Hi,
I'd like to run a simple repeated-measures analysis tetsing for change in
thickness measures between 2 time points. There is no between-subjects factor,
only the effect of time. Do I just set up a standard DOSS FSGD file, or do I
use a different format? The tutorial only covers between-subje
[EMAIL PROTECTED]
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Tue 4/11/2006 9:31 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Repeated-measures in mris_glm
There are two ways to do it:
1. You can use DOSS, making each subje
D]
Sent: Tue 4/11/2006 11:43 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Repeated-measures in mris_glm
Yes, mris_preproc is new with stable. In your FSGD file, try
specifying the title as a single string without spaces.
doug
On Tue, 11 Apr 2
ubj4
Class class_subj5
Variables Time
Input time1_subj1 class_subj1 -1
Input time2_subj1 class_subj1 +1
...
doug
On Tue, 11 Apr 2006, Fornito, Alexander wrote:
> I still get the same error message. Maybe I've coded the variable wrong?
>
> gdfReadHeader: reading
l: [EMAIL PROTECTED]
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Wed 4/12/2006 2:42 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Repeated-measures in mris_glm
How did you create the average subject? Is there a T1.mgz i
Building
161 Barry St
Carlton South Vic 3053 Australia
Ph:+61 3 8344 1624
Fax: +61 3 9348 0469
email: [EMAIL PROTECTED]
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Thu 4/13/2006 1:45 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject:
: +61 3 9348 0469
email: [EMAIL PROTECTED]
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 4/28/2006 1:35 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] 3T problems
did you check the talairach?
On Fri, 28 Apr 2006, Forn
: Fornito, Alexander
Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] 3T problems
Did you look at the raw data to make sure there were no artifacts?
Fornito, Alexander wrote:
>Hi Bruce,
>It doesn't look good; actually, I can't see anything when I load it
Hi,
I have some labels that I've drawn, which correspond to the gyral crown and
sulcal fundus of a given ROI. From what I understand, mean curvature provides
an index of the convexity/concavity of the region. I would therefore have
expected high positive values in the gyral ROI to represent a st
MAIL PROTECTED]
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thu 5/25/2006 9:09 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] ROI Curvature
Hi Alex,
the gyri will should have negative mean curvature and the sulci positive.
You
lding
161 Barry St
Carlton South Vic 3053 Australia
Ph:+61 3 8344 1624
Fax: +61 3 9348 0469
email: [EMAIL PROTECTED]
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Fri 5/26/2006 7:59 AM
To: Fornito, Alexander
Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu
Su
0469
email: [EMAIL PROTECTED]
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 5/26/2006 8:32 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] ROI Curvature
which curvature values. Can you send the output?
On Fri, 26 May
8344 1624
Fax: +61 3 9348 0469
email: [EMAIL PROTECTED]
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 5/26/2006 9:44 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] ROI Curvature
when you overlay the ?h.curv file on
: +61 3 9348 0469
email: [EMAIL PROTECTED]
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 5/26/2006 10:21 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] ROI Curvature
p.s. sorry, the mean and Gaussian curvatures dis
Hi,
I'm new to fMR and am using mri_convert to convert from siemens dicom to
analyze/spm format.I ran the command below and had a couple of questions:
1 - Why does the first INFO: line say that 807 files were found when only 805
were input?
2 - Why were only 800 of 805 files converted?
3 - As
,
Alex
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Wed 10/4/2006 2:03 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Converting DICOMs
On Wed, 4 Oct 2006, Fornito, Alexander wrote:
> Hi,
> I'm new to fMR a
Hi,
I'm trying to convert a series of siemens dicom mosaic format files to analyze
format, while reorienting at the same time. Running the command below converts
and reorients only the filename specified in the command line (which is the
first file in the series), whereas leaving out the --out_
Hi,
I was just seeking some clarification re: the legacy flag in recon-all.
