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Hi William,

I wanted to use both T1 and T2 to do the recon -all -all.

Could it be:

-

recon-all -subject subjectname -i invol1 <-i invol2> -all

El mié., 3 mar. 2021 17:16, Ammon, William WAMMON@mgh.harvard.edu escribió:

Hi Rosalia,

You can include T2 images by adding the flags -T2 /path/to/volume (to point to the T2 images) and -T2pial -all (to generate new pial surfaces using T2 images).

You can read more about this here https://secure-web.cisco.com/1-kKoxBlghDNt9knl5SHKY-AN5hisd2dv9vY-TyxuuixDypboRpqcOZD4spjJfNrqoQ7lNcImlg2d3KaMoRCCAx07RBL5eYJeluoihgs4VgUpNVlUeSCLfSXJTJWa29ulVt1tCzhDA5L3HbSAWlNzdoZsfrWxve-zkvFgPbZfK_8XhHfkvuuWIVlpTuEq_pyIXpmb_3OOQq-yg-ERdHMRgyfFQmTbUdGpCeCMfNW6NItYcf2ydKUFVaraXcXlb3iKIGaPLQxlB6hThbBwTx0EXw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23UsingT2orFLAIRdatatoimprovepialsurfaces on our wiki.

Bill Ammon

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Rosalia Dacosta Aguayo rdacostaa@gmail.com *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, March 3, 2021 at 7:36 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Include T2 in recon-all command

•    External Email - Use Caution        *
  
  

Dear Freesurfer community,

I would like to include the T2 image in the recon-all command to improve segmentation.

Any idea how I should do this in the following command?

recon-all -s Artico1 -i subj01_anat.nii.gz -all -qcache -3T

Regards,

Rosalia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1VBMQ2fXINrA7ekn-dlB3ZVLR3xICdlpTNQW6z_pii6HpWo...

External Email - Use Caution

Thank you very much for the clarification.

It helps a lot.

Regards, Rosalia

On Wed, Mar 3, 2021 at 7:53 PM Ammon, William WAMMON@mgh.harvard.edu wrote:

Sorry for any confusion, I meant that you would include the T2 flag to the end of your current recon-all command. So you could have a command that would look something like

recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume -T2pial -all

So you are inputting both T1 and T2 images. For your command in your first message, I think you should just add -T2 /path/to/T2_volume -T2pial.

Hope this helps,

Bill Ammon

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Rosalia Dacosta Aguayo rdacostaa@gmail.com *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, March 3, 2021 at 1:18 PM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Include T2 in recon-all command

•    External Email - Use Caution        *
  
  

Hi William,

I wanted to use both T1 and T2 to do the recon -all -all.

Could it be:

• recon-all -subject subjectname -i invol1 <-i invol2> -all

El mié., 3 mar. 2021 17:16, Ammon, William WAMMON@mgh.harvard.edu escribió:

Hi Rosalia,

You can include T2 images by adding the flags -T2 /path/to/volume (to point to the T2 images) and -T2pial -all (to generate new pial surfaces using T2 images).

You can read more about this here https://secure-web.cisco.com/1-kKoxBlghDNt9knl5SHKY-AN5hisd2dv9vY-TyxuuixDypboRpqcOZD4spjJfNrqoQ7lNcImlg2d3KaMoRCCAx07RBL5eYJeluoihgs4VgUpNVlUeSCLfSXJTJWa29ulVt1tCzhDA5L3HbSAWlNzdoZsfrWxve-zkvFgPbZfK_8XhHfkvuuWIVlpTuEq_pyIXpmb_3OOQq-yg-ERdHMRgyfFQmTbUdGpCeCMfNW6NItYcf2ydKUFVaraXcXlb3iKIGaPLQxlB6hThbBwTx0EXw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23UsingT2orFLAIRdatatoimprovepialsurfaces on our wiki.

Bill Ammon

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Rosalia Dacosta Aguayo rdacostaa@gmail.com *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, March 3, 2021 at 7:36 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Include T2 in recon-all command

•    External Email - Use Caution        *
  
  

Dear Freesurfer community,

I would like to include the T2 image in the recon-all command to improve segmentation.

Any idea how I should do this in the following command?

recon-all -s Artico1 -i subj01_anat.nii.gz -all -qcache -3T

Regards,

Rosalia

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