Hi Bruce,
thanks for the explanation of the p value display. I understand now and can
see what is happening using the matlab commands:
t = linspace(-4,4,1000); % t-test values
p = tpdf(t,20); % corresponding p values with df=20 (requires stats
toolbox)
plot(t,p); hold on
plot(t,-log10(p),'r')
can you send it with the neighbor threshold at it's default value (1).
thanks,
Bruce
On
Fri, 1 Nov 2002, Xiangchuan Chen wrote:
Hi Bruce,
The content of the log file is listed below. Thanks for your help.
Xiangchuan
##
it looks fine. Does the filled volume have your editing changes in it?
On
Fri, 1 Nov 2002, Xiangchuan Chen wrote:
It is as follows.
Thanks,
Xiangchuan
##
csurf0.9: log ending: Fri Nov 1 00:07:13 EST 2002
It is as follows.
Thanks,
Xiangchuan
##
csurf0.9: log ending: Fri Nov 1 00:07:13 EST 2002
##
#
Command Log
#
If the neighbor threshold is 1, it has; if the threshold is 8, it misses some added
voxels.
Xiangchuan
Start Of Original Message
Date: 2002-11-01Time: 17:36:00
From: Bruce Fischl ([EMAIL PROTECTED])
To: freesurfer ([EMAIL PROTECTED])
Subject: Re: Re: Re: Re:
Hi Darren,
you can load alternate surface configurations with file-load surface
configuration, but each one must have the same number of vertices and faces
as the main one. We are working on a new viewer that will let you load
multiple different surfaces, but it will be a while.
Bruce
p.s.
Hi all,
I found that the segmentation of the white matter near the occipital pole of my data
was not quite accurate. I tried to add some voxels to the wm volume there, but the
FreeSurfer didn't take them into account. Then, how can I improve the segmentation at
this part of brain?
Thanks,
Hi Darren,
the -log10(p) transform simply means you're looking at the exponent, with
increasing values meaning more significant. For example, if your threshold
were set to:
fthresh = 1
fmid = 2
fslope = 1
nothing with p1e-1 would be colored, the mid point of the color scale
would be p=1e-2
Hi Bruce,
thankyou, I had some minor bugs in the output asc file. It was in meters,
but more importantly the vertices started at one, where FS vertices start at
zero.
Cheers, Darren
- Original Message -
From: Bruce Fischl [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Monday, October
Hi. I converted some genesis I.??? files off a GE scanner and the
COR-.info file had a fov of 0. Everything else was OK but the surface
coordinates came out strange and the surface was sort of inside out.
I set fov to .256 by hand, and everything came out OK. Then I realized
that was wrong,
Hi Tom,
I don't believe it matters, except for displaying stuff in tksurfer.
Bruce
On Mon,
28 Oct 2002, Tom Holroyd wrote:
Hi. I converted some genesis I.??? files off a GE scanner and the
COR-.info file had a fov of 0. Everything else was OK but the surface
coordinates came out strange
Hello -
When running morph_subject, the error that vss-surf2vit command not
found was outputted. I know that this issue was addressed on the mailing
list last Feburary, with instructions to download new versions of
morph_subject, morph_subject-lh and morph_subject-rh at the given link.
I do,
G'day Bruce et al,
the template is uploading to
ftp://floyd.psy.flinders.edu.au/pub/weber/rh.wholebrain.tif (~5Mb, the
permissions should allow anonymous ftp access). Could you take a look at
it? I guess it's OK but I have no idea what it should look like, maybe it
makes sense in the light of
Hi Bob et al,
I prefer mri_strip_skull to mri_watershed. I think the former was a
previous method that has now been replaced by the latter. Please find
attached a small csh script (process_anatomy.csh) that I find useful for
doing the skull strip and segmentation (note that mri_watershed is
Hi Bob,
you'll find it here:
http://www.mail-archive.com/freesurfer@surfer.nmr.mgh.harvard.edu/
h.
On Wed, 2002-10-16 at 13:53, Bob Thoma wrote:
Hello,
I can't seem to remember the web location that contains an index of previous
emails. I would appreciate it if someone
On Wed, 16 Oct 2002, Bob Thoma wrote:
All,
I've been having some difficulty with skull stripping, it doesn't appear to
be removing enough.
Hello again,
Just a quick correction -- you'd want to increase the preflooding height
from its default of 25 if the skull strip isn't removing
Hi all,
Just for clarification sake, when people in the Freesurfer community refer
to MNI tools, is this actually a reference to the MNI_Autoreg utility?