Can I use it on subjects procssed with older versions of Freesurfer to
reconstruct surfaces that will be consistent with those generated with older
versions (i.e., I can collapse data from the two versions), or is the leg
Hi,
Is it a problem combining results from data processed using versions 3.03,
3.04, and 3.05? I have some data processed on 3.03 but I'm updating other
machines and I'd like to install 3.05.
Thanks,
Alex
Alex Fornito
JN Peters Research Fellow
Melbourne Neuropsychiatry Centre and Department o
mp; 3, Alan Gilbert Building
161 Barry St Carlton South Vic 3053 Australia
Ph: +61 3 8344 1861
Fax: +61 3 9348 0469
email: [EMAIL PROTECTED]
________
From: Fornito, Alexander
Sent: Fri 3/16/2007 1:56 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Version compatab
Hi Nick,
One thing I couldn't work out from the example image associated with the
release notes is whether the different areas are located in the non-cortical
regions of the midline. If they include cortical regions (and it appears that
subgenual portions of the cingulate are) then I am interest
Hi,
I am looking at running some thickness analyses on some MRI data we have
already collected. I noticed that the manual states that "a minimum of two
anatomical acquisitions is required for morphometric studies". Is it possible
to run a valid thickness analysis in Freesurfer if I only have 1 T
Hi all,
We've just installed Freesurfer and tried to use mri_convert and encountered
some problems. In the csurf GUI, I tried to convert a subject's image, which we
keep in analyze (.img, .hdr) format, and I got the message: "Convert (subj186)
failed - working on: orig/001/subj186.img"
I then lo
Hi,
I've been working with some images in their native space, and some of them are
tilted with respect to the superior-inferior axis. Consequently, when I attempt
to manually edit the cutting planes, the plane through the corups callosum does
not neatly cleanly separate the two hemispheres (ie.,
Hi all,
I've noticed that the tutorial's instructions for manual editing of the
ventricles stops at about slice 92 (for Bert's data). Does this mean only the
posterior portion of the lateral ventricles need to be filled, and that there
is no need to continue to fill in the ventricles up to the a
Hi all,
I've noticed you can set expert preferences to align before averaging in the
GUI, but how do you do it from the command line?
My understanding of the following from the usage is that it assumes that the
transform already exists in the /transforms dir, but how do I create this?
"The
e problem?
Than ks again for your help,
Alex
-Original Message-
From: Evelina Busa [mailto:[EMAIL PROTECTED]
Sent: Sat 5/7/2005 6:51 AM
To: Fornito, Alexander
Cc:
Subject:RE: [Freesurfer] Manual editing tips?
Hi Alex,
The normalized brain volume is created quite early on
al Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Mon 5/9/2005 10:38 AM
To: Fornito, Alexander
Cc: Evelina Busa; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Manual editing tips?
Hi Alex,
the manu
-Original Message-
From: Fornito, Alexander
Sent: Mon 5/9/2005 1:14 PM
To: Bruce Fischl
Cc:
Subject: RE: [Freesurfer] Manual editing tips?
That did the trick. So then the ?.thickness file contains data
imates too much?
Thanks again,
Alex
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Monday, May 09, 2005 10:39 AM
To: Fornito, Alexander
Cc: Evelina Busa; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Manual editing tips?
Hi Alex,
the manual editing
trying to get an idea of what is/isn't
acceptable.
Many thanks,
Alex
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wed 5/11/2005 11:30 PM
To: Fornito, Alexander
Cc: Evelina Busa; freesurfer@nmr.mgh.harvard.edu
Hi,
Does anyone know if its possible to use options with create_subject and
inflate_subject in the command line (eg., one hemisphere only). I've been
unable to bring up the usage (e.g, -u or -help).
Thanks,
Alex
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Freesurfer@
Sorry, was thinking of someting else.
That helps - thanks!
