And what is the data you analyzed in spm? You could use the mni space mask but
it won't be very accurate.
On Jun 17, 2013, at 8:44 PM, xiangbo_2010 wrote:
> Hi Bruce
>
> I use the SPM to analysis my data, and use the xjview to get a mask (have
> .img and .hdr files) as ROI, use the MNI spac
Hi Bruce
I use the SPM to analysis my data, and use the xjview to get a mask (have .img
and .hdr files) as ROI, use the MNI space in SPM analysis. Following I want to
obtain the cortical thickness from this mask in Freesurfer, and I have analyzed
all my individual subjects in FreeSurfer(recon-
can you give a complete description of your study and what you are trying
to achieve? Have you analyzed all your individual subjects in FreeSurfer
(recon-all)? What is the mask you want to use?
On Tue, 18 Jun 2013, xiangbo_2010 wrote:
I want to obtain the cortical thickness from a group of su
I want to obtain the cortical thickness from a group of subjects, thanks!
At 2013-06-18 00:13:08,"Bruce Fischl" wrote:
>are you trying to do this for a single subject or for a group of subjects
>, or group average data?
>On Tue, 18 Jun 2013, xiangbo_2010 wrote:
>
>> my subject has finis
are you trying to do this for a single subject or for a group of subjects
, or group average data?
On Tue, 18 Jun 2013, xiangbo_2010 wrote:
my subject has finished the recon-all on the structural image, whether use
the command: "mri_vol2surf --src sig.img --src_type analyze --srcreg
register.d
my subject has finished the recon-all on the structural image, whether use the
command: "mri_vol2surf --src sig.img --src_type analyze --srcreg register.dat
--hemi rh --o ./sig-rh.img --out_type analyze --float2int round --trgsubject
ico --icoorder 7" to obtain the result? thanks!
Bo
I want to get cortical thickness, and have finished the recon-all, and obtained
the mask from SPM which include the file with .img and .hdr, whether I should
convert the file (.img and .hdr) to file (.nii), and use the command:
"bbregister --s bert --mov func.nii --init-spm --reg register.dat t
and what subject do you wan to obtain thickness measures from? You could
use mri_vol2vol to map your mask to the individual using the MNI
transform
On Mon, 17 Jun 2013, xiangbo_2010 wrote:
the mask was obtained from xjview, and use the MNI space in my study,
thanks!
Bo
At 2013-06-17 23:52
the mask was obtained from xjview, and use the MNI space in my study, thanks!
Bo
At 2013-06-17 23:52:33,"Bruce Fischl" wrote:
>sorry, the formatting of your emails is lost in my reader and you may
>have said this before, but what is the mask of? What space is it in?
>
>On Mon, 17 Jun 20
p.s. you wouldn't use bert as your subject - you would specify your own
On
Mon, 17 Jun 2013, xiangbo_2010 wrote:
I want to get cortical thickness, and have finished the recon-all, and
obtained the mask from SPM which include the file with .img and .hdr,
whether I should convert the file (.img
sorry, the formatting of your emails is lost in my reader and you may
have said this before, but what is the mask of? What space is it in?
On Mon, 17 Jun 2013,
xiangbo_2010 wrote:
I want to get cortical thickness, and have finished the recon-all, and
obtained the mask from SPM which include
I have finished the recon-all, and obtained the mask from SPM which include the
file with .img and .hdr, whether I should convert the file (.img and .hdr) to
file (.nii), and use the command: "bbregister --s bert --mov func.nii
--init-spm --reg register.dat tkregister2 --mov func.nii --reg regi
please cc the list so others can answer. Do you mean get cortical
thickness? If so, then you need to run recon-all on the structural image
On Mon, 17 Jun 2013, xiangbo_2010
wrote:
I have obtained the mask from xjview (.img), I want to obtain the CT from
the mask, thanks!
Bo
At 2013-06-
what are you trying to map to the surface?
On Mon, 17 Jun 2013, xiangbo_2010
wrote:
Hi Bruce
Thank you for my help, when I use the bbregister, do not know how to choose
data for --mov, thanks!
Bo
At 2013-06-17 20:34:39,"Bruce Fischl" wrote:
>Hi Bo,
>
>tksurfer doesn't take a path to a
Hi Bruce
Thank you for my help, when I use the bbregister, do not know how to choose
data for --mov, thanks!