I have installed netcdf 3.5, but wasn't able to find a utility that is
actually called MNI tools at www.bic.mni.mcgill.ca. Also, on the
Hi Nick,
This might be occuring because you have a newer version of mri_convert that
does not support the -raw flag. You could use an older version with
register.csh or try using mri_motion_correct2 (i think that is the name).
The latter works really well, but you will need to install all of the
Hi Darren,
we usually start with one ?h.sphere, register a bunch of subjects to it to
create ?h.sphere.reg files, then create a new template with them.
cheers,
Bruce
On Fri, 11 Oct 2002, Darren Weber wrote:
Thanks, Bruce.
mris_make_template --help stops at 'valid options are:' :-(
Hi Darren,
the ico and average7 are about the same computationally. However, it is
more convenient to use average7 it has a surface that you can directly
render the results on. With ico, you'd still have to run mri_surf2surf
to convert it to another surface.
I'm not sure what you're trying to
Dear Bruce et al,
my query is about how to register cortical surfaces across X subjects, given
that we have modified the usual left/right surface separation.
Some time ago we discussed how to extract a complete cortical surface,
rather than the left/right hemi surfaces. The purpose of this
Hi Darren,
that's pretty much the way I generated the lh and rh templates we use.
There's a binary named mris_make_template,which you probably have, that
will take a bunch of surface models and construct a template (.tif) from
them. You'll have to name the individual surface lh or rh, since
Thanks, Bruce.
mris_make_template --help stops at 'valid options are:' :-(
One of the input parameters is a surface name - I suppose 'orig', 'white',
'pial' etc are valid. I'm not sure what surface to specify; is it 'sphere'
or 'inflated' or something else?
Cheers, Darren
- Original
Hi Doug et al,
from looking at the help on mris_surfglm it appears that vertices in the
analyses are not as dense as those from the subject surfaces. I'm guessing
that using the ico surface with 7 iterations of refinement (lots of
vertices!), you then locate the nearest vertex in each subject
Dear Doug et al,
surfglm looks good. I have processed 10 controls and 8 patients such that
each surface contains a whole cortical surface, without the usual split
through the corpus callosum. How would I use the surface registration
process? Should I use 'ico' as the average or can I use one
HI all,
When I first installed the latest version of Freesurfer, I did not
initially install the MNI registration utilities from
(www.bic.mni.mcgill.ca). I would now like to install these tools, but have
been unable to locate instructions on doing this. Could someone provide me
with brief
Hi Tim,
First download netcdf 3.5 and install it. I think there is an rpm for it
for some distributions on www.rpmfind.net. That makes it easier because
you will not have to compile it (not that there is anything wrong with
compiling!). Compile the latest version of MNI tools. Usually the
Brian,
Thanks for the advice, I'll give it a shot. Out of curiosity, can MNI
tools use the MNI average152 template dataset instead of the MNI average
305? We had been using the MNI_152 template in another normalization scheme
we had worked out using flirt in FSL.
Thanks,
Tim
Hi Tim,
First
Tim,
When using mritotal to fit a dataset, you can specify -model and use the
base name average152. make sure average152 and its various datasets
(average152_16_blur.mnc, average152_8_blur.mnc, average152_8_dxyz.mnc,
average152_16_mask.mnc, average152_8_mask.mnc, average152_headmask.mnc)
are in
Ver 0.9 (33y)
On 2 Oct 2002, at 2:12, Brian C. Schweinsburg wrote:
Hi Scott,
What version of freesurfer are you using?
brian
- Original Message -
From: Scott Laurence Fairhall [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Tuesday, October 01, 2002 11:20 PM
Subject:
Hi Scott,
are you still having problems? Did you try specifying the directory with
the COR files, instead of one of the individual files? What are you trying
to convert to? I you're trying to convert I.* files, you should use:
mri_convert path to I.*/I.001 $SUBJECTS_DIR/subject name/mri/orig
Hi Scott,
What version of freesurfer are you using?
brian
- Original Message -
From: Scott Laurence Fairhall [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Tuesday, October 01, 2002 11:20 PM
Subject: trouble converting to COR, can't stat ??