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Mon 5/16/2005 9:40 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
Hi all,
I've created the final surface on one of my images and noticed that
mris_euler_number has detected defects. I've gone back to edit what i think is
the problem and was wandering if I need to go through the whol process again
(create surface -> Fix topology correction -> Create final surfa
-Original Message-
From: Fornito, Alexander
Sent: Tue 5/17/2005 12:51 PM
To: Bruce Fischl
Cc:
Subject: RE: [Freesurfer] Appropriate post-editing processing
For lh.white and lh.pial it is
Hi,
When running segment_subject, I get a meesage saying THE SEGMENTATION IS
PROBABLY NOT CORRECT at the validation stage. Any hints as to what might be
causing this and how to fix?
Thanks,
Alex
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Freesurfer@nmr.mgh.harvard.
Great. Thanks!!
-Original Message-
From: florent segonne [mailto:[EMAIL PROTECTED]
Sent: Wed 5/18/2005 1:22 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Segmentation error
Hi,
Just to toss my hat into the ring, can I ask why the transform is kept. Is it
used later on?
I've also been having trouble with the MNI tools, and was thinking of using
FLIRT or AIR to align the images first. What is th point of having the .xfm?
Thanks,
Alex
-Original Message
5/18/2005 10:55 AM
To: Fornito, Alexander
Cc: peggy christidis; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] WMFilll and talairach coordinates
1. to report talairach coords.
2. To get cutting planes to separate the hemispheres
Wouldn't that occur by using the MNI tools anyway?
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wed 5/18/2005 9:39 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] WM
-Original Message-
From: Fornito, Alexander
Sent: Thu 5/19/2005 10:27 AM
To: Bruce Fischl
Cc:
Subject: RE: [Freesurfer] WMFilll and talairach coordinates
Now I understand. And this information has to be in
Hi,
I've been having some problems with the MNI tools (I can't create the
talairach.xfm) and was hoping for some help.
If I run mri_convert in the command line, I get the following:
mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/
mri_convert -it spm 190/mri/orig/001/1000190
Hi all,
Sorry to labour this point, but I'm stuck with the MNI tools and am
having trouble progressing through my freesurfer analyses. I can't
create the talairach.xfm and was hoping for some help.
If I run mri_convert in the command line, I get the following:
mri_convert -it spm 190/mri/orig/001
Hi,
We're really stuck on this one...
We are running a linux kernel 2.4.26 debian 3.0 (woody).
We've installed the freesurfer and the packaged MINC tools in the apporpriate
directories and set the appropriate environment variables.
We can't get the MNI tools to work through freesurfer, and only so
Hi all,
The page about using FSL with freesurfer on the FSL website recommends using
BET to skull strip the images before feeding them into freeusrfer. I've had a
bit of play with this, and have noticed some marginal improvements. Would you
generally recommed this practice? Are there any reasons
Hi,
I've come across some problems when I run morph_subject. It seems to work fine
until near the end. I've included the final bit of the log below. The problem
seems to occur after it calls MNI programs. I've been having trouble using the
MNI tools through freesurfer, so I created the talairach
Thanks Nick,
We'll give it a try and keep you posted.
A.
-Original Message-
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Sat 6/4/2005 7:41 AM
To: Fornito, Alexander
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] Mi
is conformed to 1 mm size and 256 voxels for all directions
writing to nu...
-Original Message-
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Sat 6/4/2005 7:41 AM
To: Fornito, Alexander
Cc: Freesurfer Mailing List
Subject:Re: [Freesurfer] Missing
Hi all,
I've created my the fional surface for some people and am trying to register
them using recon-all -stage4b.However, I get an error message saying that I
needed to do average labels (see output below). I've noticed that I get the
same message if I try to morph_subject, except morph_subjec
That worked, thanks, Doug.
To expand on the labels issue, from my understanding, the labels are used to
check that the registration worked, and that these are automatically created.
I don't have any files in my labels directory.
Do you need to run parcellate_subject to get them?
Is there any docu
: Thu 6/9/2005 1:10 AM
To: Bruce Fischl
Cc: Fornito, Alexander; Elizabeth Fenstermacher;
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all-nmr -disable-autoseg
I think it looks in the average7 directory for a few labels (ce
Hi,
A couple of questions;
1 - The skull stripping feature has overstripped some of my brains, and using
-wsmore doesn't completely fix the problem. Are there any other options?
