/space/barlab_002/users/cibu/dep_LGI does not exist
Cibu Thomas wrote:
Hello
When I run the mri_preproc command I am getting the message
ERROR: cannot find fsaverage in /space/barlab_002/users/cibu/dep_LGI
But the fsaverage folder is in the path and subjects_dir is set
correctly.
So I am not
Watson, Christopher wrote:
Hello Freesurfers,
Lately I've been scratching my head about image orientation problems. What I do
here is take the DICOM images and use mri_convert to convert them into SPM
Analyze format. The command I use is:
mri_convert.x86_64.dev -dicomread2 "$experiment" --n
You can create labels for each of the cortical annotations with
mris_label2annot, then merge the labels for your lobe together with
mri_mergelabels, then run mris_anatomical_stats on the final label. This
will give cortical volume for your lobe (will exclude white matter).
doug
Tadeu Kubo wr
Iris, the registration targets were derived differently. With version 4,
we automatically fill in all the ventricles. In verion 3, they were
partially filled in manually. Version 3 creates a surface around the
ventrical making it look like a sulcus, and this affects both the target
and the regi
We don't have anything that will do it explicitly. If you have FSL
installed, you can use fslsplit. Otherwise, you can write your own
script to convert to spm analyze, then convert each file to nifti
(nothing is lost as we keep the .mat files around).
doug
Watson, Christopher wrote:
Hi, I'm
You can use mri_surf2vol to create a mask. Is that what you mean?
doug
On Tue, 30 Sep 2008, Tommaso De Marco wrote:
Hi,
I'm a freesurfer user beginner. I need to discretize the gray matter in a
cubic mesh. I have extracted the $h.pial and $h.white surfaces, and I would
know if it is possib
I'm sure there are some out there, but we cant do it in FS.
doug
On Mon, 29 Sep 2008, Qianqian Fang wrote:
hi
I know that mri_convert and a few other tools are able to convert
a series of dicom files into a 4D (multi-frame?) nifti file. However,
is there a way, either using freesurfer or o
main labeled as "None", apparently propagated from aseg.mgz).
Do I have this summary correct?
thanks,
Mike H.
On Tue, 2008-07-22 at 14:54 -0400, Doug Greve wrote:
Actually, the construction of aparc+aseg and wmparc do use info about
where the surface is to refine the aseg cortical
Hi Joost, you can load the label into matlab with read_label.m and then
convert it into the vector you want. Alternatively, there is a new
version of mri_annotation2label (x64 below) which you can use to create
a "segmentation" surface in nifti or mgz from an annotation. Then find
"voxels" th
one uses ?h.aparc.annot and one uses ?h.aparc.a2005s.annot. These are
two different parcellations.
Hwee Ling Lee wrote:
Hi!
I hope this finds you well.
What is the difference between aparc+aseg.mgz and aparc.a2005s+aseg.mgz?
I tried to extract the label for 1180 but I get nothing
Hi Joost, can you look at the original sig map thresholded at 1.3 to see
if there is a cluster of that size?
Hi,
version 4.0.5
after:
mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf
fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/newperm_lh
--glmdir st
One method that leaps to mind is to have new RAs analyze a relatively
small set of data (say 10), then do a vertex-wise paired t-test between
your gold standard set and the new RA's set.
doug
Derin Cobia wrote:
Nick,
Yes, our tcltktixblt directory was intact and set correctly. The reason I
I just added those changes to stable, so it should be in our next stable
release.