Hello,
I'm probably doing something
Hi Scott,
when specifying a COR volume, just give it a directory name (not the name
of one of the files).
cheers,
Bruce
Bruce Fischl email: [EMAIL PROTECTED]
Mass. General Hosp. NMR Center.tel:(617)-726-4897
Hi Brian,
I just finished that program a few weeks ago. This program allows you to
do cross-subject/cross-group analysis of surface data by solving a GLM
with ordinary least-squares (OLS). It also allows you to pre-smooth the
surface values as well as include covariates (eg, age, gender, etc).
Hi Brian,
you probably need to specify a target subject (--trgsubj). I've put a
newer version of mri_surfglm at
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/FreeSurfer/. The
guts of it have not changed, but it does better command-line error
checking.
doug
Brian C. Schweinsburg
Hello,
I'm probably doing something very stupid but I can't figure out what.
When I attempted to load in my anatomical files through the GUI I
recieved an error saying:
Convert (scott) failed - working on:
orig/a/I.%03d
So I tried the tutorial (bert) files through the command line and got:
I was able to answer my own question regarding thickness parameter maps
from the other day by poking through the Linux/bin directory. Looking
forward to using it.
brian
Hi Arvid,
I did not find a correction for that problem yet. mris_convert may not be
causing the problem, because I obtained the same result with an older
version of it. Maybe something went wrong in the make final surfaces step. I
am still looking for the source of the mismatch between the white
Hi Brian and Arvid,
could you run the binary mris_euler_number on each of the relevant surfaces
(?h.sphere.reg, ?h.orig, ?h.white, ?h.pial) and make sure that they all
have the same number of vertices and faces, and that that matches what is
in the ?h.thickness.asc file? If there is a
Bruce,
As suggested, I ran mris_euler_number on all of my surfaces. Comparing
this output to that of the rh.thickness.asc shows that each surface has
the same number of vertices as the thickness curvature.
9 ucsd-ybp00ib7lt:brian:surf mris_euler_number rh.pial
euler # = v-e+f = 2g-2: 159216 -
what are the first couple of lines of the rh.thickness.asc file?
On 30 Sep 2002, Brian Schweinsburg wrote:
Bruce,
As suggested, I ran mris_euler_number on all of my surfaces. Comparing
this output to that of the rh.thickness.asc shows that each surface has
the same number of vertices as the
Dear Bruce
I have:
[freesurfer@arvid surf]$ mris_euler_number rh.inflated
euler # = v-e+f = 2g-2: 138843 - 416523 + 277682 = 2 -- 0 holes
F =2V-4: 277682 = 277686-4 (0)
2E=3F:833046 = 833046 (0)
total defect index = 0
[freesurfer@arvid surf]$ mris_euler_number
here are the first 7 lines
000 12.61563 -89.76370 -3.82580 0.0
001 11.95849 -89.71229 -3.96183 0.0
002 10.82764 -89.53942 -4.15206 0.0
003 10.03118 -89.17944 -3.95924 0.0
004 14.26332 -89.59046 -5.39858 0.0
005 13.91159 -89.66550 -4.88632 0.0
006 12.91290 -89.80223
When using the the snapshot distribution fsa-20020917.tar.gz I get the
following error messages when running:
mris_convert -c thickness rh.white rh.thickness.asc
MRISreadBinaryCurvature: incompatible vertex number in file
./rh.thickness
the ascii file output, but all thickness values are zero:
Hi All,
I am interested in being able to do parametric
analyses with the cortical thickness data (e.g., one patient group, one control
group, and a t-test for each registered vertex similar to Rosas et al.
2002).
I have completed the process of fixing topology,
sphering, and registering.
In attempting to use the surface-stats button to
see functional overlay, in the View Functional Data
option, this error is generated and tksurfer does not start:
'Error: can't read scandirpref: no such variable.'
The stack trace is at the end of this message if that helps in locating
where the
Hi - no, it doesn't - that is part of the initial freesurfer processing
(which estimates white matter and then estimates bias field on the basis
of white matter points), not the format conversion.
ttfn, Steve.
On Thu, 29 Aug 2002, Darren Weber wrote:
Dear Bruce et al,
does mri_convert
p.s. what we do is not really bias field estimation/correction, but
something much more aggressive, really a pre-segmentation, which accounts
for bias fields as well as tissue inhomogeneity. If what you want is really
the bias field for some other purpose, you're probably better of using the
EM
I am referring to a command line option to mri_convert:
--unwarp-gradient-nonlinearity ...
