I am so sorry about that Dr. Greve.
The post I made earlier is reference from the following thread:
On 02/16/2017 12:28 PM, Anderson Napolitano wrote:
>
> Thank you Dr. Greve. Just to clarify, the 'inputfile.nii.gz' file in
> the command:
>
> fscalc inpu
Thank you Dr. Greve. Just to clarify, the 'inputfile.nii.gz' file in the
command:
fscalc inputfile.nii.gz div value -o outputfile.nii.gz
,is the gtm.nii.gz file generated after the command:
mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
--default-seg-merge --au
Hi Experts!
Quick question: is it possible to re-scale intensities relative to the full
brain atlas?
Details:
Per step 3 of the following tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
I wanted to re-scale the the intensities relative to the full brain atlas. The
command:
Hi Experts!
Per step 3 of the following tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
I wanted to re-scale the the intensities relative to the full brain atlas. The
command:
--no-rescale
removes scaling relative to the Pons and the command:
--rescale
rescales the intensit
Hi Dr. Greve,
Thank you very much. That worked beautifully. For those who are having the same
problem as I did, the command:
mri_coreg --s subject_name --mov static_template.nii.gz --reg
registration_matrix.reg.lta
creates a text file named registration_matrix.reg.lta on your current
direc
Hi Dr. Greve,
Ah I see. If that's the case, is the command:
mri_coreg --s subject_name --move dicom_template --reg registration_matrix
generating the registration matrix? I have ran a search on the subject folder
for any *.reg* file and has only found lh.sphere.reg and rh.sphere.reg on the
Hello Experts!
I am having trouble running the following command:
tkregisterfv --mov
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm
--reg
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016
?Thank you Dr. Greve and Don. Unfortunately adding '\' after spaces and
removing the spaces all together doesn't seem to resolve the said error.
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Freesurfer@nmr.mgh.harvard.edu
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Hello Experts!
I am having trouble checking the registration per step 2 of the pet surfer
tutorial: http://freesurfer.net/fswiki/PetSurfer. The line:
mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta
worked just fine but when checking the registration using the line:
tkregist
I can.
Thank you,
Anderson Napolitano?
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = --mov
shift
switch ( $flag )
switch ( --mov )
if ( $#argv < 1 ) goto arg1err ;
if ( 4 < 1 ) goto arg1err
set movvol = $argv[1] ;
:
tkregisterfv --mov template.nii.gz --reg template.reg.lta --surfs
I get the following output:
set: Variable name must begin with a letter
Any advice as to how to resolve this issue will be greatly appreciated.
Thanks,
Anderson Napolitano?
tkregisterfv --mov
/Users/djsandoval/Desktop
Hi Zeke,
That resolved the issue. Thank you very much.
Warmest Regards,
Anderson Napolitano
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
freesurfer-requ...@nmr.mgh.harvard.edu
Sent: Wednesday, January 18, 2017 10:00 AM
To: freesurfer
help us resolve this issue.
Thank you for your time.
Warmest Regards,
Anderson Napolitano?
Mon Jan 9 13:19:45 MST 2017
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
cd /usr/local/freesurfer
/usr/local/freesurfer/bin/gtmseg --s M87151031-2016002-BL
freesurfer-Darwin-OSX-stable-v6-beta
help us resolve this issue.
Thank you for your time.
Warmest Regards,
Anderson Napolitano
Mon Jan 9 13:19:45 MST 2017
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
cd /usr/local/freesurfer
/usr/local/freesurfer/bin/gtmseg --s M87151031-2016002-BL
freesurfer-Darwin-OSX-stable-v6-beta
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