Michael Harms wrote:
At some point in early 2008, Doug had created a version of tkregister2
that he graciously provided us, which had --gca-skull and --gca flags,
which greatly simplified the process of confirmin
You can use mri_binarize with the --match option to spec the index, eg:
mri_binarize --i aseg.mgz --match 17 --o hippo.lh.nii
doug
Martin Ystad wrote:
Hi, I'd like to create binary masks in the nifti-format from each of
the subcortical segmentations in freesurfer, separately (one for
hippoc
If you've reconned a subject, you can use the aparc+aseg.mgz volume.
doug
Ryan Scotton wrote:
Hi Freesurfers,
Some associates of mine are working on a pipeline that generates
cortical parcellations and we are looking to compare its measurements
to some measurements generated by the freesurf
one way to do it is with mri_concat, something like
mri_concat f???.img --o f.nii.gz
if your individual volumes are f000.img f001.img etc
Kara Dyckman wrote:
I'm not sure. When I just tried it, it converted to .nii.gz. Maybe
it has to do with the version of fsl being used? I'm posting this
Hi, for subcortical segmentations, is it then better to use the
volumes in wmparc.stats than those in aseg.stats?
On Tue, Jul 22, 2008 at 2:54 PM, Doug Greve
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
>
> Actually, the construction of aparc+aseg
You need to set up the psdwin to span the duration of a hemodynamic
response to your event as if it were presented in isolation. For a 3sec
event, you can probably use something like 24 sec (so min=0, max=24).
Since your TR=2, but your event duration is 3sec, I'd set dpsd=1 (so
that both the TR
If you go into the qdec output directory, you will find a contrast for
each group (class). In the contrast directory, you will find a file
called gamma.mgh. This will be the average thickness for the group. You
can load it into tksurfer, something like:
tksurfer fsaverage lh inflated -overlay
mean
difference in thickness between groups. How do I get it to save out one file
for each group? Where is there a good explanation of the output files from qdec?
Thanks
Jen
On Oct 28, 2008, at 4:30 PM, Doug Greve wrote:
If you go into the qdec output directory, you will find a contrast for
You can also use mri_concat, like
mri_concat \
010130_vc6126/surf/lh.thickness.fsaverage.mgh \
zmaps/OCplusYC/lh_mean.mgh \
--paired-diff \
--o 010130_vc6126/surf/lh.thick_min_OCADmeanthick.mgh
Masking can be done by mri_mask, and thresholding with mri_binarize.
doug
On Fri, 31 Oct 2
I just modified fscalc.fsl to take surfaces. This is a front-end to
FSL's fslmaths command. You give it the exact same arguments, but the
files can be of any format. If the underlying data are on a surface,
then add --surf subject hemi, and it will reshape the surface to fit
in nifti (as long as
It creates a file called ".xdebug_tkmedit", not sure if it puts all
the commands there, though.
doug
On Sat, 1 Nov 2008, Kellen Mobilia wrote:
Hi
Would anyone happen to know the location where Freesurfer hides its error
logs? Especially for the "medit tool. Are the located in the local
Freesur
Do you mean one for each subject? If you output a cluster number
volume (--ocn) from mri_surfcluster, then you can pass the ocn to
mri_segstats as a segmentation, and pass the mri_glmfit input (--y)
as --in, then save the result as an ascii file with --avgwf.
doug
On Wed, 29 Oct 2008, Carl Sc
Can you try specifying "-run 15" instead of "-run 015"? Not sure that
will make a diff, but it might.
doug
[EMAIL PROTECTED] wrote:
Hi,
Running the following command line :
unpacksdcmdir -src /media/AJB_CERV1A/07311357 -targ
/space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti -
What is your tkmedit command line?
Alexa Nardelli wrote:
Hi, I am new to freesurfer and to automated segmentation in general
and I am having a problem using tkmedit's segmentation. I am able to
open my images with freesurfer but I am having problems with the
segmenation function. I am not
They are in aseg.mgz, you can extract them into a nifti file with
mri_binarize --i aseg.mgz --match 251 --o CC_Posterior.nii
251 is the code for CC Posterior (found in
$FREESURFER_HOME/FreeSurferColorLUT.txt)
doug
vin wrote:
hi,
I am trying to export segmented regions as NIFTI, and it wo
nifti generally does not have the capability to save patient info. I
might if the software that created it has a nifti extension (FreeSurfer
does not, yet). There is a comment field in the nifti header, so it is
possible it could be there, but unlikely (it would not be with a
FreeSurfer program
SurfArea is the surface area of the parcellation in mm^2.