- Original Message -
From: Bruce Fischl [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Thursday, August 29, 2002 9:30 PM
Subject: Re: RF bias correction with mri_convert
p.s. what we do is
Hi Bruce, et al,
The Markov random field approach with FSL FAST is intensive (~ 2000 sec on
Athlon 1700, 1Gb PC2700 on VIA KT333A) and the results appear to be good.
Of course, it could be better to measure the quantity on the scanner. Would
this approach require access and modification of the
Hi Darren,
I think you'll find that this option refers to the fact that the
gradients in many of the latest generation MRI systems from several
manufacturers are not exactly linear, particularly in z. Obviously, this
has implications for the imaging experiments performed on them,
Greig is correct. The --unwarp-gradient-nonlinearity option corrects for
the 3-D image distortions caused by departures from linearity in the
magnetic fields produced by the x-, y- and z- gradient coils. These
distortion patterns are specific to each scanner/gradient model (e.g.,
Sonata,
Hi Anders,
Many thanks for this reply. We have been grappling with the
non-linearity on our new Sonata systems, and will face the same hurdle
with our 4T (Sonata gradients). Would it be possible to continue the
discussion off-list about your correction procedure and how it is
implemented in
Dear Bruce et al,
does mri_convert automatically apply RF bias field estimation/correction?
If it can do the RF bias correction, what is the best command line option
for this?
Take care, Darren
--
Darren Weber, PhD Student
Cognitive Neuroscience, School of Psychology
Flinders University of
check the fov field in the subject's mri/T1/COR-.info file. If it is 0,
then change it to .256.
cheers,
Bruce
On Mon, 26 Aug 2002, Rutvik Desai wrote:
Hello,
During the Edit Segmentation stage, the Tksurfer window
does not seem to recognize any mouse operations. The TkMedit
display and
Hi,
I have solved the problem using Eirik's suggestion. When the initial square
for the TkMedit window appears, I move it towards the center of the desktop
and it works fine. The initial tkmedit window always shows up at the edge
of the desktop so, as you suggest, it may be that it exits when
Hi,
I am having some difficulties performing motion correction on multiple
structural runs in Freesurfer. In order to ensure that it is not my data
which is problematic, I have tried to use register.csh on bert tutorial
data. Following the instructions in the tutorial, I used the command:
Arun Bokde wrote:
Hi,
I am having a problem with the TkMedit window.
I am going through the tutorial using the example data set. When I wish
to view one of the volume images after the various segmentation steps,
the window in which TkMedit would appear does not work properly. The
Hi Darren,
speaking for myself, I don't consider this off-topic for the freesurfer
list. Congratulations on getting it done.
Bruce
On Fri, 16 Aug 2002, Darren Weber wrote:
Hi,
there is a new release of the matlab eeg-toolbox/mri-toolbox available via
http://eeg.sourceforge.net/.
This
Hi,
I am having a problem with the TkMedit window.
I am going through the tutorial using the example data set. When I wish
to view one of the volume images after the various segmentation steps,
the window in which TkMedit would appear does not work properly. The
window initially appears
[Arun]
window initially appears as a small grey square (perhaps 2 x 2 inches)
while the other window, in which the image appears, is being drawn. As
the window with the image is completed, the TkMedit window closes.
Are both windows being closed and the program exited? Or just the window
Hi,
there is a new release of the matlab eeg-toolbox/mri-toolbox available via
http://eeg.sourceforge.net/.
This release incorporates a new mesh_shrinkwrap function (alpha release) for
generating a surface from an Analyze MRI volume. If given the Analyze
version of the original input to
I am a new user of freesurfer. I was able to complete
the first three steps of the process, namely, convert/average,
process volume, and create surface. However, I do not get any
graphic displays showing surfaces or slices. When I go to the next step,
Edit Segmentation, no displays open up and
Hi Folks,
When I convert and load images (from gelx, analyze,
or brik format), the contrast and brightness are way off. In some cases the
entire brain looks bright white. This creates a problem for segmentation edits
because when I adjust the contrast for the auxiliary image (mri/orig) the
Hi Brian
The tkmedit View-- Configure Brightness Contrast option allows you to
configure the main and/or aux volume(s) to your liking. I suppose you
could set an environment variable once you determine to which degree you
want the aux volume brightness reduced -- assuming this would be the
We've got 2 subjects where we've gotten a segment fail error reading
that the corpus callosum can't be found.
I've retransferred and remotion corrected them and I still get the same
error message when I segment them.
Any suggestions on how to fix this or to find the CC at this stage?