2 - I'd like to check my registrations by mapping labels from the average back
onto the individual's brain. What's th
Hi,
I got an error when running recon-all -stage3.I've included the relevant part
of the log below. Any ideas as to what went wrong?
Thanks,
alex
writing spherical brain to
/data/flanders/work/alex/freesurfer/subjects/1000192/surf/lh.qsphere
spherical transformation took 0.91 hours
navgs=32 and
Hi,
I've been using freesurfer with only one run (image) pers subject and have
generally been obtaining good results. I've just noticed a few quirks in the
estimation of the pial surface that I was seeking some clarification.
1 - the algorithm consistently misses portions of grey matter in the me
ler: NHoles = 0
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 6/14/2005 10:12 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject:Re: [Freesurfer] recon-all stage3
Hi Alex,
that's a starnge one. Did the partition run out
2:33 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject:RE: [Freesurfer] recon-all stage3
then you should just run the rest of the analysis I guess and see if it
works. In general all the surfaces of a hemisphere should have the same #
of edges/faces/vertices *e
Hi,
I was seeking some clarification re: the relationship
between the fsgdf and design matrix file for use with mris_glm. It seems to me
that the two contain very similar info, the examples in the –help don’t
use the fsdf at all. Is it necessary to create one, or can you just run an
analys
g?
Thanks again,
Alex
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Tuesday, June 21, 2005 4:11 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_glm
You can run with just the design matrix, but you won't be able t
Fantastic. I really appreciate all your help!!
-Original Message-
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Tuesday, June 21, 2005 11:00 PM
To: Fornito, Alexander
Cc: Freesurfer Mailing List; Bruce Fischl
Subject: RE: [Freesurfer] mris_glm
Alex,
Attached is the
Hi again,
So many questions!!
Is there some sort of correspondence between vertices on the
inner (wm) and outer (pial) surfaces? Ie., for every vertex on the inner
surface, is there a point on the outer surface, and if so, does Freesurfer retain
this information in any of the files?
A
shed link between the
points on each surface.
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wed 6/22/2005 9:20 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] vertex corre
you please give me an example of a command line?
Thanks,
Alex
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wed 6/22/2005 10:02 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject:RE: [Freesurfer] vertex correspondance
t
EMAIL PROTECTED]
Sent: Tue 6/21/2005 11:00 PM
To: Fornito, Alexander
Cc: Freesurfer Mailing List; Bruce Fischl
Subject:RE: [Freesurfer] mris_glm
Alex,
Attached is the make_average_surface script. Copy it to the
freesurfer/bin directory, and be sure to make it executable (run '
ing subject s1000186...
The following must be revisited**
Segmentation fault
-Original Message-
From: Itamar Kahn [mailto:[EMAIL PROTECTED]
Sent: Tue 6/28/2005 9:51 AM
To: Fornito, Alexander
Cc: Freesurfer Mailing List
Subject:Re: [Free
EMAIL PROTECTED]
Sent: Wed 6/29/2005 2:26 AM
To: Fornito, Alexander
Cc: Itamar Kahn; Freesurfer Mailing List
Subject:RE: [Freesurfer] mris_glm
Alex,
I'm trying to track down the source of the segmentation fault. In the
meantime, can you re-run the script with the parameter -
a/flanders
--
recon-all exited with errors at Tue Jun 28 14:41:03 EST 2005
-Original Message-
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Wed 6/29/2005 2:26 AM
To: Fornito, Alexander
Cc: Itamar Kahn; Freesurfer Mailing List
Subject:RE: [Freesurfer] mri
Hi,
I'm trying apply ROI masks that I've manually traced in volume space to the
same image's surface using mri_vol2surf. mri_vol2surf seems to requires a
register.dat file, and I'm unsure what needs to be registered, since the volume
that I traced the masks on is exactly the same as the one that
o Source Subject Surface
vol2surf_linear: nhits = 152789/152789
Done mapping volume to surface
Number of source voxels hit = 96553
Warning: all vertex values are zero
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 7/1/2005 11:06 AM
To: Fornito, Alex
tkregister.tcl: default macro interface (to change: macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Fri 7/1/2005 12:47 PM
To: Fornito, Alexander
Cc: Bruce Fischl; freesu
152789/152789
Done mapping volume to surface
Number of source voxels hit = 96553
avg = 1.000, stdev = 0.000, min = 1.000, max = 1.000
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Fri 7/1/2005 10:11 PM
To: Fornito, Alexander
Cc: Bruce Fischl; freesurfer@nmr.mgh
this happen?
