc file using SureFit
* you imported this .mnc as a segmentation volume into Caret
* you used Volume:Segmentation: Edit Voxels to patch the .mnc
* you tried and failed to flatten the
is of the occipital lobe, is it necessary to create
a functional volume with a mask that masks out everything except the
occipital lobe? Or does Caret ignore what the flat map does not cover?
Thanks again!!
marc
- Original Message -
From: Donna Hanlon [EMAIL PROTECTED]
To: Caret
to be fixed.
it runs, but how do I go about fixing this?
marc
- Original Message -
From: Donna Hanlon [EMAIL PROTECTED]
To: Caret, SureFit, and SuMS software users
[EMAIL PROTECTED]
Sent: Tuesday, June 15, 2004 12:07 PM
Subject: Re: [caret-users] generating fMRI metric file for flat map
Hi
uploaded the files.
marc
- Original Message -
From: Donna Hanlon [EMAIL PROTECTED]
To: Caret, SureFit, and SuMS software users
[EMAIL PROTECTED]
Sent: Wednesday, June 16, 2004 9:55 AM
Subject: Re: [caret-users] generating fMRI metric file for flat map
Hi Marc,
For what you're
See inline comment below.
On 06/18/2004 07:58 AM, David Field wrote:
Dear Caret users,
I am new to Caret, and am trying to import fMRI data from a group study
analysed using SPM2 as a metric file so that I can view it on the Colin
atlas. I'd be very grateful for some help with the following
uploaded the files
marc
- Original Message -
From: Donna Hanlon [EMAIL PROTECTED]
To: Caret, SureFit, and SuMS software users
[EMAIL PROTECTED]
Sent: Friday, June 18, 2004 3:59 PM
Subject: Re: [caret-users] generating fMRI metric file for flat map
See inline responses below
Hi Sandra,
On 06/18/2004 07:15 PM, Sandra Basic wrote:
Can you tell me if it is neccessary to align lower scale mark of the
section to the origin although the contours, once I do it, appear out of
alignment.
I don't think it needs to be the origin, but it should be consistent
throughout all
Hi Timothy,
Hmmm. I just to recreate your problem using the output of 3dAFNItoMINC
Human.colin.LR.TLRC-711-2B.111+tlrc.HEAD, and my initial segmentation
after filling ventricles, but before automatic error correction, had no
missing chunks like yours. I'd like to see your cropped structural
through FSL's
fast and see how the bias-corrected volume does in SureFit.
Donna
On 06/23/2004 02:20 PM, jarv0075 wrote:
On 23 Jun 2004, Donna Hanlon wrote:
Hi Timothy,
Hmmm. I just to recreate your problem using the output of 3dAFNItoMINC
Human.colin.LR.TLRC-711-2B.111+tlrc.HEAD
After Tim Jarvis reported problems with SureFit omitting large parts of
cortex near the eye, we carried on further discussion off-list.
While some of you may have experienced cases where SureFit failed to
fully remove all the eye fat (requiring well-placed zaps in either the
segmentation or
Hi Albena,
John Harwell is out of the office today, but let's just make sure caret5
is actually finding the libstdc++.so.5 you installed.
1. Enter which caret5 on the command line.
2. Enter ldd /usr/local/caret/bin/caret5 on the command line
(replacing the full pathname of caret5 with the
Hi Sandra,
If these are volume files, if you can save them as old Analyze 7.5
.hdr/.img format, caret5 can open them directly as volume
anatomy/functional files.
I understand you can also save .obj files as volume (.hdr/.img) files
in Analyze, so you can open them as a volume segmentation
Malloy wrote:
Hi Donna
the matrix file is part of my spec file and I loaded it when I made my spec
file selections.
I did File: Open Data File: Volume Comm Matrix right after I created the
matrix file.
marc
- Original Message -
From: Donna Hanlon [EMAIL PROTECTED]
To: Caret, SureFit
Hi Marc,
What happens when you move your cursor over the narrowest part of the
connecting bridge in the surface window and press 'p' (for 'pick') on
your keyboard? This should take your slice window cross-hairs to the
corresponding voxel in the segmentation (assuming you have *segment*mnc
. We
tried zapping voxels at that point and regenerating the surface, but this
did not disconnect the skull from the brain.
