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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" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Subject ID error with bbregister To: freesurfer@nmr.mgh.harvard.edu Message-ID: 6f0565c8-c4f3-8289-d41b-0558a1fb69f9@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 CautionHi 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_eM4ShAKwlFflhqDPeh22njZyomMazJzeiBX6fxvFT...
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 CautionHi 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" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Subject ID error with bbregister To: freesurfer@nmr.mgh.harvard.edu Message-ID: 6f0565c8-c4f3-8289-d41b-0558a1fb69f9@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 CautionHi 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_eM4ShAKwlFflhqDPeh22njZyomMazJzeiBX6fxvFT...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Tisdall, Dylan