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 <wam...@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-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia > Dacosta Aguayo <rdacos...@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 <wam...@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-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia > Dacosta Aguayo <rdacos...@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 > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1_qf7LurH93xX2kY1ZXt7VCV5yp2ETHxblrJoGEOtxZm3DWoarMCk139LLsURmisn5Hfn9C04kH-AX0ykPwVSlHdfQWcHIix4ruSDL0WIiftJ_VTt9hNZ8_UriFhECRIEQ5S0viT83eT-X9AI2yrOQQozrNcz8IQjIvb_m7Mx1XYbjT852iFruCALGEj4P-UV2Pnre5LpKsqERacaXTLu6wTiQmHYgVQfVP5TE2bt6JocAg5r7b_WFoN6Bqc7UtdxY_yjXtvUTB8AHWqx3RXqQw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > <https://secure-web.cisco.com/1VBMQ2fXINrA7ekn-dlB3ZVLR3xICdlpTNQW6z_pii6HpWoqpunKpYFrq5bo9blmsBAhzG7FHGYWVgo6Fm6iftCHp7ChcMiVTAmSSlDOuKeAsTj047zBSr3GZAiWvXBoLYQXj_9w5LPyf4ul5_HF8TlvQNwlvP_ZfNVF6hFggdQB6Md0ViFPswLKcKVRY73u8q2XvaQl5G_FE-PUr63fKMoNyEMybLHUiCzTjViac-Ncce1066gc2_n21Ib3iPQCkYRM-9LA07LZur6pciv5kJg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1_qf7LurH93xX2kY1ZXt7VCV5yp2ETHxblrJoGEOtxZm3DWoarMCk139LLsURmisn5Hfn9C04kH-AX0ykPwVSlHdfQWcHIix4ruSDL0WIiftJ_VTt9hNZ8_UriFhECRIEQ5S0viT83eT-X9AI2yrOQQozrNcz8IQjIvb_m7Mx1XYbjT852iFruCALGEj4P-UV2Pnre5LpKsqERacaXTLu6wTiQmHYgVQfVP5TE2bt6JocAg5r7b_WFoN6Bqc7UtdxY_yjXtvUTB8AHWqx3RXqQw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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