Marc
- Original Message -
From: Donna Hanlon [EMAIL PROTECTED]
To: Caret, SureFit, and SuMS software users
[EMAIL PROTECTED]
Sent: Thursday, July 15, 2004 12:50 PM
Hi Mellanie,
First, make sure your *segment_vent_corr.fiducial*vtk surface is loaded as
surface 1, and the inflated surface as surface 2. This is because the
coordinates of surface 1 are used for the picking function, and the fiducial
surface's coordinates will be closer to the offending
On 07/21/2004 02:58 PM, Jeff Browndyke, Ph.D. wrote:
Hello all,
Sorry in advance for the annoying newbie question but, can CARET / SUREfit
do the following:
1.) generate cortical thickness data for later use in VBM
No, but Freesurfer can.
2.) generate fMRI activity group maps based upon
Hi all,
The Van Essen Lab is switching our web and mail server from
pulvinar.wustl.edu to brainvis.wustl.edu.
I'm going to turn off the list for a short while to bring over the
archives, etc. I'll also redirect list traffic from pulvinar to brainvis.
When the list is back online, I'll let
We should be back in business now.
On 07/22/2004 11:01 AM, Donna Hanlon wrote:
Hi all,
The Van Essen Lab is switching our web and mail server from
pulvinar.wustl.edu to brainvis.wustl.edu.
I'm going to turn off the list for a short while to bring over the
archives, etc. I'll also
since '_corr' was not appended to the
file name
and even the object list remained the same. Why didn't error correction
occur?
Also, what is the difference between a cavity and a handle? Which of
these
errors is worse?
-Mellanie
- Original Message -
From: Donna Hanlon [EMAIL
Marc,
First, make sure the fiducial cited in the matrix file is the one whose
center matches the ORIGIN in the afni anatomical volume.
It's a good idea in afni to move to where the x,y,z coordinate in the
afni main window shows 0,0,0 (or very close to it). This should match
the anatomical
Actually, before tranlating by minus the SPM originator less one, you'd
need to translate +Xmin,+Ymin,+Zmin.
But I doubt that it is necessary to do this at all.
On 07/29/2004 11:37 AM, Donna Hanlon wrote:
Hi Sophie,
Some things to check:
1. The anatomical to which the EPI scans were
SPM users,
I agree with John that using the caret built-in mapper is often quicker
and easier than using the map_fmri_to_surface program. But I'd like to
qualify this statement in John's reply below:
* Your fiducial surface should have its origin at the anterior
commissure.
This is true
in the maptoindividual parameters cropping box to
align them together?
Sophie
*/Donna Hanlon [EMAIL PROTECTED]/* wrote:
SPM users,
I agree with John that using the caret built-in mapper is often
quicker
and easier than using the map_fmri_to_surface program. But I'd
like to
qualify
Mellanie,
When I'm flattening and get only 89 crossovers, sometimes I'm relieved.
But I was able to see the two areas that could be improved in your
segmentation.
In caret, when you try to flatten, you can see two patches in the
compressed medial wall view (see attached file
Hi Mark,
Try setting the MESA_NO_3DNOW environment variable as shown here:
http://brainmap.wustl.edu/SureFit/RELEASE_NOTES.html#mesa3dnow
Cross your fingers and retry SureFit. I'm hoping it works.
Donna
On 08/12/2004 11:40 AM, Mark Bolding wrote:
I have installed SureFIT per the included
Hi Mellanie,
Actually, there are seven handles after you press FloodFill Vol2. But I
could spot only two looking at the inflated surface.
One was in the familiar trouble spot, the parahippocampal gyrus (medial
surface view), while the other was near the temporal pole (ventral
surface
Hi Marc,
First, if you literally cannot see them on the surface, then they're
probably not worth worrying about.
But when you view the ellipsoid surface in Caret, if you can see the
handles, then you probably need to address the problem on the
segmentation side.
Otherwise, if it appears
Hi Mellanie,
Sure -- but you uploaded these files, which are necessary, but not
sufficient:
jan11_2003.L.full.sMRI.mnc
jan11_2003.L.full.sMRI.params
I still need the segmentation file.
Donna
On 09/03/2004 01:48 PM, [EMAIL PROTECTED] wrote:
Hi Donna,
There is a single handle left and it
For some reason, the archive search feature isn't working. I'm trying
to fix it.
