Hi
I loaded an annotation file (that i generated using the command annot2label
then label2annot) on a pial surface using tksurfer :
tksurfer subj lh pial
then i loaded my annotation file (frontal association cortex). is it possible
to reload it with a unique color for all the g
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,
20130617 Stelle_postdoc_fMRT_EEG.docx
Description: 20130617 Stelle_postdoc_fMRT_EEG.docx
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is
Dear Doug,
I can not download the files needed for Xhemi in mentioned link. Would you
please advise how to download them?
--
Best regards,
Amir
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/
Hi list,
I am interested in a Cortical Thickness analysis in the Visual Word Form
Area.
I have been suggested to use a MNI152 coordinate and make an sphere (circle
in this case) of 5mm around it.
Has anybody got any experience or any recommendation on how to establish
the visual word form area f
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
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
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-
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
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
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
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
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
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
Dear Freesurfer experts,
I am trying to prepare my data for linear mixed modeling using the
matlab add ons, with this command
mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh
--meas thickness --out lh.thickness.mgh
However I keep getting this error message ERROR: flag
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
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
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
Hello Freesurfer Experts,
I am relatively new to FS'r and was wondering if there were any references I
could use to establish criteria for editing my results (pial surface, GM, and
WM classifications). I am using two MPRAGE files (which gives me great
results), but still would like to do some
Hi list,
I have performed cortical thickness analysis and I have individuated a ROI.
Now, I'd like to perform a correlation analysis by qdec (if possible) between
cortical thickness in this ROI and neuropsychological test score.
I'm reading some previous post such as
http://www.mail-archive.com/f
Hi Freesurfers,
I am trying to use Freesurfer to convert DICOM files to nii f.nii files.
Freesurfer is able to find all the DICOM files but always gives me an
error: "ERROR: reading DICOM/59175096 tag 28 30".
Can anyone help?
Thanks,
Luc
--
Luc Amdahl
Brown University '14
Sc.B. Neuroscience
69
it really depends on the goals of your study. If you are doing fMRI
analysis then it's not so important that the surfaces be accurate to the
sub-millimeter level, but if you are doing a thickness study it probably
is. Unfortunately there is no easy way to validate accuracy in vivo - you
just ha
can you send the complete command line and screen output, and tell us
what version of FS you are using and where the dicoms are from?
On Mon, 17
Jun 2013, Luc Amdahl wrote:
> Hi Freesurfers,
> I am trying to use Freesurfer to convert DICOM files to nii f.nii files.
> Freesurfer is able to find a
Hello Doug,
it worked perfectly, thanks !
Marcel
2013/6/16 Douglas Greve
>
> Oh, I see what the problem is. You can try replacing this line in the
> script:
>
> set cmd = (mri_concat --sum $surfvol $involmasked --o $outvol)
>
> with
>
> set cmd = (fscalc $surfvol add $involmasked -o $outvol)
Hi All,
There is a label named White-matter hypo-intensities (77), is it the
same as white matter hyper-intensity? If not, can anyone tell me the
difference?
Thanks in advance,
Akshay
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https:/
Hello,
I have an annotation file for fsaverage, which I would like to map it to
a particular subject. What would be the best way to do so?
I tried a combination of calls to mris_ca_train and mris_ca_label, but
the latter gave me an error.
First I ran
mris_ca_train lh lh.sphere.reg fsaverage/l
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
Hi Peter,
mri_surf2surf is what you want to use for this.
-Louis
On Mon, 17 Jun 2013, Peter Savadjiev wrote:
> Hello,
>
> I have an annotation file for fsaverage, which I would like to map it to
> a particular subject. What would be the best way to do so?
>
> I tried a combination of calls to mri
Hi Marie
After checking that Matlab on FSL indeed has the image processing toolbox,
I ran the batch command (-localGI for every subject) through FSL, and it
all worked fine - although it took something like 3 days to complete for
all 38 subjects :)
Unfortunately, for two of my subjects, ?h.pial_l
Hi Tudor,
Good to know that it went fine! Normally the lGI takes about 2-3h per subject
to complete, so if you launched them sequentially and not in parallel, I'm not
surprised that it took about 3 days. (you can shorten the computational time by
launching as many parallel sessions as you have
-- Forwarded message --
From: Luc Amdahl
Date: Mon, Jun 17, 2013 at 3:45 PM
Subject: Re: [Freesurfer] DICOM unpacking error
To: Bruce Fischl
Hi Bruce,
Thanks for responding.
Here is the command line and screen output:
[Sheinberg-Lab-MRI-iMac:~/MRI/Solar_System] lab% unpacksdc
Hello everyone,
I was trying out FS-FAST tutorial with my set of images (converted to NIFTI
from AFNI BRIK format using 3dAFNItoNIFTI). However, I get this error
'nifti1Read(): unsupported slice timing pattern 5 in … '.
Looking at NIFTI.h, this value (#define NIFTI_SLICE_ALT_INC2 5) is added
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-
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
Luc, it is missing the pixel spacing (ie, voxel size), which is a
fundamental quantity which should not be missing. Have you anonymized
the data or done something else too it?
doug
On 6/17/13 2:36 PM, Luc Amdahl wrote:
-- Forwarded message --
From: *Luc Amdahl* mailto:luc
Hi Bo, you should run the MNI152 template through recon-all, then map
your mask to the surface, create a label, then map the label to each
individual subject with mri_label2label
doug
On 6/17/13 7:24 PM, xiangbo_2...@126.com wrote:
I analysis the volume of grey matter, and MNI152 as the mask
Hi Mariam, I don't know why it does not read this particular code. I can
modify it when I get back from HBM and send you a new version of
mri_convert. Or you might be able to change the way you convert from
BRIK to use a different slice code.
doug
On 6/17/13 4:13 PM, Mariam Sood wrote:
> He
Hi Amir, if you are using 5.2 or 5.3, then you should already have it.
If not, I'll have to recreate the links. let me know
doug
On 6/17/13 6:52 AM, amirhossein manzouri wrote:
Dear Doug,
I can not download the files needed for Xhemi in mentioned link. Would
you please advise how to download
Hi Matt, was I supposed to get back to you on this? I generally leave
these types of questions to Nick and Zeke.
doug
ps. Please post to the list instead of us indivudally. thanks!
On 6/16/13 12:46 PM, Matthew Hoptman wrote:
> Hi Dr. Greve,
> Any news on the libboost_program_options.so.5 issue?
39 matches
Mail list logo
