It looks like cvs failed. Can you send the log? Also, please remember to
post to the list and not us personally.
On 7/30/2020 11:13 AM, Camargo, Aldo wrote:
External Email - Use Caution
Hi Douglas,
I was able to run the script to create the cvs folder and its files
but still I can not run the script that does the coregistration of the
Pet image to the MNI space.
I am getting the following error:
(base)
acamargo@acamargo-System-Product-Name:~/PET/MPRAGE/2006-09-27_14_15_46.0/S19445/subj1/mri$
mri_vol2vol --gcam
/home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/meanPET.nii.gz
register.dof6.lta
$SUBJECS_DIR/subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
$FREESURFER_HOME/subject/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1
pet.cvs.2mm.sm00.ni.gz
Loading mov
/home/acamargo/PET/ADNI_Brain_PET__Raw/2006-11-01_11_56_37.0/I28835/meanPET.nii.gz
Loading source LTA register.dof6.lta
Loading GCAM /subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
ERROR: cannot find or read
/subj1/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
------------------------------------------------------------------------
*From:* Douglas N. Greve <dgr...@mgh.harvard.edu>
*Sent:* Wednesday, July 29, 2020 10:39 AM
*To:* Camargo, Aldo <acama...@som.umaryland.edu>; Freesurfer support
list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Coregistration to MNI
Here is the command
mri_cvs_register --mov $subject --mni --openmp N
This command can take a very long time to run. The --openmp N
indicates the number of processors to use if you have a multiprocessor
system. Even with N=3, it can take 18 hours.
On 7/29/2020 12:35 AM, Camargo, Aldo wrote:
External Email - Use Caution
Hi Douglas,
I don't have the folder cvs and I don't have the files bellow:
cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta
How can I get these files,
Aldo
------------------------------------------------------------------------
*From:* Camargo, Aldo <acama...@som.umaryland.edu>
<mailto:acama...@som.umaryland.edu>
*Sent:* Monday, July 27, 2020 11:46 PM
*To:* Douglas N. Greve <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Coregistration to MNI
Thanks a lot Douglas for your great input,
Aldo
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Monday, July 27, 2020 10:46 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Coregistration to MNI
This command will allow you to have a registration file and sample
into MNI152 2mm space
mri_vol2vol --gcam pet.nii.gz register.dof6.lta
$SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1
pet.cvs.2mm.sm00.nii.gz
you can get the registration file with
mri_coreg --mov pet.nii.gz --s $subject --reg register.dof6.lta
On 7/26/2020 9:19 AM, Zollei, Lilla,Ph.D. wrote:
Hi Aldo,
If you have a recon-ned structural MRI corresponding to your PET
scan then the answer is yes.
Lilla
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Camargo, Aldo <acama...@som.umaryland.edu>
<mailto:acama...@som.umaryland.edu>
*Sent:* Saturday, July 25, 2020 12:19 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] Coregistration to MNI
External Email - Use Caution
Hi Freesurfer experts,
I want to coregister a PET image to the MNI space, can I use
mri_cvs_register ?
Thanks a lot,
Aldo Camargo
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