Many
Jill,
you may need to set this manually. it is described in the
FreeSurferGuide.pdf ~page 31 available at the FreeSurfer site. It
descirbes how to fix this within csurf.
you can also use the command mri_fill with the -C flag and the talairach
coords of the cc you want to use. run
Thanks. I overlooked the aux adustment for some reason. The environment
variable would be nice because my contrasts are off for every participant,
to varying extents. I suspect that the display contrast and brightness do
not impact the segmentation, etc. Although, I would like to confirm this.
Hi Brian,
You're right, the display contrast and brightness don't actually impact
the segmentation; it's just for visualization purposes.
Cheers!
Ev
On Tue, 13 Aug 2002, Brian C. Schweinsburg wrote:
Thanks. I overlooked the aux adustment for some reason. The environment
variable would be
[Brian]
Thanks. I overlooked the aux adustment for some reason. The environment
variable would be nice because my contrasts are off for every participant,
Are you running tkmedit from the command line or from csurf? If the
former, you can use a startup script to set the brightness and
Hi all,
I'm a fairly new user of Freesurfer, although I have been a user of AFNI
for some time. I have a question related to using MNI space in freesurfer.
Currently we have been normalizing our data to the MNI_avg_152 template,
using FLIRT in FSL. I understand that Freesurfer can be set up to
Hi Tim,
you could spatialize normalize the data before running mri_convert, the
only down side is that you have added an interpolation to the processing
that you didn't need to, and so sacrificed some resolution. You will
probably want to create a talairach.xfm file in the subject's
Thanks Kevin.
I am able to do it.
Is there any way to change the scale of the color bar, or the colors
within the scale color bar?
-Brad
On Friday, August 9, 2002, at 02:42 PM, Kevin Teich wrote:
[Brad]
How do I paint and view a map I created with another analysis package
onto an
Thanks Doug.
Those links don't seem to work. In any case, I am running Freesurfer on
an SGI.
-BRad
On Wednesday, July 31, 2002, at 11:35 AM, Doug Greve wrote:
Ah, I think you must have an old vesion. You can get a new Linux version
of mri_convert from
Ah, that is a problem. The IRIX we use to build new binaries is down, so
I can't get a new version for you. One work-around (if you don't have a
Linux box handy) is to use matlab to read in as analyze and write out as
bfloat. If you have a version of FS-FAST (probably in
Ah, I think you must have an old vesion. You can get a new Linux version
of mri_convert from
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/FreeSurfer/
Or an entirely new version of FreeSurfer from
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/FreeSurfer/fsa-20020724/
Hello,
Perhaps you will be happy to have some feed-back on the fsa-20020724
version.
(using csurf : I dont know the command line, lack of doc).
tkmedit works pretty well,
tksurfer doesn't want to display anything, but give the messages :
env tksurferinterface=csurf patchname=occip.patch.flat
Thanks Doug.
didn't work though.
I'm looking to create bshorts.
I keep getting a can't determine type of output volume, even when I
try using --out_data_type float.
-Brad
On Friday, July 26, 2002, at 09:43 AM, Doug Greve wrote:
Use mri_convert. Here's an example for an spm functional
Use mri_convert. Here's an example for an spm functional volume
spm001.img, spm002.img ...
mri_convert spm001.img --in_type spm spm_000.bfloat
This should create the spm bfloat volume.
doug
Bradley Goodyear wrote:
Which parameter from the .HDR file does spm_to_b use as the number of
Hi there,
I've got a question, this time about FS-FAST (if this isn't the
appropriate place to ask these questions, feel free to let me know).
I'm running the latest version of the FS-FAST software (with fsfast
directory fsfast-20020510). When running commands that use Matlab (such
as
Hi Nick,
what does the -tty do? Is that new to version 6? Will it work for
version 5?
doug
Nicholas Knouf wrote:
Hi there,
I've got a question, this time about FS-FAST (if this isn't the
appropriate place to ask these questions, feel free to let me know).
I'm running the latest
I'm not sure if it works for version 5 or not (since I only have 6.1 to
work with). Typing matlab -tty on my system causes matlab to startup in
the same terminal window (instead of spawning a separate command window).
Looking through an older version of FS-FAST that we use (fsfast-010328), I
Would there be any benefits by using a Beowulf cluster for FS-FAST and
Freesurfer computations?
