recon-all -autorecon2 -autorecon3 -subjid
Actually, I am sorry, I just noticed the processing is not over yet. I
will check after it is done and get back to you.
> What command did you run? Do you want to upload the dataset?
>
>
>
> On Sep 16, 2011, at 10:52 PM, "Sindhuja Tirumalai Govindarajan"
What command did you run? Do you want to upload the dataset?
On Sep 16, 2011, at 10:52 PM, "Sindhuja Tirumalai Govindarajan"
wrote:
> Hi Khoa and Bruce,
>
> I added control points along the white surface - it did not help much in
> extending the pial surface.
>
>
>> Looks like there might
Hi Khoa and Bruce,
I added control points along the white surface - it did not help much in
extending the pial surface.
> Looks like there might be some kind of gray matter pathology there as well
>
>
>
> On Sep 16, 2011, at 3:07 PM, Khoa Nguyen wrote:
>
>> Hi,
>>
>> How is the intensity of the
Looks like there might be some kind of gray matter pathology there as well
On Sep 16, 2011, at 3:07 PM, Khoa Nguyen wrote:
> Hi,
>
> How is the intensity of the wm between the putamen and the
> white surface? If it's lower than 110, you can place a string of control
> points along the insid
when I want to get the timecourse from vertex number, what is the option
name can I use?
YUMI
>
> Yes, that is correct. You can have it produce one time course with --id
1
> doug
>
> YUMI MAEDA wrote:
>> Doug,
>> thank you very much. I tried with --ctab-out
>> my timecourse data and annot has di
Yes, that is correct. You can have it produce one time course with --id 1
doug
YUMI MAEDA wrote:
> Doug,
>
> thank you very much. I tried with --ctab-out
> my timecourse data and annot has different dimention and I got this message.
>
> ERROR: dimension mismatch between input volume and seg
> i
You are right, it turned out there was an issue with $SUBJECTS_DIR and
when I fixed it, everything worked fine.
Thank you very much for your help!
Peter
On 09/16/2011 03:22 PM, Douglas N Greve wrote:
> Is that subject in your $SUBJECTS_DIR ?
>
> Peter Savadjiev wrote:
>> Hi Douglas,
>>
>> I rem
Doug,
thank you very much. I tried with --ctab-out
my timecourse data and annot has different dimention and I got this message.
ERROR: dimension mismatch between input volume and seg
input 96 32 96
seg 119778 1 1
Then I tried this to get the same dimension,
mri_label2vol --label ./ROI.labe
Is that subject in your $SUBJECTS_DIR ?
Peter Savadjiev wrote:
> Hi Douglas,
>
> I removed the --surf curv option from the command, but had exactly the
> same error output.
>
> Also, if curv is not a surface, how can I get the curvature values
> into a 3D volume? This is all I'm really intereste
Hi Douglas,
I removed the --surf curv option from the command, but had exactly the
same error output.
Also, if curv is not a surface, how can I get the curvature values into
a 3D volume? This is all I'm really interested in.
Thank you once again,
Peter
On 09/16/2011 02:39 PM, Douglas N Greve
Hi,
How is the intensity of the wm between the putamen and the
white surface? If it's lower than 110, you can place a string of control
points along the inside border of the white surface. That might help
extend the pial surf to include all the gm.
-Khoa
On Fri, 16 Sep 2011, Sindhuja Tirumala
Oh, don't use --surf curv. The curv is not a surface (which has vertex
XYZ and neighborhood relationships). Leave that option off (to get
white) or specify a real surface.
doug
Peter Savadjiev wrote:
> Hi Douglas,
>
> Yes, I know that, I just put subjid in the email not to enter a long
> pathna
Hi Douglas,
Yes, I know that, I just put subjid in the email not to enter a long
pathname and an actual subject id that is irrelevant to the email. Sorry
about the confusion. Do you see any other problem with the command?