Hi Mellanie,
Since intensities in the occipital lobe tend to be higher (especially
with volumes that have not been pre-processed with bias correction
software such as FSL's fast, MNI's nu_correct, or AFNI's 3dUniformize),
it's not unusual for sulci to fuse over in that region. Handles often
the segmentation:
jan21_2003.R.full.segment_vent_corr.patch2_corr.patch2_corr.patch4.mnc
Thanks,
Mellanie
Quoting Donna Hanlon [EMAIL PROTECTED]:
Hi Mellanie,
Since intensities in the occipital lobe tend to be higher (especially
with volumes that have not been pre-processed with bias
Hi Roland,
Weren't you with uni-oldenburg before? Did you relocate or did they
change their name?
I can't answer most of your questions; I hope John Harwell can. But
regarding question #2, I can understand the confusion, and I'm not sure
which context you saw this term in. If it was how
This message also was intended for the list, but mailman had a problem
with the attachment.
Original Message
Subject: [caret-users] Brainvoyager
Date: Thu, 21 Oct 2004 14:12:47 -0500
From: Donna Hanlon [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
CC: John Harwell [EMAIL PROTECTED
Hi Phtseng,
You have drawn attention to a well-known deficit in SureFit: There is no
quick, easy way to update the ERROR_CORRECTION_INTERMEDIATES/*errors*mnc
file, from which the SURFACES/*errors*RGB_paint is generated. This is
the same mnc file that is the default file selection when you press
Note: Mellanie's original post included a powerpoint capture of the
flat map whose size exceeded the list's limit. I've replaced that file
with the attached gif, along with my response to her query.
Hi Mellanie,
In caret, the black cross shows the location of the surface's origin.
The
on surface (Donna Hanlon)
--
Message: 1
Date: Thu, 11 Nov 2004 16:27:56 +0800
From: pohetsn [EMAIL PROTECTED]
Subject: [caret-users] about painting error on surface
To: caret-users@brainvis.wustl.edu
Message-ID: [EMAIL PROTECTED
SureFit users,
Some of you already may have installed this patch, but I don't recall
ever announcing it publicly (probably because I was afraid the 'fixes'
might break something). This gzipped tar file contains four python modules:
http://brainmap.wustl.edu/pub/donna/surefit_patch.tar.gz
Hi Dr. Ramon,
First, I should mention that we soon plan to release a new version of
Caret that not only revises the entire mapping interface, but also adds
support for the PALS_B12 (population-average landmark and surface based,
Buckner 12 individuals) atlas. The software and data are ready,
Hi Mellanie,
It might help to refer to Caret 4.6 Tutorial Part I, p. 25-26
(http://brainmap.wustl.edu/caret/pdf/CARET_UsersGuide.03-06.Part-I.pdf).
It shows how you can select one bucket (e.g., intensity bucket) for
viewing and another bucket for the threshold.
Whatever number is stored in
On 11/21/2004 10:16 PM, pohetsn wrote
By the way, I'd like to confirm that whether SureFit aims for a
segmentation
whose boundary runs approximately midway of inner bourndary and
outher boundary
or layer 4?
Yes -- this is correct.
I see, so I must be 100% sure about all handles are fixed
I'm trying to fix the broken archive searching here:
http://brainvis.wustl.edu/pipermail/caret-users/
Hi Ben,
It truly makes my day when I can find a fix this easy:
http://brainmap.wustl.edu/SureFit/RELEASE_NOTES.html#mesa3dnow
Donna
On 12/15/2004 07:14 PM, Ben wrote:
Ugh, please change the working kernel to 2.4.20-30 (it's been a long day)
Cheers!
-Original Message-
From:
Hi Po-He,
Your anterior commissure (AC) setting was WAY off. It was set to
66,46,21 while it should have been set to 69,95,45. Using that AC, I got
an excellent segmentation with no skull whatsoever. The Set AC tab has
an image that shows where the AC should be set.
Also, your white matter peak
Hi Dr. Smiley,
Correct: If you've somehow generated a surface from your anatomical MRI
outside of Caret, then you'll likely be able to import it into Caret to
display it. In most cases, you also can flatten and register it, as
well, but there can be problems drawing borders on surfaces
Hi Dr. Paraskevas,
Erin Reid already did something like this with the Paxinos atlas. Have
a look at Tutorial 9 in Part II of the Caret 4.6 manual. (This tutorial
has not yet been updated to reflect the Caret 5.1 interface, but at
least one other user has managed to find his way through this
Hi Dr. Theoharis,
Another user ran into similar trouble last week. Evidently, Caret 5.1
doesn't support opening tif images, but it supports jpeg and some other
file formats.