I've been wondering about this lately, and wanted to hear the thoughts of
other Freesurfer users. I don't know much about the underlying design of
the code and whether or not it would be
Hi Tom,
we've never really used our skull stripping for primates, so I'm not
surprised to hear that it fails. It's good to know that BET works well, so
I would definitely use it instead of ours. In general, we have been working
over the last year or so to integrate with the Oxford tools, so
one workaround is to use tksurfer.static, which will be slower, but
should work.
Bruce
On Thu, 11 Jul 2002, Nicholas Knouf wrote:
I'm having problems running tksurfer on a couple Linux machines (they are
running a modified version (MIT athena) of RedHat 7.1). Here is the
output of the log
apologies for any inconvenience
some of my email to the list has not been working
Hi Bruce,
Tried the downloading the mris_convert from
surfer.nmr.mgh.harvard.edu:/space/outgoing/fsdev and again doing:
mris_convert -c ./lh.area lh.orig lh.area.asc
(after renaming the old lh.area.asc file). However the output is the
same, as far as I can tell. Here are the first 8 lines
Hi again,
On Friday, June 7, 2002, at 06:38 PM, Bruce Fischl wrote:
Hi Tom,
we write out an ?h.area file that contains the area of every vertex in
the tessellation (the average area of all triangles it is a member of).
You
should be able to convert it to ascii using mris_convert in the
Thanks Bruce,
A few more questions:
On Thursday, June 13, 2002, at 03:00 PM, Bruce Fischl wrote:
Hi Tom,
the mris_convert command line for converting curvature files is a bit
arcane (my fault). You need to specify that it is a curvature format
file
with the -c option, and which one you
you should convert the patch to ascii using mris_convert -p and get the
vertex #s from the ascii file. Also, I think you must have an old version
of mris_convert (as every other area is 0, which it certainly shouldn't
be). Try taking a new one from
Hi,
I've been experiencing some problems with the rh.orig and lh.orig files in
the surf/ directory.
The problem manifests itself as an inability to find the proper saved
vertex on a T1 volume displayed in TkEdit following selection of that
vertex on an inflated surface. The error arises in the
Hi Petr,
this almost certainly means that you didn't reinflate after running the
topology correction, so that there is no longer a correspondence between
the orig (which has been corrected) and the inflated surfaces. The reason
the orig doubles in size is that the corrected surfaces have to be
Is there any way to get a measure of absolute surface area of, e.g., the
pial surface of an individual? If so, can this be run on cut portions
of the cortical surface (e.g., the occipical pole)? We worked our way to
the point at which freesurfer has created a model of the surface of each
Hi Tom,
we write out an ?h.area file that contains the area of every vertex in
the tessellation (the average area of all triangles it is a member of). You
should be able to convert it to ascii using mris_convert in the usual way.
Also, note that the vertex index is invariant across the
Hi,
I got the following problems when using the latest version of freesurfer
(fsa-20020521) downloaded from the surfer site:
1) Segmentation fault when trying to check the registration using tkregister:
[phoebe@taz rnnmean]$ tkregister local
tkregister: starting register
register: cwd scan =
Hi All,
I am aware that the FreeSurfer manual has typical MRI parameters for various
MRI scanners. Are these the best to use?
In other words, given the techniques employed by FreeSurfer, are there any
ideal MRI scanner parameters (or scanning sequences) that are known to give
the best
Dear Bruce, Kevin and others,
Thank you for your fast reply. Sorry, to tell you Kevin, that the new
tcl-script does not work either, the same error occurs, using the
alpha-version (October release). In the last mail I was meaning the colour
of the surfaces in tksurfer (e. i. red-green and
Hi Bruce,
I tried everything again and again, and the
area file is created after orig. But still the
command mris_convert produces the error:
mris_convert -c area
/li2/freesurfer/freesurfer_alpha/subjects/t1xxl/surf/rh.orig
/li2/freesurfer/freesurfer_alpha/subjects/t1xxl/surf/rh.area.asc
Sorry to take so long to get back to you.
sorry to bother you again with my questions. I was wondering how I can
change the colour of the surfaces and of the blobs of the functional
overlay. Is there an easy way for doing it? An other problem is, when I try
Is this in tkmedit? You can change
Hi Bruce,
I downloaded the updated
mris_smooth.Linux
from the path you indicated below and I moved the file
to /freesurfer_alpha/bin/Linux/mris_smooth.
Then I restartet the CREATE_SURFACE process and got
a new ?h.area file.
Then I transformed to ascii again:
mris_convert -c area
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