Bo
At 2013-06-17 20:34:39,"Bruce Fischl" wrote:
>Hi Bo,
>
>tksurfer doesn't take a path to a file. Read the help on it - you need to
>reconstrcut the subject with recon-all t
Hi Bo,
tksurfer doesn't take a path to a file. Read the help on it - you need to
reconstrcut the subject with recon-all then give it the subject id. To
project a volumetric map onto the surface use mri_vol2surf, with the
registration typically computed by bbregister.
cheers
Bruce
On Mon,
Hi doug
Thank you for giving this information, I used the command: "/tksurfer
fsaverage lh inflated -aparc -mni152reg -overlay
/pathname/to/spm/roi/yourfile.img/", but do not have results for me, and do not
know how to do next? thanks!
Bo
At 2013-06-06 23:04:30,"Douglas N Greve" wr
ehalf Of Douglas N Greve
Sent: Tuesday, June 04, 2013 1:48 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] SPM ROI to Cortical Thickness
Make sure that your SPM volume is registered to the anatomical, then use
mri_vol2surf to map the volume to the surface, then mri_segstats to ex
I don't know anything about XjView. You will need to be very specific
and detailed about what you did in order for us to help you. Eg, what
space is the ROI in?
doug
On 6/15/13 8:40 AM, xiangbo_2010 wrote:
Dear experts,
I was wondering if anyone can advise on the best way to use an ROI
Dear experts,
I was wondering if anyone can advise on the best way to use an ROI mask created
in SPM (XjView) to extract cortical thickness values in freesurfer. Though
which was pointed out by reseachers, but I still can not know it. I hope some
experts help me, Thanks!
Bo
Thank you i
Hi Stephanie, I don't know which recommendation you are referring to. We
get a lot of emails, and I can't remember each one. Can you repost with
the full thread?
doug
On 06/06/2013 10:40 AM, McMains, Stephanie wrote:
> I am wondering why you didn't tell them to go through fsvarege space?
> I
I am wondering why you didn't tell them to go through fsvarege space? I
thought that was an easy way to go from SPM MNI to freesurfer land.
tksurfer fsaverage lh inflated -aparc -mni152reg -overlay
/pathname/to/spm/roi/yourfile.img
I am wondering because when I look at the segmentation for f
Create a label with this vertex in it and use mri_label2label. See
subject/label/lh.cortex.label for any subject as an example.
doug
On 06/05/2013 03:43 PM, Ozranov-Palchik, Ola wrote:
> Hi Doug,
>
> Thanks for the response. I'm still a bit confused.
>
> Let's just say that I have a vertex index
Hi Doug,
Thanks for the response. I'm still a bit confused.
Let's just say that I have a vertex index that I determined on the surface of
my FS average surface (created by 'make_average_subject'). Now I simply want to
find the corresponding vertex index on all the source subjects.
How can I do
Hi Ola, this probably will not work. The tal coordinate is notoriously
inaccurate in cortex. You are verylikely to totally miss the area you
are looking for. A better way is to run the MNI template through
recon-all, map your VBM result to the surface of that, then use
mri_surf2surf to map the
Hi Doug,
Thank you, again! I decided to try to use the Talairach coordinates from my
analysis for ROI extraction. I created an average subject and preprocessed the
data (mris_preproc). I obtained the vertex index based on the coordinates from
the average subject. Any ideas on how I can now fi
PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] SPM ROI to Cortical Thickness
Make sure that your SPM volume is registered to the anatomical, then use
mri_vol2surf to map the volume to the surface, then mri_segstats to extract the
mean
; http://www.childrenshospital.org/research/gaablab
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Tuesday, June 04, 2013 1:48 PM
> To: freesurfer@nmr.mgh.harvard
Make sure that your SPM volume is registered to the anatomical, then use
mri_vol2surf to map the volume to the surface, then mri_segstats to
extract the mean of the thickness
doug
On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote:
>
> main lab: (617) 355-0400
Dear FreeSurfer Experts,
I w
Dear FreeSurfer Experts,
I was wondering if anyone can advise on the best way to use an ROI mask created
in SPM (XjView) to extract cortical thickness values in freesurfer.
Thank you in advance for your help!
Ola
Ola Ozranov-Palchik M.S.
Research Coordinator, Gaab Lab
Laboratories of Cognitive
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