Hello, I'm wondering what is the first step in reconstruction when working with rhesus macaque. script 01.05 requires files to be in mgh format initially ?
I understand that the recon-all scipt is not setp to work with monkey data
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Thanks, Rafael
Hi Rafael,
On Feb 1, 2016, at 19:46 , Casas, Rafael (NIH/CC/DRD) [F] rafael.casas@nih.gov wrote:
Hello, I’m wondering what is the first step in reconstruction when working with rhesus macaque. script 01.05 requires files to be in mgh format initially ?
One simple solution would be to either use mri_convert to convert the input volumes into mgh/mgz format, or just change the “set anat_name = mprage.mgz” line to reflec the actual format your files are in… (this requires a reasonably modern 01.05_average_anatomicals_mgz.csh though, not sure which version you are using over at NIH). Anyway I attached a recent enough version of the scripts, t this email, I do fear that they will not make it through the list server…
Thanks Sabastian! I received the new version of the scripts.
So I can run 01.05 as the first step and just modify the locations and names of my files?
Regards, Rafael
-----Original Message----- From: Moeller, Sebastian [mailto:sebastian.moeller1@rwth-aachen.de] Sent: Monday, February 01, 2016 2:56 PM To: Freesurfer support list Cc: Casas, Rafael (NIH/CC/DRD) [F] Subject: Re: [Freesurfer] Recon for Rhesus Macaque
Hi Rafael,
On Feb 1, 2016, at 19:46 , Casas, Rafael (NIH/CC/DRD) [F] rafael.casas@nih.gov wrote:
Hello, I’m wondering what is the first step in reconstruction when working with rhesus macaque. script 01.05 requires files to be in mgh format initially ?
One simple solution would be to either use mri_convert to convert the input volumes into mgh/mgz format, or just change the “set anat_name = mprage.mgz” line to reflec the actual format your files are in… (this requires a reasonably modern 01.05_average_anatomicals_mgz.csh though, not sure which version you are using over at NIH). Anyway I attached a recent enough version of the scripts, t this email, I do fear that they will not make it through the list server…
Hi Rafael,
On Feb 1, 2016, at 21:18 , Casas, Rafael (NIH/CC/DRD) [F] rafael.casas@nih.gov wrote:
Thanks Sabastian! I received the new version of the scripts.
So I can run 01.05 as the first step and just modify the locations and names of my files?
As you have not offered enough information about your exact setup/file formats I have no way of answering this question, sorry. You could start by reading the files I sent you and then just try it, though. For NHPs I would always start with making sure that the orientation information in the files really describes the anatomy of the animals, which typically are used in sphinx position, and only do all the rest after fixing this.
Best Regards Sebastian
Regards, Rafael
-----Original Message----- From: Moeller, Sebastian [mailto:sebastian.moeller1@rwth-aachen.de] Sent: Monday, February 01, 2016 2:56 PM To: Freesurfer support list Cc: Casas, Rafael (NIH/CC/DRD) [F] Subject: Re: [Freesurfer] Recon for Rhesus Macaque
Hi Rafael,
On Feb 1, 2016, at 19:46 , Casas, Rafael (NIH/CC/DRD) [F] rafael.casas@nih.gov wrote:
Hello, I’m wondering what is the first step in reconstruction when working with rhesus macaque. script 01.05 requires files to be in mgh format initially ?
One simple solution would be to either use mri_convert to convert the input volumes into mgh/mgz format, or just change the “set anat_name = mprage.mgz” line to reflec the actual format your files are in… (this requires a reasonably modern 01.05_average_anatomicals_mgz.csh though, not sure which version you are using over at NIH). Anyway I attached a recent enough version of the scripts, t this email, I do fear that they will not make it through the list server…
freesurfer@nmr.mgh.harvard.edu
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Casas, Rafael (NIH/CC/DRD) [F] -
Moeller, Sebastian