GrayVol is the volume of gray matter in the parc (basically thickness
time area) in mm^3
ThickAvg is the average thickness (use this for your thickness study)
MeanCurv is the average mean curvature.
GausCurv is the average gaussian cu
How many vertices does that subject have and is there a prime factor
less than 2^15?
doug
On Thu, 6 Nov 2008, Akram Bakkour wrote:
Hello,
Thanks for adapting fslcal.fsl to work on surfaces Doug. This is very
helpful. It was working for me until today.
I'm working on thigpen.
setenv SUB
Hongchuan Zhang wrote:
> Hi, list,
> I am new to optseq2 so I really need advices to my questions. We have
> an experiment of 2 factors with36 trials for each factor, and another
> 24 null trials. So in total we have 96 trials. We also have 3 random
> jitters which make our trials could last for
Use mri_vol2vol, something like:
mri_vol2vol --mov ribbon.mgz --targ rawavg.mgz --regheader --o
ribbon-in-rawavg.nii --interp nearest
doug
Arthur Mikhno wrote:
Hi,
I am trying to convert the ribbon (amongst other mgz files) from a
freesurfer run to the native space ANALYZE file I initial
There are two things you can do here. One is to create your own design
matrix in a text file and pass it to mri_glmfit with the --X (instead of
using an fsgd file). If you want to stay with the fsgd, then you can
spec DODS (this will set up one regressor for MMSE instead of two).
doug
Martin
Have you looked at my presentation on group analysis? The slides are here:
http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/freesurfer.groupanalysis.pdf
There's a very similar design on slides 23 and 24.
doug
Zhangyuanchao wrote:
> Dear Mr or Ms,
> I have read the FreeSurfer Tutorial: Gr
All those commands will do the same thing. When you pass mri_convert a
single dicom file, it looks at all the files in that directory and finds
all the dicoms that have the same series number, and puts them into one
volume.
Alexa Nardelli wrote:
Hi,
I have a question regarding converting fi
In general, this is a bit of a mess. The way that I do it is to use
piecewise and set the min and mid to the same thing (this is what linear
opaque was supposed to do). This way, anything that is over threshold
has color, everything else is transparent. BTW, everything over the mid
will be opaq
did you create a subject called "average"? This is done with
make_average_subject. Alternatively, we distribute an average subject
called fsaverage, so you can just use that instead if you want.
doug
Alexandru Hanganu wrote:
Dear Freesurfer Users,
We have a little problem with mri_surf2surf.
from a freesurfer standpoint, it looks like you've done the right
thing. Sorry, can't help out much on slicer. It is possible that slicer
is expecting an integer data set, so you can try
mri_convert FSParcel_FSorient.mgz FSParcel_FSorient.int.mgz
--out_data_type int
doug
joel bruss wrote:
Lúcia Garrido wrote:
Dear all,
I have a few questions about stats in freesurfer that I'd be very grateful
if you could answer.
1. Is it possible to reduce the search from the whole brain to a smaller
region of interest to apply corrections for multiple comparisons? For
example, if I'm intere
The cortical segmentation from the aseg does not often line up very well
as it is only based on a voxel/volume analysis. The aseg is not informed
by the surface analysis.
doug
[EMAIL PROTECTED] wrote:
Hello all-
I'm having some trouble with sessions in which the pial surface is not
matching
Hi Scott, you should skip steps 2-6 (that is the old stream). Instead,
run isxconcat-sess after #1, then smooth on the surface either in
isxconcat-sess or with mri_surf2surf before running mri_glmfit.
doug
Scott Gorlin wrote:
Hi,
I'd like some clarification on the recommended procedure for
The aseg.stats is computed with a partial volume correction at the
boundaries of the structures, tkmedit just counts voxels.
Yuan Xu wrote:
Hi FreeSurfer:
when I compare a brain structure volume count on the aseg.stats
files with a volume of same structure measured using tkmedit
"Se
significance in the sphere
space? This didn't seem true to me, which is why I tried to recreate
the significance maps as below.