Here is an archive that contains jpg files for the tif images cited in
Caret 4.6 tutorial 9:
Hi Joern,
First, for the benefit of most caret-users members, we still haven't
officially released PALS_B12, but we're getting pretty darned close.
The 40+ page paper has been submitted to Neuroimage, but it hasn't yet
been reviewed. Harold Burton's lab found some blemishes affecting a few
Hi Johannes,
Did you try generating the latlon on the individual's surface (i.e.,
before deformation), and then applying the deformation map to that
latlon file?
Donna
On 04/04/2005 03:46 AM, Johannes Klein wrote:
Hi everyone,
I'd like to show how a particular spherical surface gets
Hi Surya,
My guess is that it's more likely a png version issue, as John
suggested, rather than a size issue. Your best bet is to try converting
to another format. Try entering convert at the Linux command line.
If you get Command not found then you probably don't have ImageMagick
Hi Marco,
I remember you! You helped educate me about the differences between
talairach and MNI space a couple of years ago.
Is there any chance you're trying to segment both hemispheres at once?
If not, then can you upload your cropped .HEAD and .BRIK structural
volumes along with your
Hi Marco,
Very nice structural volume. My Caret gives a very nice segmentation
with no complaints, but I had to scale it from float to byte (not sure
what your original datum type was). We ported the SureFit algorithm
almost completely as is, and its SureFitOps utilities work only on
Hi Marco,
Could you also upload the topo file?
Thanks,
Donna
On 06/20/2005 04:48 PM, marco tettamanti wrote:
Hi Donna!
I am back and was finally able to check. The metric file, as you suspected,
only contains the header. I have uploaded the metric file, the functional
volume (.hdr and
. The correct offsets are 0, +19, and +5.5. I would be
happy to share the files if anybody is interested.
Best,
Jochen.
Donna Hanlon wrote:
Hi Dr. Ditterich,
No, I don't think you're doing anything wrong. I think the problem
is that we need a fiducial coord file that is aligned to the
inter
Hi Dr. Giffard,
Make sure you have the source surface (e.g., flat or inflated) loaded
in the main Caret window. Make sure the reference (e.g., fiducial
surface) is loaded; it need not be opened in a window.
Then, so Surface: Measurements: Generate Distortion. Select OK. Then,
use D/C:
. Note also that Caret includes several useful
utilities (e.g., mathematical operations) under the Attributes: Surface
Shape menu.
On 07/13/2005 09:09 AM, Donna Hanlon wrote:
Hi Dr. Giffard,
Make sure you have the source surface (e.g., flat or inflated)
loaded in the main Caret window. Make
Hi Joe,
Upload your volume here (if Analyze/SPM format, upload the .hdr first,
which won't take long, so I can get the dimensions and other header
information; gzip or zip the .img before sending):
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
If you're resampling to cubic 1mm, then I'm
Hi Brige,
I am not someone who has had success (or failures) with mouse brain
segmentation, but I tried segmenting the map015 left hemisphere using
Caret, just to see what would happen. I made these selections:
* left the voxel size at 0.056mm
* GMpeak=45 ; WMpeak 60
* toggled off
from Freesurfer to Caret
would indeed be useful. Is there documentation on how exactly to do this?
thanks,
Brad
-Original Message-
From: Donna Hanlon [mailto:[EMAIL PROTECTED]
Sent: Monday, September 19, 2005 3:52 PM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret
Hi Morgan,
Many of our best users are FSL users, so we want to make life as easy as
possible for them. While we don't have Colin in FSL (what we're calling
flirt) grid, we do have the PALS_B12 surfaces that way:
http://brainvis.wustl.edu/help/pals_volume_normalization/
We're recommending
get much more of his attention
than the colin atlas does.
BTW, the PALS paper hit NeuroImage early views. I don't have the link
handy but it is there as well.
Cheers,
-Morgan
On Tue, 2005-09-20 at 08:59 -0500, Donna Hanlon wrote:
Hi Morgan,
Many of our best users are FSL users, so we
in touch with Johannes
too.
Cheers,
-Morgan
On Thu, 2005-09-22 at 08:04 -0500, Donna Hanlon wrote:
Hi Morgan,
See comments below.
