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 <dgreve@mgh.harvard.edu>
Sent: Wednesday, July 29, 2020 10:39 AM
To: Camargo, Aldo <ACamargo@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:

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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 <ACamargo@som.umaryland.edu>
Sent: Monday, July 27, 2020 11:46 PM
To: Douglas N. Greve <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Coregistration to MNI
 
Thanks a lot Douglas for your great input,

Aldo
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Monday, July 27, 2020 10:46 AM
To: freesurfer@nmr.mgh.harvard.edu <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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Camargo, Aldo <ACamargo@som.umaryland.edu>
Sent: Saturday, July 25, 2020 12:19 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Coregistration to MNI
 

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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

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