You can create a ribbon volume with the command below:
mris_volmask \
--label_left_white 2 --label_left_ribbon 3 \
--label_right_white 41 --label_right_ribbon 42 \
--save_ribbon --save_distance youraveragesubject
Note this when you make the aparc+aseg in this way, it should
definitely use the individuals. Use mri_vol2surf to convert the motion
corrected (and otherwise unsmoothed) fmri time courses to the
surface. Then use mri_segstats with the --avgwf and --annot options
to compute the mean time course over the parcellations.
doug
On Sat, 17 Jul 2010, liang
Probably the AA matlab file is using dicom coordinates which are LPS
whereas my software uses RAS.
On Thu, 15 Jul 2010, Xu, Jun wrote:
Hi,
I found out something that I do not understand when I was trying to create
rotation matrix from scratch. I have used two methods and hope they
The stats files are computed with partial volume correction.
doug
On Thu, 15 Jul 2010, Yunjo Lee wrote:
Hi,
I am a new user of FreeSurfer and trying to figure out gray matter
segmentation.
A volume that I extracted from aparc+aseg.mgz using mri_segstats did not
match the volume
wow, I have no clue. You can tar up the data and drop it to me at the
file drop. But I just want to warn you that it might take me a while
to get to.
doug
On Thu, 15 Jul 2010, Scott Hayes wrote:
Hi,
I am trying to convert .ima files, and my command seems to work fine for
some series:
It computes the p-values first.
doug
On Thu, 15 Jul 2010, James Porter wrote:
Hello-
Does the built-in FDR function in tksurfer and QDEC run the calculations
upon the actual values in the .mgh files, or does it take the exponent
of those -log10(p) values first?
--
Douglas N. Greve,
Hi Keta, this is a pretty old version. Are you sure you don't want to
upgrade? The ipr is the in-plane resolution stored in the seq.info
file in the bold directory. Newer versions don't use this anymore.
doug
On Thu, 8 Jul 2010, ±¬Ìî¸ÂÀ wrote:
Hi,Freesurfers
I'm going to analyze the
The auto is what is automatically created. The other will be the same
as the auto unless you have made manual adjustments.
doug
On Wed, 23 Jun 2010, Corey Keller wrote:
Hi freesurfers,
I am trying to convert electrode coordinates from RAS to talairach
space. I have 128 electrodes sitting
/label1.label -temp subject/orig.mgz
-fillthresh .5 -o label1.bshort
However, it prompted me for a register.dat file and I do not have this.
Using the advice from Dr. Doug Greve, I have tried to use the -identity:
mri_label2vol -label subject/label/label1.label -temp subject/orig.mgz
You need a registration between the space in which your label is
defined and the fmri. The problem is that there are many definitions
of what Talairach space means. Can you get your label into the
fsaverage space? Ie, look at it with tkmedit using fsaverage as the
subject?
doug
On Wed, 9
You can use mri_label2vol. It takes the same registration matrix that
you used to get to the surface.
doug
On Wed, 9 Jun 2010, Hansen, Kathleen (NIH/NIMH) [F] wrote:
We have another question that is very related, so I will ask that at the same
time:
We have a region of interest defined
What do you mean by the UCSD freesurfer? A long time ago I re-wrote
a stream that Anders was using, and it gave similar results. I've just
re-written it again and it will be released with version 5.
doug
On Wed, 9 Jun 2010, francesca strappini wrote:
Hi all,
I would ask you about freesurfer
I don't have anything explicitly that will compute a map of z-scores,
but you could do a two group analysis with your subject as the only
one in one group and then do a group analysis. Alternatively, you can
transform you individual to the fsaverage space (mri_surf2surf), then
compute the z using
look in the subject/stats/?h.aparc.stats file
doug
On Tue, 8 Jun 2010, Weisinger, Brian (NIH/OD) [E] wrote:
Hello I am trying to retrieve the fusiform volumes of a sample. I looked in
the subject output files but didn't see any mention of the fusiform and when
I searched the website so
It was created by mapping all the individual asegs of the
input subjects to mni305, then detertermining the
most frequently occuring label. It should only be used for display
purposes.
doug
On Tue, 8 Jun 2010, Michael Waskom wrote:
Hi all,
How was the fsaverage aseg.mgz (in the 4.5
How did you create the .label files? mri_label2vol (your last step)
does not produce them. Maybe with mri_cor2label run on the output of
mri_label2vol?
doug
On Mon, 7 Jun 2010, Tina Jeon wrote:
Hello freesurfers!
After creating some labeling files from aparc.a2005s.annot, I noticed that
The corpus collosum is labeld in the auotmatic volume segmenation
(aseg.mgz). The prefrontal cortex is subdivided into a number of
regions in the auotmatic surface parcellation (lh.aparc.annot or
rh.aparc.annot)
doug
On Tue, 8 Jun 2010, Ahmed, F, Me fah...@sun.ac.za wrote:
Hello FS experts,
for that Doug, I just had a look in the aseg.mgz file, but unless
I'm blind, I can't seem to see it...could you tell me what it's labelled as
please?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Doug Greve
cmd line?