Thanks again,
A.
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Mon 7/4/2005 11:25 AM
To: Fornito, Alexander
Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu
Subject:RE: [Freesurfer] mri_vol2surf
Hi Alex,
no, label files are text files
me to apply the image
as an ROI to the surface to get regional anatomical info.
Thanks,
Alex
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Mon 7/4/2005 11:25 AM
To: Fornito, Alexander
Cc: Doug Greve; frees
Sorry Doug,
Could you please give me an example of how I would implement this?
Thanks,
Alex
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Tue 7/5/2005 1:40 AM
To: Bruce Fischl
Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu
Subject:RE
vertex dist (mm) = 1.00548 +/- 0.427572
avg vertex radius (mm) = 61.0534 +/- 17.1529
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Tue 7/5/2005 1:40 AM
To: Bruce Fischl
Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu
Sub
k?
Thanks,
Alex
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wed 7/6/2005 11:22 AM
To: Fornito, Alexander
Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu
Subject:RE: [Freesurfer] mri_vol2surf
Hi Alex,
you can click inside the ROI region on the surface,
ent: Wed 7/6/2005 11:22 AM
To: Fornito, Alexander
Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu
Subject:RE: [Freesurfer] mri_vol2surf
Hi Alex,
you can click inside the ROI region on the surface, then use custom fill
to create a label and save it to a file.
cheers,
Bruce
On
Hi,
I've noticed that when I run mris_anatomical stats on a label, I get a
different value for "total gray matter volume" if I run it on the pial surface,
compared to if I run it on the white surface. Just wondering why this is, how
the total gray matter volume is calculated, and which one rep
s
included.
Hope this makes sense!
Thanks,
Alex
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 7/12/2005 1:09 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject:Re: [Freesurfer] Anatomical stats for labels
Hi Alex,
th
Makes sense. If the lable is only defined along the wm surface, how are the
pial surface vertices defined/identified?
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wed 7/13/2005 9:32 PM
To: Fornito, Alexander
Cc
ace area between the white and pial come
about as a result of shearing forces as the wm surface is deformed outward. Is
that correct?
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thu 7/14/2005 8:04 AM
To: Fornito, Alexander
Hi,
recon-all stage1 overstrips some of my images during the skull-stripping stage.
I've played with the different options, but they don't seem to make any
difference at all. Any suggestions?
I've tried feeding in a pre-stripped brain (stripped using BET), but the
intensity normalization doesn't
Hi,
The new version of recon-all certainly sounds exciting. Any dates for Linux
release planned?
I'm looking at starting processing on a large set of images and wouldn't want
to begin and then re-do some of the processing because a superior method came
out.
Regards,
Alex
-Original M
Hi Nick,
I tried running the script you attached to this thread, and the error was
similar, albeit slightly different (see below). Any ideas?
Thanks,
Alex
make_average_surface --subjects 1000186 1000187 1000188 --out test_avg --echo
if ( 0 ) then
breaksw
end
while ( 0 != 0 )
goto parse_args_retu
Hi,
Is there anyway to print the output of mri_anatomical_stats to a text file?