Thanks,
-S
Doug Greve wrote:
Hi Scott, you should skip steps 2-6 (that is the old stream).
Instead, run isxconcat-sess after #1, then smooth on the surface
Hi Susie, I have a tool that works very well on this type of thing, but
I am not quite ready to release it (a few more weeks). It will be
greatly facilitated if you acquired a whole-brain image during your scan
(this can include the MPRAGE itself). If not, then you'll have to do
some hand regis
what is your command line?
On Fri, 28 Nov 2008, Steinmann, Iris wrote:
Hi Freesurfers,
there is a little problem: I load fsaverage in tkmedit and marked with
tools-'Configure-Brush-Info...' an area in the volume, then I saved it as a
label (newarea.label).
I want to create a binary mask wi
try just running tksurfer with the -label-outline option.
j janssen wrote:
Hi,
using version 4.0.5
my goal: to display in tksurfer an inflated brain with curvature and
an *outlined* label, using a tcl-script.
there are probably numerous ways, i did:
tksurfer "subject" rh inflated -gray -
We don't have a good way to do this yet. I've have been working on one
but have dropped the ball. Some people will analyzed both the
correctly-oriented data and left-right reversed for each subject, but
this is not the best way to do it.
doug
Frederic Andersson wrote:
Hi,
Is there any wa
Do you just want to do a paired analysis? Do you want to include other
covariates?
Burmicz, Ryzarda wrote:
Hello,
Could you please advise as to whether or not the following analysis is
suitable?
I would like to compare groups of monozygotic twins (MZ concordant vs.
MZ control ; MZ discor
Looks like matlab is having trouble running from the shell. I have no
idea what causes this, you may have to ask your system administrator for
help.
doug
wrote:
Hi, Mr or Ms
My name is Kenta in Japan. I'm undergraduate student.
Please help me!
I've tried some things to solve the error
Yea, there's not a mask to label. There is a mask to brain, but I'm not
sure if you can substitute your own mask for it. I just tried to run it,
and could not get FDR to work at all in tkmedit. Is it working for you
at all?
doug
Dan Dillon wrote:
Dear FreeSurfers,
I've created a basal g
It was likely converted thru an intermediate format that did not retain
those values (eg, nifti or analyze) before being imported into freesurfer.
Jared Price wrote:
Dear freesurfer gurus,
I noticed something unusual in some of our data today. When the
command mri_info was run on some of the
Yes, the max stat is stored in the CSD, and it's purpose is to enable
voxel-wise correction, but I've never gotten around to it (and this is
the 1st request:). You might be able to program something in matlab
pretty quickly. You can use FS's load_csd.m to load the CSD file, and
MRIread() to l
Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd lines.
doug
Alexandru Hanganu wrote:
Dear Freesurfer users,
We have an MNI mask and we want to apply this mask on a group of
subjects for small volume correction.
so we did the following steps:
1. cd $SUBJECTS_DIR/fsaverage/
I would probably use --ocn with mri_volcluster to create a single volume
in which each voxel value is the cluster number it belongs to. Then
split them out like:
mri_binarize --i ocn.mgh --match 1 --o cluster-0001.mgh
doug
Gregory Dierksen wrote:
Hi,
I'm trying to use the mri_volcluster c
what's your cmd? You need to make sure to add --in lh.thickness to get
thickness in the summary file
Alexandru Hanganu wrote:
Thank you Nick, and Doug for your answers. I used both "--reshape"
flag and "--noreshape" flag and the results after "mri_segstats" were
in both cases:
.
.
Try looking at the docs on
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
esp the fscoords.{pdf,ppt}
doug
Julien Dubois wrote:
Hi
I need one piece of info that I can't seem to find anywhere (after 1h
of searching).
What exactly do the numbers in register.dat correspond to (I
Hi Y'all, I've completed some new documentation on the FreeSurfer Group
Descriptor (FSGD) files. They can be found in these locations:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat
https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss
I just created another wiki page to document how to perform a paired
statistical analysis in FreeSurfer (someone was asking me about it, but
I lost the email). The page is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
It is admittedly a little rough, so let me know if you fi
Sorry, try it now.
doug
wrote:
Hi, Mr. and Mrs
I want Tutorial file of fsfast.