On Tue, 8 Jun 2010, Ahmed, F, Me fah...@sun.ac.za wrote:
I'm running version 4.3.1
-Original Message-
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: 08 June 2010 11:01
To: Ahmed, F, Me fah...@sun.ac.za
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer
Is there total overlap between group and number of slices? Sounds not
very good. I don't have a feel for what the MR on this and whether
changing the number of slices would create systematic differences in
SNR or contrast. Maybe Andre would like to weih in.
doug
On Tue, 8 Jun 2010,
This tests whether the quantity = (controls-patients)-(males-females)
is different than 0. Note the order of the inputs may be different
(making the final sign different). The order depends on the order that
you specfied in the levels file you passed to qdec.
doug
On Thu, 3 Jun 2010,
Do you just mean the volume in mm^3 of the caudate, etc? These numbers
are in the aseg.stats files in each subject. You can create a spread
sheet using asegstats2table (including just specifying the segs you
want).
doug
On Tue, 1 Jun 2010, Weisinger, Brian (NIH/OD) [E] wrote:
Is there any
Hey Libby, try using mri_label2vol. It will ask for a template volume
and registration. If you are mapping it to each functional run use
example_func as the template and the register.dat created by
reg-feat2anat as the registration. If you are mapping it to a gfeat of
the combined runs of each
You can do a cluster-based correction for multiple comparisons to
compute the p-value of the cluster. Is that what you mean?
doug
On Thu, 20 May 2010, Rajagopalan, Venkateswaran wrote:
Thanks Doug, but for instance in my result the inferiorparietal region is
significantly different in some
Try running mri_annotation2label with --lobes lh.lobes.annot
doug
On Thu, 20 May 2010, Rudolph Pienaar wrote:
Hi all --
Is there a simple way to create an annotation for
frontal/temporal/occipital/parietal lobes based off the ?h.aparc.annot
files in a FS 'label' dir? Ideally speaking,
Just run
mri_convert dicom-from-series.dcm 001.mgz
where dicom-from-series.dcm is a single file from the T1 series (it
will find the rest).
doug
On Sun, 29 Nov 2009, Jesse Bledsoe wrote:
I have all of the dicoms - what is the best way to run mri_convert on all of
the dicoms in the t1
Here's Tom Nichols explanation. He points out that you use the maximum
i, not the minimum, so you don't have to get past i=1. Thanks Tom!
-- Forwarded message --
Date: Fri, 16 Oct 2009 23:11:09 +0100
From: Thomas Nichols t.e.nich...@warwick.ac.uk
To: Doug Greve gr
Good point (meaning that I don't know the answer). I'll see if I can
find out.
doug
On Fri, 16 Oct 2009, Donna Dierker wrote:
Regardless: FDR's sensitivity appears resolution-dependent to me.
On 10/16/2009 10:39 AM, Michael Harms wrote:
Interesting post Donna, but my understanding of
you might try mris_volmask. It expects two surfaces (usually white and
pial),
so you might have to generate a 2nd surface with mri_surf2surf with
--surf-xyz, --targ-xyz, and --projabs XXX (XXX =? 1mm).
doug
On Fri, 16 Oct 2009, Daniel G. Wakeman wrote:
Hi,
I need to generate a mask from a
isxconcat-sess creates the files that you pass to mri_glmfit (ie,
multi-frame volumes and/or surfaces where each frame is a
subject). Something like:
AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor/tal.ces.nii
You can then use this as input to mri_glmfit
using a command like this:
mri_glmfit --y tal.ces.000.nii --osgm --glmdir tal.rfx.osgm --nii --mask
../tal.mask.nii
Thanks
Mx
2009/10/15 Doug Greve gr...@nmr.mgh.harvard.edu
isxconcat-sess creates the files that you pass to mri_glmfit (ie,
multi-frame volumes and/or surfaces where each
On Sat, 26 Sep 2009, Asaf Kaftory wrote:
Hello list,
I'm new to optseq, and would like your help with the following issues:
1. What exactly does DPSD mean? and why does the TR has to be an integer of
it?
Delta Post-Stimulus Delay. The time between samples in the
FIR. Usually, it is just
You can just use tksurfer, something like
tksurfer subject lh hippocampus
assuming you called it lh.hippocampus
There will be a lot of warnings/errors printed to the terminal. These
just have to do with the fact that the number of vertices will be
different than the cortical surfaces.
You can
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 vertex for
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
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
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
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
(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) You
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
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
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
---
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
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
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
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
On 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 2009
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
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
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 nifti header
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
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 with this. Can
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
something like
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
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
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
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
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
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
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
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
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
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
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
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
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
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
(or anyone)
help me with the command line flags?
regards,
sid.
On Mon, Dec 15, 2008 at 12:11 PM, Doug Greve
gr...@nmr.mgh.harvard.edu 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
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.
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:
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
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
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
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
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
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
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
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:
.
.
.
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
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
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
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
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
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
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
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
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
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
either in isxconcat
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
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
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
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
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.
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
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
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
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
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