Also, have you met Johannes Klein, who also works in the FMRIB? He has
extensive experience with Caret registration.
Donna
On 09/22/2005 06:49 AM, Morgan
Hi Rishi,
Is this preventing you from flattening, or is it just complaining at the
console?
If the former, please upload a zip/tar.gz archive of your dataset,
including the paint file, so I can try to replicate it. Also, is it
possible you have multiple paint files loaded?
Donna
On
(San Antonio Talairach Daemon database),
for example.
Donna
On 12/15/2005 09:13 AM, [EMAIL PROTECTED] wrote:
Hi Donna,
Using that average brain would be very nice. I just wanted to make sure that it
is in taliarch space.
Thanks,
Erin
Quoting Donna Hanlon [EMAIL
and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
From: [EMAIL PROTECTED] on behalf of Donna Hanlon
Sent: Sat 17/12/2005 12:56 AM
To: Caret, SureFit, and SuMS software users
Subject: Re: [caret-users] Tutorial troubles
Hi Alex,
I recognize
. Smith
Research Scientist/Engineer
phone: 206-616-7343
fax: 206-616-7791
University of Washington
Neuroimaging Research Group
Box 354940
Seattle, WA 98105
~
Date: Wed, 21 Dec 2005 07:20:23 -0600
From: Donna Hanlon [EMAIL PROTECTED]
Subject: Re
expensive process.
Does anyone have any thoughts on this?
Donna Hanlon
inline: tmap_hfavcon_young_left_3.0_variance_smoothed.jpginline: tmap_hfavcon_young_left_3.0_variance_unsmoothed.jpg
Hi Roland,
I got your log file. Could you upload your structural volume here:
http://pulvinar.wustl.edu/cgi-bin/upload.cgi
If AFNI, I need both .HEAD and .BRIK; for Analyze, both .hdr and .img.
Also, let me know which peaks you used. The crash is occurring pretty
early in segmentation --
/caret5_exe_linux.zip
Don't think the whole distribution will be needed in your case.
Let us know if this helps, hurts, etc.
Donna
On 01/09/2006 09:36 AM, Roland Marcus Rutschmann wrote:
On Monday 09 January 2006 15:24, Donna Hanlon wrote:
Hi Roland,
Hi again,
I got your log file
can visualize all the foci together on a single surface (e.g., the
inflated or flat surface). Projecting the foci associates them with a
surface tile.
Hope this helps,
Donna
On 01/17/2006 11:43 AM, Simone Kamphuis wrote:
Donna Hanlon schrieb:
Hi Dr. Kamphuis,
The coordinates in the ID
Hi Ashley,
Are you mapping group functional data onto the PALS atlas or individual
data onto a surface reconstruction of that individual's hemisphere? The
former is covered in this tutorial:
http://sumsdb.wustl.edu/sums/download.do?id=6363278
Either way, thresholding for both metric (the
Hi Aaron,
The caret_file_convert command below will just convert lh.orig to Caret
-- not average lh.orig with lh.pial. John Harwell recently wrote a
command line utility, caret_command, for this an other purposes. If
you're willing to wait until tomorrow morning, I'm planning to write a
On 02/13/2006 03:37 PM, Fornito, Alexander wrote:
Ok,
I had a look under attributes and I saw the ROI I created, so I assume this is
correct.
I tried to create a new ROi under the attributes area color tab named ???. This
got rid of the WARNING: Paint names with no corresponding area
file?
Thanks,
Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
-Original Message-
From: [EMAIL PROTECTED] on behalf of Donna Hanlon
Sent: Tue 14/02/2006 9:19 AM
To: Caret
Alex and John,
While I think it might be useful to have a command line equivalent of
the Generate inflated, ellipsoid, etc. from fiducial for other reasons
(to be explained in a later message to caret-users), I don't think this
is necessary for your purposes. I'll explain further in a reply
Hi caret-users,
This script may be helpful to those who import Freesurfer surfaces into
Caret for various purposes.
http://brainmap.wustl.edu/pub/donna/SCRIPTS/FREESURFER/freesurfer2caret.sh
login pub
password download
It does the following:
* calls mris_convert to convert the Freesurfer
Only one member so far (me), but we hope there will be more soon.
Subscribe here:
http://pulvinar.wustl.edu/mailman/listinfo/surefit-users
94 matches
Mail list logo
