[Freesurfer] norm.mgz
Hi, I am using recon-all and the norm.mgz's so far are only about half the brain. I checked the input volumes and looked though the output to std and everything seemed fine, so I am not sure what to do: on machine vader source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /autofs/space/boba_001/users/nrecon/ which mri_ca_normalize /usr/local/freesurfer/stable/bin//mri_ca_normalize cd /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz output: using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... Note: program considers input volume #1 as the most T1-like using real data threshold=56.0 using (109, 110, 82) as brain centroid... mean wm in atlas = 109, using box (94,96,73) --> (123, 124,90) to find MRI wm before smoothing, mri peak at 484 after smoothing, mri peak at 484, scaling input intensities by 0.225 scaling channel 0 by 0.224939 using 242283 sample points... INFO: compute sample coordinates transform 1.724 -0.639 -2.451 142.880; 0.122 1.661 -0.265 -85.128; 2.012 0.112 1.598 -322.680; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter found 38929 control points for structure... bounding box (121, 85, 50) --> (177, 152, 94) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0 87 of 225 (38.7%) samples deleted finding control points in Right_Cerebral_White_Matter found 38531 control points for structure... bounding box (116, 86, 62) --> (172, 156, 102) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 108.0 90 of 179 (50.3%) samples deleted finding control points in Left_Cerebellum_White_Matter found 3087 control points for structure... bounding box (132, 135, 50) --> (150, 158, 68) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 96.0 18 of 52 (34.6%) samples deleted finding control points in Right_Cerebellum_White_Matter found 2900 control points for structure... bounding box (123, 136, 61) --> (144, 161, 76) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 102.0 23 of 58 (39.7%) samples deleted finding control points in Brain_Stem found 3414 control points for structure... bounding box (138, 130, 62) --> (152, 170, 78) Brain_Stem: limiting intensities to 89.0 --> 97.0 37 of 66 (56.1%) samples deleted using 580 total control points for intensity normalization... bias field = 1.037 +- 0.088 0 of 219 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 29 seconds. But when I look at norm.mgz, the whole brain is not shown: tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/norm.mgz I checked the inputs brainmask.mgz and nu.mgz, and they seem ok: tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/brainmask.mgz tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/nu.mgz how do I check if the transforms/talairach.lta is ok? Thanks, Vasanth ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fsaverage
Is fsaverage used in recon-all processing? Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] norm.mgz
Vasanth, When I tried to load the nu.mgz and brainmask.mgz into tkmedit it complained that they weren't the same size. mri_info confirms this: ukase [mri] mri_info nu.mgz Volume information for nu.mgz type: MGH dimensions: 256 x 256 x 128 voxel sizes: 1., 1., 1.3300 ukase [mri] mri_info brainmask.mgz Volume information for brainmask.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. This is likely causing the error to the norm.mgz volume. How have you run things up to now - within recon-all, or with individual commands? If you conform your nu.mgz volume: mri_convert --conform nu.mgz nu.mgz and then try again! Jenni On Fri, 24 Mar 2006, Vasanth Pappu wrote: Hi, I am using recon-all and the norm.mgz's so far are only about half the brain. I checked the input volumes and looked though the output to std and everything seemed fine, so I am not sure what to do: on machine vader source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /autofs/space/boba_001/users/nrecon/ which mri_ca_normalize /usr/local/freesurfer/stable/bin//mri_ca_normalize cd /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz output: using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... Note: program considers input volume #1 as the most T1-like using real data threshold=56.0 using (109, 110, 82) as brain centroid... mean wm in atlas = 109, using box (94,96,73) --> (123, 124,90) to find MRI wm before smoothing, mri peak at 484 after smoothing, mri peak at 484, scaling input intensities by 0.225 scaling channel 0 by 0.224939 using 242283 sample points... INFO: compute sample coordinates transform 1.724 -0.639 -2.451 142.880; 0.122 1.661 -0.265 -85.128; 2.012 0.112 1.598 -322.680; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter found 38929 control points for structure... bounding box (121, 85, 50) --> (177, 152, 94) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0 87 of 225 (38.7%) samples deleted finding control points in Right_Cerebral_White_Matter found 38531 control points for structure... bounding box (116, 86, 62) --> (172, 156, 102) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 108.0 90 of 179 (50.3%) samples deleted finding control points in Left_Cerebellum_White_Matter found 3087 control points for structure... bounding box (132, 135, 50) --> (150, 158, 68) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 96.0 18 of 52 (34.6%) samples deleted finding control points in Right_Cerebellum_White_Matter found 2900 control points for structure... bounding box (123, 136, 61) --> (144, 161, 76) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 102.0 23 of 58 (39.7%) samples deleted finding control points in Brain_Stem found 3414 control points for structure... bounding box (138, 130, 62) --> (152, 170, 78) Brain_Stem: limiting intensities to 89.0 --> 97.0 37 of 66 (56.1%) samples deleted using 580 total control points for intensity normalization... bias field = 1.037 +- 0.088 0 of 219 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 29 seconds. But when I look at norm.mgz, the whole brain is not shown: tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/norm.mgz I checked the inputs brainmask.mgz and nu.mgz, and they seem ok: tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/brainmask.mgz tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/nu.mgz how do I check if the transforms/talairach.lta is ok? Thanks, Vasanth ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fsaverage
