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:

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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

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*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

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*From:* Camargo, Aldo ACamargo@som.umaryland.edu mailto:ACamargo@som.umaryland.edu *Sent:* Monday, July 27, 2020 11:46 PM *To:* Douglas N. Greve dgreve@mgh.harvard.edu mailto: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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@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:

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Hi Aldo, If you have a recon-ned structural MRI corresponding to your PET scan then the answer is yes. Lilla

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Camargo, Aldo ACamargo@som.umaryland.edu mailto:ACamargo@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

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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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