Thank you,
Peter
On 09/16/2011 02:22 PM, Douglas N Greve wrote:
> subjid
subjid should be the name of your subject (not literally "subjid")
Peter Savadjiev wrote:
> Hi,
>
> I am trying to convert the "curv" surfaces to a volume, using the
> mri_surf2vol command in the following manner:
>
> cd subjects/subjid
> mri_surf2vol --surf curv --hemi lh --template ./mri/orig.m
Hi,
I am trying to convert the "curv" surfaces to a volume, using the
mri_surf2vol command in the following manner:
cd subjects/subjid
mri_surf2vol --surf curv --hemi lh --template ./mri/orig.mgz --outvol
/tmp/curv.mgz --surfval ./surf/lh.curv --fillribbon --volregidentity subjid
I get the fo
unfortunately, all the annotations have to have different colors. The
identity of an annotation is coded by its color.
Antonella Kis wrote:
> Hi,
>
> Based on Group Analysis tutorial by loading the cluster annotation in
> tksurfer you can visualize all clusters, regardless of significance.
>
great, thanks
Bruce
On Fri, 16 Sep 2011, Yang Liu wrote:
It worked. Thanks.
On Fri, Sep 16, 2011 at 12:06 PM, Bruce Fischl
wrote:
hmmm, looks like it's not linked. Just try doing a redraw in the
interface and see what happens
On Fri, 16 Sep 2011, Yang Liu wrote:
Hi Bruce,
It worked. Thanks.
On Fri, Sep 16, 2011 at 12:06 PM, Bruce Fischl
wrote:
> hmmm, looks like it's not linked. Just try doing a redraw in the interface
> and see what happens
>
> On Fri, 16 Sep 2011, Yang Liu wrote:
>
> Hi Bruce,
>> 'set scalebar_bright 240' works.
>> But when I type 'draw_scaleba
hmmm, looks like it's not linked. Just try doing a redraw in the
interface and see what happens
On Fri, 16 Sep 2011, Yang Liu wrote:
Hi Bruce,
'set scalebar_bright 240' works.
But when I type 'draw_scalebar',
it says 'invalid command name "draw_scalebar".
Did I miss anything?
Yang
On Fri,
Hi Bruce,
'set scalebar_bright 240' works.
But when I type 'draw_scalebar',
it says 'invalid command name "draw_scalebar".
Did I miss anything?
Yang
On Fri, Sep 16, 2011 at 11:57 AM, Bruce Fischl
wrote:
> at the tksurfer tcl prompt (%)
>
> On Fri, 16 Sep 2011, Yang Liu wrote:
>
> Hi Bruce,
>>
Hi,
Based on Group Analysis tutorial by loading the cluster annotation in tksurfer
you can visualize all clusters, regardless of significance. Then changing
the label mode to "Outline" by hitting the outline button and loading the
cluster p-value overlay I can see all the significant cluste
at the tksurfer tcl prompt (%)
On Fri, 16 Sep 2011, Yang Liu wrote:
Hi Bruce,
Where can I set these parameters?
Yang
On Fri, Sep 16, 2011 at 11:40 AM, Bruce Fischl
wrote:
Try something like:
set scalebar_bright 240
draw_scalebar
the scalebar is 1cm, so I don't thin
Hi Bruce,
Where can I set these parameters?
Yang
On Fri, Sep 16, 2011 at 11:40 AM, Bruce Fischl
wrote:
> Try something like:
>
> set scalebar_bright 240
> draw_scalebar
>
>
> the scalebar is 1cm, so I don't think tthere's any need for text. The
> default scalebar_bright is 128
>
>
> On Fri, 16
Try something like:
set scalebar_bright 240
draw_scalebar
the scalebar is 1cm, so I don't think tthere's any need for text. The
default scalebar_bright is 128
On Fri, 16
Sep 2011,
Douglas N Greve wrote:
> I don't think there is text. The scale bar is 1cm long.
>
> Yang Liu wrote:
>> Hi,
>>
Hi Adam, try rescaling the brain volume to be around 1 (demeaning it
might help too). The next version of FS will remove these scaling problems.
doug
Adam David Felton wrote:
> Hello,
>
> I am using Qdec to analyze thickness (etc) using various IVs (e.g.,
> Verbal IQ) while controlling for cor
I see. Thanks!