But I didin't get it from the following pass.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsfast-tutorial/fsfast-tutorial.subjects.tar.gz
If you know about that please let me know.
Thank y
I just noticed this about a week ago and have not been able to track it
down. The w file (or anything created by mri_vol2surf, which is run by
paint-sess) is the gold standard. When tksurfer loads in a
volume/registration, it is slightly off. I'm working on why.
doug
Jesse Friedman wrote:
H
Christian Scheel wrote:
Dear all,
I have got several questions about the analysis of my data. Maybe you
can help me out:
1) Regarding the different levels of smoothing (FWHM) in Qdec are
there already some 'standards' that one should usually stick to? My
results look better when I set th
it is automatically computed by mri_glmfit and used to compute the fwhm
(saved in fwhm.dat). I'm working on an RFT-based correction for multiple
comparisons correction, and that requires fwhm. You also need it if you
are going to use the monte-carlo-based simulation.
doug
Michael Harms wrote:
I would have thought that that mri_convert cmd (with .img) would have
worked. what went wrong?
Susie Heo wrote:
Hello,
I am hoping that someone can help me to solve my orientation/angle acquisition
problem:
1) I have an EPI oblique slice in Analyze format with incorrect
orientation/angle a
Hi Petr, when you list your subjects, just use the subject's name. It
looks like you put path specifiers in there, ie, "./1013" shoudl be
simply "1013"
doug
p.s.bjer...@studmed.uio.no wrote:
Hi,
Trying to make an average of about 60 subjects. The problem is that the
proper files are not pro
Hi Xin, the problem is that neither the sform nor the qform are valid.
Did the message below not appear when you ran tkmedit?
WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented
Fix that, and everything will work fine.
doug
Wang, Xin w
the registration without
the information on qform and sform in case I can not get them. Does
convert to ANALYZE format or manually correct in tkregister2 work?
Thank you again,
Xin
-Original Message-
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 12/15/2008 1:09 PM
To
There are two things you can do,
mri_concat spm_*.img --o 4d.img
you can also do it with mri_convert, but I don't think it buys you
anything over using mri_concat.
doug
Siddharth Srivastava wrote:
hi everyone,
is it possible to combine, using mri_convert, a set of
3D s
anyone)
help me with the command line flags?
regards,
sid.
On Mon, Dec 15, 2008 at 12:11 PM, Doug Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
There are two things you can do,
mri_concat spm_*.img --o 4d.img
you can also do it with mri_convert, but I don't think
it's only positive for the contrast that you have specified. the roi
summary reports the HRF amplitudes for each condition. When you compute
the contrast of those, you should get the right sign.
doug
Dave Brohawn wrote:
Hello,
In the stable 3 environment, I ran the func2roi-sess command. Th
it wants the number of dimensions to be either 3 or 4, even if the size
of those dims is only 1. You'll probably have to edit the header, though
I'm not sure how to do that.
Susie Heo wrote:
Hello,
When I try to use the Freesurfer command 'tkregister2' (or 'mri_convert', or
any Freesurfer co
if you have the voxel index (col, row, slice) then you can:
V2R = [
-1.00.00.0 128.0
0.00.01.0 -128.0
0.0 -1.00.0 128.0
0.00.00.01.0 ]
crs = [col row slice]';
xyz = V2R[crs+1; 1];
then f
make sure you're not using a 0-based index with matlab
Yunjie Tong wrote:
Hi Doug and Bruce,
Thanks for your answers. One more question, why the vertex RAS of the
same spot on the brain given in TkSurfer is not the ones I read by
Matlab program freesurfer_read_surf?
The commands I am using
how are you defining your ROI? Below is some info Im putting together on
segmentations, parcellations, and labels. It's still pretty raw, but it
might be useful to you.
