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Hi Bruce,

Thank you for your quick and helpful reply. Unfortunately, I wasn't able to figure out what comes between -f and -ss... Would you mind explaining what you meant with ... ?

Thanks a lot, Stephanie

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, February 15, 2019 11:03 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2surf QC

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Hi Stephanie

I guess visually. You can write a script to run freeview and save a snapshot using something like:

foreach s ($SUBJECTS) freeview -f ... -ss <subject snapshot name) end

then you can zip through them in nmovie (or nmovie_qt, which I guess is what we support now)

cheers Bruce

On Fri, 15 Feb 2019, Winkelbeiner, Stephanie A wrote:

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Hi Freesurfers,

I ran mri_surf2surf and registered self-created parcels from fsaverage to all my subjects. What is the best way to do QC and check if everything went right?

Thanks for your help!

Stephanie

The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Dear Bruce

Thanks a lot for this very helpful explanation! This is much appreciated and it is now much clearer to me what I have to do.

Thank you, Stephanie

On Feb 19, 2019, at 11:09 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

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Hi Stephanie

if you have an annot named lh.myannot.annot you could use:

freeview -f lh.inflated:annot=lh.myannot.annot -ss filename.tif

where of course you will need paths to the various files and will want to change the filename for each subject

cheers Bruce

...

On Tue, 19 Feb 2019, Winkelbeiner, Stephanie A wrote:

  External Email - Use Caution

Hi Bruce,

Thank you for your quick and helpful reply. Unfortunately, I wasn't able to figure out what comes between -f and -ss... Would you mind explaining what you meant with ... ?

Thanks a lot, Stephanie

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, February 15, 2019 11:03 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2surf QC

External Email. Use Caution.

Hi Stephanie

I guess visually. You can write a script to run freeview and save a snapshot using something like:

foreach s ($SUBJECTS) freeview -f ... -ss <subject snapshot name) end

then you can zip through them in nmovie (or nmovie_qt, which I guess is what we support now)

cheers Bruce

...

On Fri, 15 Feb 2019, Winkelbeiner, Stephanie A wrote:

    External Email - Use Caution

Hi Freesurfers,

I ran mri_surf2surf and registered self-created parcels from fsaverage to all my subjects. What is the best way to do QC and check if everything went right?

Thanks for your help!

Stephanie

The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.