On Fri, Sep 16, 2011 at 11:27 AM, Douglas N Greve wrote:
> I don't think there is text. The scale bar is 1cm long.
>
> Yang Liu wrote:
>
>> Hi,
>>
>> I want to get a distance scale bar on tksurfer's window. I can get a very
>> dark bar on the black background, but I can't see an
Hi Ansgar,
If you have your own bvals and bvecs, you should add the following extra
lines to your dmrirc file.
set bvalfile = /path/to/bvals.txt
set bvecfile = /path/to/bvecs.txt
set nb0 = *No. of low-b images* (In your case you can set nb0 to 5 and
tracula will use the first 5 images to get an a
Hi Jerry, what is the command you are running? I mean the full command
line including the arguments.
doug
Chen, Xu wrote:
> Hi,
>
> Just installed FreeSurfer 5.1 ( stable ) to my 64 bit Ubuntu 10.04
> LTS (kernel 2.6.32-33). Playing with it to test the Freesurfer
> installation. Everything se
I don't think there is text. The scale bar is 1cm long.
Yang Liu wrote:
> Hi,
>
> I want to get a distance scale bar on tksurfer's window. I can get a
> very dark bar on the black background, but I can't see any text
> around it. I guess it is because the text is also black, which is
> buried
Hi,
I want to get a distance scale bar on tksurfer's window. I can get a very
dark bar on the black background, but I can't see any text around it. I
guess it is because the text is also black, which is buried under the black
background. Is there a way to change the text color?
Thanks,
Yang
__
Thanks Bruce.
Jing
> Date: Fri, 16 Sep 2011 08:38:55 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: k...@nmr.mgh.harvard.edu
> CC: s...@nmr.mgh.harvard.edu; jennifer_g_gold...@rush.edu; vy_d...@rush.edu;
> freesurfer@nmr.mgh.harvard.edu; mj_com...@hotmail.com
> Subject: Re: [Freesurfer] manual
Thanks much Khoa.
Jing
> Date: Thu, 15 Sep 2011 22:00:39 -0400
> From: k...@nmr.mgh.harvard.edu
> To: mj_com...@hotmail.com
> CC: s...@nmr.mgh.harvard.edu; jennifer_g_gold...@rush.edu; vy_d...@rush.edu;
> freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] manual editting problem
>
> Hi
p.s. sorry, then you'll need to rerun the cortical parcellation steps
afterwards (mris_ca_label). The full mris_register command line would be:
set sd=$SUBJECTS_DIR/$subject
set ldir=$SUBJECTS_DIR/$subject/label
set sdir=$SUBJECTS_DIR/$subject/surf
mris_register -l $ldir/lh.central_sulcus \
Hi Omer,
there is actually a work-around for this kind of thing. You need to
create a central sulcus label in tksurfer:
1. Load the inflated surface with sulc as the "curvature" overlay.
2. Draw a path across the central sulcus near the vertex to prevent the
filling (see below) from escaping
Hi Ed,
yes, that's true. We found that the N3 correction sometimes made the
intensities too low to be well represented by an 8 bit voxel, so we keep
it as float now.
cheers
Bruce
On Fri, 16 Sep 2011, Ed Gronenschild wrote:
> Hi,
>
> I noticed a difference in the file nu.mgz between FreeSurfer
p.s. you also have topological defects there, which you can tell as the
orig (green) surface doesn't follow the voxels in the wm.mgz. The
interventions Khoa suggests should help this as well. If you are missing
that much wm you probably want to use control points.
cheers
Bruce
On Thu, 15 Sep
Hi,
I noticed a difference in the file nu.mgz between FreeSurfer
version v5.0.0 and v5.1.0 (running on Mac OSX10.6). It looks
as if nu.mgz in v5.1.0 is an intensity scaled-down version of
nu.mgz in v5.0.0.
The release notes tell that a bug is fixed in mri_nu_correct.mni,
I don't know if that may c
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