Thanks,
Alex
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
Sorry to keep bugging you about this, but I ran tyhe new script and got a
slighlty different message (below). Any ideas?
make_average_surface --subjects 1000186 1000187 1000188 --echo
if ( 1 ) then
set getting_subjects = 0
endif
breaksw
end
while ( 1 != 0 )
set flag = --echo
if ( ! 0 ) t
Hi,
I've been trying to edit some labels in tkmedit and have noticed that if I save
a label in tkmedit and then project it back onto the surface in tksurfer, it
appears fragmented (ie., speckled). This happens even if I save a label that
was created in tksurfer in tkmedit without even editing it
. Quinn [mailto:[EMAIL PROTECTED]
Sent: Sat 7/30/2005 4:27 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject:Re: [Freesurfer] anatomical_stats
sure:
cd $SUBJECTS_DIR
mris_anatomical_stats -f file.txt -b -a subjid/label/hemi.aparc.annot
subjid hemi
On Sat, 30
ected onto the surface (?).
-Original Message-
From: Kevin Teich [mailto:[EMAIL PROTECTED]
Sent: Thu 8/11/2005 5:18 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject:Re: [Freesurfer] Editing labels
> I've been trying to edit some labels i
Hi,
I'm trying to resample a volume (representing a subregion of the subjects T1)
onto the surface using mri_vol2surf. When I try to load the output as an
overlay in tksurfer, nothing appears. The output is below. Any help would be
appreciated (note, I;ve also tried to output in analyze format w
lto:[EMAIL PROTECTED]
Sent: Thu 8/11/2005 1:42 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject:Re: [Freesurfer] mri_vol2surf help
Definitely do not use cor as the output. Use "paint" format (also
known as .w). See the examples.
doug
On Thu,
Hi,
Can labels be loaded in different colours in tkmedit?
Alexander Fornito
M.psych (Clin. Neuro.)/PhD candidate
Melbourne Neuropsychiatry Centre and Department of
Psychology
The University of Melbourne
[EMAIL PROTECTED]
___
Fre
ertex numbers to label...
-Original Message-
From: Kevin Teich [mailto:[EMAIL PROTECTED]
Sent: Fri 8/12/2005 7:56 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject:RE: [Freesurfer] Editing labels
The internal representation of the label form
Hi,
We've recently installed the freesurfer-Linux-rh9-dev20050729.tar.gz
distribution along with fs_supportlibs.tar.gz.
csurf works ok, but if i try to run tksurfer, I get the error message below.
We'd appreciate any help as we've been stuck for a while.
Thanks!
tksurfer 127 rh wh
HI Nick,
I downloaded the new redhat distribution from this site and the GUIs seem to
work ok, but got an error message when reunning recon-all (see below). We are
running Debian 3.1.
Thanks heaps for your help.
recon-all -autorecon1 -subjid 27_new -hemi lh -echo
breaksw
end
while ( 0 != 0 )
got
Hi,
We've recently installed the freesurfer-Linux-rh9-dev20050905-full.tar.gz
distribution on our systems, which run Debian 3.1. I noticed that unpacking the
distribution did not place the perl5 directory in
$FREESURFER_HOME/lib/mni/lib,as the readme file says it should. I then
downloaded the m
Sent: Thu 9/8/2005 1:43 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Intstallation problems on new dev?
That's due to a problem I created a few days ago. Fixes are at:
way?
Thanks again,
Alex
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thu 9/8/2005 10:45 PM
To: Fornito, Alexander
Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu
Subject:RE: [Freesurfer] Intstallation problems on new dev?
Hi Alex,
you probably wa
Do you mean you're not sure if it will work?
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Fri 9/9/2005 9:28 AM
To: Fornito, Alexander
Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Frees
31 AM
To: Fornito, Alexander
Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Intstallation problems on new dev?
we just have to test it. We've run the equivalent process many times,
just not in the recon-a
Sent: Fri 9/9/2005 9:36 AM
To: Fornito, Alexander
Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Intstallation problems on new dev?
probably. The safest thing to do is to rerun everything to make sure
that
al
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