Segmentation
- each voxel has an index
- index into lookup table (LUT), eg FreeSurferColorLUT.txt
- only one index per vox
Hi Y'all, I've recently found an error in the way that mri_surfcluster
reports the area of a cluster when using a group surface such as
fsaverage. The bottom line is that the area reported is about 25% too
big. However, the cluster-wise p-values reported by mri_surfcluster
based on simulatio
Try adding -unpackerr
Adrienne McCallister wrote:
Hello,
I am unpacking recent functional data and during a function run we
needed to stop it early and so now when I view it in unpacksdcmdir, it
has a err next to the run. Since those runs are typically skipped when
unpacking, is it possibl
Hi Dave, I'm not sure where to begin with this. Can you give more info?
In particular, you might look at
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for ways to report issues
efficiently.
doug
Dave Brohawn wrote:
Hello,
Josh Roffman and I recently ran an fMRI scan. Our subject's data vi
yes, it is
Bruce Fischl wrote:
actually Doug can confirm, but I think the average surface RAS are
already Talairach coords
On Wed, 24 Dec 2008, Nick Schmansky wrote:
Corey,
I'm not 100% sure how to do this but a starting point is to use
mris_info on the surface file you are getting coordina
Siddharth Srivastava wrote:
Hi all,
I am trying to understand the --surf flag in the mri_glmfit
command, and the 2 parameters that follow it. The tutorial mentions
--surf average lh .
1) what should "average" contain? should it point to the average of
the population, of fsaverage, or
reference points I can use?
Thank you in advance for any suggestion.
Xin wang
-Original Message-----
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 12/15/2008 1:26 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed
There is a flag in the ni
You can use feat2surf (or mri_vol2surf directly), this will create
something like lh.zstat1.mgh. You can then use
lhz1 = MRIread('lh.zstat1.mgh');
doug
Yunjie Tong wrote:
Hi
I was able to view the statistical maps (from FSL) on the subject's
surface following the tutorial (FsTutotial/FSL
Xin Wang
----
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 1/5/2009 2:03 PM
To: Dave Brohawn
Cc: jroff...@partners.org; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Problem with post-spm registered data
Hi Dave, I'm not sure where to begin
s dimensions of 1x9022x17. What does that mean? I am
looking for the vertex and faces, with which I could display them in
Matlab using patch. Do I miss something? Thanks.
Best,
YJ
On Jan 6, 2009, at 12:44 PM, Doug Greve wrote:
You can use feat2surf (or mri_vol2surf directly), this will create
Christine Ecker wrote:
I would like to export cortical thickness measures and compare the data
across subjects in a vertex-by-vertex fashion.
Please could you confirm that similar functions such as mri_glmfit are based
on the parameters in template space e.g. lh.thickness.fsaverage.mgh and no
On Sun, 22 Mar 2009, Avram Holmes wrote:
All,
I have generated a mask of the cingulate regions for each of my participants
from their aparc+aseg.mgz files (see attached image) and I would like see how
these masks overlay with the group average brain I have generated for my
study. Is there a
you can get something like what you want with
cd $SUBJECTS_DIR/subject
mri_binarize --i mri/ribbon.mgz --min .0001 --o mri/tmp.mgh
mri_tessellate mri/tmp.mgh 1 surf/lh.both
mris_smooth -nw surf/lh.both surf/lh.smboth
tksurfer subject lh smboth
Note that eventhough you call it "lh" it has both h
Sorry, I have not used this toolbox much. Maybe Don can chime in.
doug
On Fri, 3 Apr 2009, Zhong Jidan wrote:
Hi,
I was trying to figure out if there is any way to determine the exact
size at which clusters becomes significant given a specified
significance on the surface data.