No, it's only there for display purposes, it is not used in recon-all in any way. Sasha Wolosin wrote: Is fsaverage used in recon-all processing? Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] norm.mgz
Hi Vasanth, your orig.mgz hasn't been conformed. That is, it should be 1mm isotropic in a 256^3 volume, but it's not: mri_info /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/orig.mgz Volume information for /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/orig.mgz type: MGH dimensions: 256 x 256 x 128 voxel sizes: 1., 1., 1.3300 type: FLOAT (3) fov: 256.000 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -85.1, zend: 85.1 . . . how did you generate it? Bruce On Fri, 24 Mar 2006, Vasanth Pappu wrote: Hi, I am using recon-all and the norm.mgz's so far are only about half the brain. I checked the input volumes and looked though the output to std and everything seemed fine, so I am not sure what to do: on machine vader source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /autofs/space/boba_001/users/nrecon/ which mri_ca_normalize /usr/local/freesurfer/stable/bin//mri_ca_normalize cd /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz output: using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... Note: program considers input volume #1 as the most T1-like using real data threshold=56.0 using (109, 110, 82) as brain centroid... mean wm in atlas = 109, using box (94,96,73) --> (123, 124,90) to find MRI wm before smoothing, mri peak at 484 after smoothing, mri peak at 484, scaling input intensities by 0.225 scaling channel 0 by 0.224939 using 242283 sample points... INFO: compute sample coordinates transform 1.724 -0.639 -2.451 142.880; 0.122 1.661 -0.265 -85.128; 2.012 0.112 1.598 -322.680; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter found 38929 control points for structure... bounding box (121, 85, 50) --> (177, 152, 94) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0 87 of 225 (38.7%) samples deleted finding control points in Right_Cerebral_White_Matter found 38531 control points for structure... bounding box (116, 86, 62) --> (172, 156, 102) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 108.0 90 of 179 (50.3%) samples deleted finding control points in Left_Cerebellum_White_Matter found 3087 control points for structure... bounding box (132, 135, 50) --> (150, 158, 68) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 96.0 18 of 52 (34.6%) samples deleted finding control points in Right_Cerebellum_White_Matter found 2900 control points for structure... bounding box (123, 136, 61) --> (144, 161, 76) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 102.0 23 of 58 (39.7%) samples deleted finding control points in Brain_Stem found 3414 control points for structure... bounding box (138, 130, 62) --> (152, 170, 78) Brain_Stem: limiting intensities to 89.0 --> 97.0 37 of 66 (56.1%) samples deleted using 580 total control points for intensity normalization... bias field = 1.037 +- 0.088 0 of 219 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 29 seconds. But when I look at norm.mgz, the whole brain is not shown: tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/norm.mgz I checked the inputs brainmask.mgz and nu.mgz, and they seem ok: tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/brainmask.mgz tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/nu.mgz how do I check if the transforms/talairach.lta is ok? Thanks, Vasanth ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] norm.mgz
Thanks Bruce and Jenni, I see that I left out the conform step when going from rawavg.mgz to orig.mgz. I was grad_unwarping the 00?.mgz's before averaging them, and I started recon-all with the -nomc flag. I conformed nu.mgz and it's norm.mgz is a full volume now. Thanks, Vasanth On Fri, 24 Mar 2006, Bruce Fischl wrote: Hi Vasanth, your orig.mgz hasn't been conformed. That is, it should be 1mm isotropic in a 256^3 volume, but it's not: mri_info /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/orig.mgz Volume information for /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/orig.mgz type: MGH dimensions: 256 x 256 x 128 voxel sizes: 1., 1., 1.3300 type: FLOAT (3) fov: 256.000 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -85.1, zend: 85.1 . . . how did you generate it? Bruce On Fri, 24 Mar 2006, Vasanth Pappu wrote: Hi, I am using recon-all and the norm.mgz's so far are only about half the brain. I checked the input volumes and looked though the output to std and everything seemed fine, so I am not sure what to do: on machine vader source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /autofs/space/boba_001/users/nrecon/ which mri_ca_normalize /usr/local/freesurfer/stable/bin//mri_ca_normalize cd /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz output: