Try just adding a line at the end of the lta file like subject 126346 On 2/22/2022 9:45 AM, Tisdall, Dylan wrote: > External Email - Use Caution > > Hi Doug and Matt, > > I'm pretty confident my $SUBJECTS_DIR is correct, its the same one I used for > recon-all on this subject and the files seem to be in the right place; wee > below: > > [mtisdall@ftdc-gpu01 126346]$ echo $SUBJECTS_DIR > /home/mtisdall/Research/7TAnalysis/subjects > > [mtisdall@ftdc-gpu01 126346]$ ls $SUBJECTS_DIR/126346 > label mri scripts stats surf tmp touch trash > > > I don't see a blank subject line in the lta file. I tried to make the initial > transform manually in Freeview by just loading the two volumes, using > `Transform Volume` until they were close, and then saving the resulting > transform. I then re-loaded my 7T data, using the option in FreeView to apply > the transform on load, and it looks right. See the file contents below: > > [mtisdall@scisub 126346]$ cat 7Tto3Tinit.lta > type = 1 # LINEAR_RAS_TO_RAS > nxforms = 1 > mean = 0.0000 0.0000 0.0000 > sigma = 1.0000 > 1 4 4 > 9.961947798728943e-01 8.715574443340302e-02 4.656613983300417e-10 > -1.702789425849915e+00 > -8.682409673929214e-02 9.924039244651794e-01 -8.715574443340302e-02 > -7.269048690795898e+00 > -7.596124429255724e-03 8.682409673929214e-02 9.961947798728943e-01 > 1.319813346862793e+01 > 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 > 1.000000000000000e+00 > src volume info > valid = 1 # volume info valid > filename = /home/mtisdall/Research/7TAnalysis/126346/niis/3T_MPRAGE.nii > volume = 208 240 256 > voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 > xras = 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 > yras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 > zras = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 > cras = 5.000000000000000e-01 1.455932617187500e+01 -1.323728942871094e+01 > dst volume info > valid = 1 # volume info valid > filename = /home/mtisdall/Research/7TAnalysis/126346/niis/3T_MPRAGE.nii > volume = 208 240 256 > voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 > xras = 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 > yras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 > zras = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 > cras = 5.000000000000000e-01 1.455932617187500e+01 -1.323728942871094e+01 > fscale 0.100000 > > > Note that, when I move the --s flag to the end of the command line, it runs > slightly further, but ultimately fails searching for `subject-unknown` within > my subjects directory: > > [mtisdall@scisub 126346]$ bbregister --mov mgz/7T_MEMPRAGE.mgz --init-reg > 7Tto3Tinit.lta --reg 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 --s 126346 > ... > Loading mov > error: > mghRead(/home/mtisdall/Research/7TAnalysis/subjects/subject-unknown/mri/orig.mgz, > -1): could not open file > > > Any other suggestions on what I'm doing wrong here? > > > Thanks again, > Dylan > > > >> Date: Mon, 21 Feb 2022 16:58:22 -0500 >> From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> >> Subject: Re: [Freesurfer] Subject ID error with bbregister >> To: freesurfer@nmr.mgh.harvard.edu >> Message-ID: <6f0565c8-c4f3-8289-d41b-0558a1fb6...@mgh.harvard.edu> >> Content-Type: text/plain; charset=UTF-8; format=flowed >> >> Is there a blank subject line in the lta file? If so, it is probably >> trying to get the subject from there. You can try putting the --s after >> the --lta >> >> On 2/21/2022 3:43 PM, Tisdall, Dylan wrote: >>> External Email - Use Caution >>> >>> Hi all, >>> >>> Quick question on a puzzling error with bbregister version 7.1.1. When I >>> run: >>> >>> bbregister --s 126346 --mov mgz/7T_MEMPRAGE --init-reg 7Tto3Tinit.lta --reg >>> 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 >>> >>> I get the error: >>> >>> ERROR: must spec a subject id >>> >>> which I thought I'd done with the --s flag. What am I missing? >>> >>> Even more odd, if I just move the to the end of the command, bbregister >>> will run, but eventually fails with: >>> >>> error: >>> mghRead(/hom/mtisdall/Research/7TAnalysis/subject//subject-unknown/mri/orig.mgz, >>> -1): could not open file >>> >>> Is there something obvious I'm doing wrong with these two command lines >>> that cause these behaviors? >>> >>> >>> Thanks, >>> Dylan >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://secure-web.cisco.com/12zXL_eM4ShAKwlFflhqDPeh22njZyomMazJzeiBX6fxvFTbzWQT4dDrbh7VHCxXpC9zVzYXpf8J_kHA3NFDtsVRx1_W-j2zIYz_oBIPjeLRZCLseGMLP_Hx83KDx_30NhLniAmeL0LXEiqIasVZppSibro6mJADhi-Xa6_I_j8IlT9XwUQs3oo7eGVjbskQtINNx3LmsOipdJerlqWTj5IRyp23YH18wndzp-dSYuGfYWhBZYFQKaGQsoR4gfyyK4uNc7XWGE5Ai6Ho8RO6w7jTBZpaGJxAJ7_3082X2Xzn1Rony2mJaU_0N3SF3axidPyUAxxt5sv07fPElehYO1g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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