Then i foun
Falk, it looks like that file was somehow converted to DOS. try:
dos2unix recon-all
chmod a+x recon-all
then re-run
doug
On Mon, 6 Apr 2009, Falk Lüsebrink wrote:
Hi Nick,
I tried using your modified recon-all today but as soon as I try to process any
data I receive following error mess
I thought it was 4.0.3, so maybe that's not it. Can you look at the
ribbon.mgz file? You can load it as a segmentation, ie,
tkmedit subject orig.mgz -seg ribbon.mgz
aparc+aseg is suppossed to inherit the cortex from ribbon.mgz
doug
On Mon, 6 Apr 2009, Martin Kavec wrote:
Hi Dough,
this
Monday 06 April 2009 22:17:18 Doug Greve wrote:
I thought it was 4.0.3, so maybe that's not it. Can you look at the
ribbon.mgz file? You can load it as a segmentation, ie,
tkmedit subject orig.mgz -seg ribbon.mgz
aparc+aseg is suppossed to inherit the cortex from ribbon.mgz
doug
On Mon, 6 Apr
Are you loading the one created by mri_glmfit (in the output
directory)?
doug
On Mon, 6 Apr 2009, Jeff Sadino wrote:
Thank you for the advice Sid. I added those lines, and now my errors
disappear, but I still get a blank screen where there should be a scatterplot.
Is this a graphics is
Is this for a permutation test? Sorry, this is my fault. I've put a
new version here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim
that should fix the problem. Can you test it out?
thanks
doug
On Mon, 1 Jun 2009, Georg Homola wrote:
Hi All (and especially Dou
The sig.mgh is the input that creates the sig.cluster.mgh (and the
summary table).
doug
On Thu, 4 Jun 2009, Judith Segall wrote:
Doug.
Again, I am only asking about the sig.cluster.summary. This was a thickness
study, where monte-carlo simulations where used to correct for multiple
compariso
just
mri_convert brainmask.mgz brainmask.nii
doug
On Thu, 4 Jun 2009, Jose Luis Cantero Lorente wrote:
Dear Freesurfers,
is it feasible to save to nii the MR images after stripping the skull in
Freesurfer? If so, please let me know how to do it.
Thanks in advance.
Best,
Jose
---
Jos
You can mri_convert the output specifying the output type as -odt
short. Sorry, don't have any easy way to change the slicing.
doug
On Wed, 10 Jun 2009, xfore...@ucla.edu wrote:
Dear Freesurfer experts,
I'm trying to convert the annotation file into (binary Analyze file),
I tried the com
yes, it is
On Thu, 11 Jun 2009, Nasim Maleki wrote:
Dear Freesurfer developers,
I'm wondering whether the wmparc.stats is computed with a partial volume
correction at the boundaries of the structures.
Thank you,
Nasim
___
Freesurfer mailing lis
(1) probably using mri_segstats with "--annot fsaverage lh aparc" and
specifying the --y input to mri_glmfit as the "--i invol" and specify
a "--avgwf" output to get all the subjects.
(2) Yes, you would expected it. I'm not sure what it means if you
don't see it. Maybe a bug somewhere.
(3)
In this case you would have six regressors:
1. control-offset
2. hiv-offset
3. control-age
4. hiv-age
5. control-ed
6. hiv-ed
If you want to test group thickness "regressing out" the effect of age
and ed, then you would just set the contrast to:
1 -1 0 0 0 0 0
Note that this will test it at ag
This cmd is not going to work. I don't think we have a way to convert
between the two. Sorry,
doug
On Wed, 17 Jun 2009, Yigal Agam wrote:
Hi all,
Is there a way to convert results that I have on fsaverage to average7? I
need to do that to be compatible with some average7 results that go
we often have problems reading philips dicoms, not sure why.
doug
On Fri, 17 Jul 2009, Jose Luis Cantero Lorente wrote:
Hi,
I am trying to convert from dicom to mgz (or nii) in Freesurfer by using dicom
files as the one attached to this message. However, Freesurfer reports that
this file
Yes, this is what our group analysis tools do. You can find tutorials
on the wiki. You'll probably start with mris_preproc.
doug
On Thu, 20 Aug 2009, Feng-Xian Yan wrote:
> Hi,
>
> Thank you for your responses before.
>
>
>
> I have another problem want to solve. I check the number of verte
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