using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... Note: program considers input volume #1 as the most T1-like using real data threshold=56.0 using (109, 110, 82) as brain centroid... mean wm in atlas = 109, using box (94,96,73) --> (123, 124,90) to find MRI wm before smoothing, mri peak at 484 after smoothing, mri peak at 484, scaling input intensities by 0.225 scaling channel 0 by 0.224939 using 242283 sample points... INFO: compute sample coordinates transform 1.724 -0.639 -2.451 142.880; 0.122 1.661 -0.265 -85.128; 2.012 0.112 1.598 -322.680; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter found 38929 control points for structure... bounding box (121, 85, 50) --> (177, 152, 94) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 111.0 87 of 225 (38.7%) samples deleted finding control points in Right_Cerebral_White_Matter found 38531 control points for structure... bounding box (116, 86, 62) --> (172, 156, 102) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 108.0 90 of 179 (50.3%) samples deleted finding control points in Left_Cerebellum_White_Matter found 3087 control points for structure... bounding box (132, 135, 50) --> (150, 158, 68) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 96.0 18 of 52 (34.6%) samples deleted finding control points in Right_Cerebellum_White_Matter found 2900 control points for structure... bounding box (123, 136, 61) --> (144, 161, 76) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 102.0 23 of 58 (39.7%) samples deleted finding control points in Brain_Stem found 3414 control points for structure... bounding box (138, 130, 62) --> (152, 170, 78) Brain_Stem: limiting intensities to 89.0 --> 97.0 37 of 66 (56.1%) samples deleted using 580 total control points for intensity normalization... bias field = 1.037 +- 0.088 0 of 219 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 29 seconds. But when I look at norm.mgz, the whole brain is not shown: tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/norm.mgz I checked the inputs brainmask.mgz and nu.mgz, and they seem ok: tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/brainmask.mgz tkmedit -f /autofs/space/boba_001/users/nrecon/ARSS70_nrecon/mri/nu.mgz how do I check if the transforms/talairach.lta is ok? Thanks, Vasanth ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question about format conversion
Hi Freesurfer Help, I am trying to get the wm.mgz file into matlab. Is there a way to change the mgz into dicom format, or any othe matlab compatible formats? Thanks, Camilo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Question about format conversion
Hi Camilo
[v,M,p] = load_mgh('wm.mgz');
will load the volume (v) into matlab, in addition to the vox2ras matrix M
and the MR parameters p. The .m file is in
$FREESURFER_HOME/matlab/load_mgh.m.
cheers,
Bruce
On Fri, 24 Mar 2006
[EMAIL PROTECTED] wrote:
Hi Freesurfer Help,
I am trying to get the wm.mgz file into matlab. Is there a way to change
the mgz into dicom format, or any othe matlab compatible formats?
Thanks,
Camilo
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Re: [Freesurfer] Question about format conversion
Or
v = MRIread('wm.mgz');
v is a struct, and v.vol will give you the volume.
Bruce Fischl wrote:
Hi Camilo
[v,M,p] = load_mgh('wm.mgz');
will load the volume (v) into matlab, in addition to the vox2ras
matrix M and the MR parameters p. The .m file is in
$FREESURFER_HOME/matlab/load_mgh.m.
cheers,
Bruce
On Fri, 24 Mar 2006 [EMAIL PROTECTED] wrote:
Hi Freesurfer Help,
I am trying to get the wm.mgz file into matlab. Is there a way to change
the mgz into dicom format, or any othe matlab compatible formats?
Thanks,
Camilo
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] load_mgh question
Hi Freesurfer help, Thanks for the prompt response. I now am using the load_mgh function but it is giving me the following error: ??? SWITCH expression must be a scalar or string constant. Error in ==> load_mgh at 126 switch type Does anyone have an idea why this is happening? Thanks, Camilo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] load_mgh question
did you add $FREESURFER_HOME/matlab to your matlab path? You probably need to On Fri, 24 Mar 2006 [EMAIL PROTECTED] wrote: Hi Freesurfer help, Thanks for the prompt response. I now am using the load_mgh function but it is giving me the following error: ??? SWITCH expression must be a scalar or string constant. Error in ==> load_mgh at 126 switch type Does anyone have an idea why this is happening? Thanks, Camilo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to register subcortical segmentation with the original image
Hello, I have subcortical segmentations from freesurfer. I have automatically extracted one of the segmented objects (binary). I need to get the grayscale map of the object and do not know how to register the segmented object with the original image (analyze) so it can be overlayed for masking? Any comments? Thanks Shahab Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to register subcortical segmentation with the original image
you shouldn't have to register it - it will be in register. And what kind of grayscale map do you mean? On Fri, 24 Mar 2006, Shahabuddin Ansari wrote: Hello, I have subcortical segmentations from freesurfer. I have automatically extracted one of the segmented objects (binary). I need to get the grayscale map of the object and do not know how to register the segmented object with the original image (analyze) so it can be overlayed for masking? Any comments? Thanks Shahab - Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
