External Email - Use Caution
Hi,
I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii
I now have something registered to the T1.nii and would like to move it back to Freesurfer space. How would you go about doing that? I am assuming I would do the inverse of the mri_convert, but I can't seem to find the option to write the matrix.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
External Email - Use Caution
Hi Victor,
in case you used mri_convert like this only, there is no change in orientation or spacing between orig.mgz and T1.nii. So, whatever you registered to the T1.nii should also be in space of the orig.mgz.
Best,
Falk
...............................................
[http://secure-web.cisco.com/1bMxxPB2IQvUkA27JpoN6uYF_qZIvBhG7A1lEk_pEPVLjceS...] Universitätsklinik für Neurologie
Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg
Telefon: +49-391-6117-512
falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de http://secure-web.cisco.com/1Ot95tcBSI8NwAu9j3-MCi-WNazHI1x3J_Wd7KLcLqqDxbYO... ________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Zeng, Victor (BIDMC - Keshavan - Psychiatry) vzeng@bidmc.harvard.edu Gesendet: Donnerstag, 5. Mai 2022 10:09:26 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Reversing mri_convert
External Email - Use Caution
Hi,
I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii
I now have something registered to the T1.nii and would like to move it back to Freesurfer space. How would you go about doing that? I am assuming I would do the inverse of the mri_convert, but I can't seem to find the option to write the matrix.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
External Email - Use Caution
For some reason it isn't displaying the same i/j/k ras. The T1 and the registered image (ASL) is in the same dimension/voxel sizes. The TR is different at 7ms (T1) vs ~9000ms (ASL). When I try mri_convert -tr 7 asl.nii asl.mgz, it doesn't change the incorrect i/j/k ras matrix
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.de Sent: Thursday, May 5, 2022 4:17 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Reversing mri_convert
External Email - Use Caution
Hi Victor,
in case you used mri_convert like this only, there is no change in orientation or spacing between orig.mgz and T1.nii. So, whatever you registered to the T1.nii should also be in space of the orig.mgz.
Best,
Falk
...............................................
[https://secure-web.cisco.com/1OC7if2MmAqtO5LsFetXxMvabgQVMtCLToGm04c-ZSvPThe... ] Universitätsklinik für Neurologie
Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg
Telefon: +49-391-6117-512
falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de https://secure-web.cisco.com/12VV1Zuktq-dOaOs2OFkciZgmD7fNFdt3i2XPDRjKwQTNpX... ________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Zeng, Victor (BIDMC - Keshavan - Psychiatry) vzeng@bidmc.harvard.edu Gesendet: Donnerstag, 5. Mai 2022 10:09:26 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Reversing mri_convert
External Email - Use Caution
Hi,
I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii
I now have something registered to the T1.nii and would like to move it back to Freesurfer space. How would you go about doing that? I am assuming I would do the inverse of the mri_convert, but I can't seem to find the option to write the matrix.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1td8aV2ri352TR9VpVlXrbsb7IaSAo2-icYdNvCin2ONbSE... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1bPNZTQeAO_ytwQ-hmKMYJlbcqOzKlQMyhItm8U_PbEUOws... <https://secure-web.cisco.com/1bPNZTQeAO_ytwQ-hmKMYJlbcqOzKlQMyhItm8U_PbEUOws... > .
What does "isn't displaying the same i/j/k ras" mean? In what tool? What is the result of running mri_info on each volume?
On 5/5/2022 4:54 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
For some reason it isn't displaying the same i/j/k ras. The T1 and the registered image (ASL) is in the same dimension/voxel sizes. The TR is different at 7ms (T1) vs ~9000ms (ASL). When I try mri_convert -tr 7 asl.nii asl.mgz, it doesn't change the incorrect i/j/k ras matrix
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab
--
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.de *Sent:* Thursday, May 5, 2022 4:17 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] Reversing mri_convert External Email - Use Caution
Hi Victor,
in case you used mri_convert like this only, there is no change in orientation or spacing between orig.mgz and T1.nii. So, whatever you registered to the T1.nii should also be in space of the orig.mgz.
Best,
Falk
...............................................
[https://urldefense.com/v3/__http://secure-web.cisco.com/1bMxxPB2IQvUkA27JpoN... ] Universitätsklinik für Neurologie
Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg
Telefon: +49-391-6117-512
falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://urldefense.com/v3/__http://secure-web.cisco.com/1Ot95tcBSI8NwAu9j3-M... https://secure-web.cisco.com/1zKilxLvUtOcslJ-NeZ-r6q6_ihlUtPUwQi5aENW7AlA2XGBDTAThmSOjDC6OEs9n2lSaPhs0XJSMBudXQxuxfLWnkcTQa2GSCmYp0osiECuFZWqhJgETRmchOqWX9A4kp8HnqoyrF_i9nqpqLv8XebTBMEWXote0H5zoAkPv5ukQp-lPH2zlsCIAmll2Wsfbu_IU8dvoLthf7o5x2pzg6KSvqv_sk9nnNH1uGPHyp5ePJPJW6Icx2cToEZRfaQUc0Fvyy2oemRECy8qdhl5V1KYHNSprV74P50X5pomOQy1rsgW-J3Ezda1aDR6Erd8maGZPNbftDq1i16TKS18kmQ/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fsecure-web.cisco.com%2F1Ot95tcBSI8NwAu9j3-MCi-WNazHI1x3J_Wd7KLcLqqDxbYOgUclzwlyOXOLYHH412QcBGDnXDUOxzgguWCcQel8L9ZaACvmWHS4zTEdK8m4QYnGS7xdkGY5RGp0vFAppqrzydZAf5JmpYcPyBnyWZKvGyEXVs4m-zIc-l0qYdee1xdYpnuNye9cAN_EA7WpEICaRtzUMDWnXay-IFvAa1sx-CEhdTWl_sspDuOZKqHB0SYGJ-szyMlAYGZFOOg42NNc91WEMisk0SlaKG7_cgfvjHUrowbBBNtrdR_lL3mwsJ8-Tq9I_Xgwp-2hdoPYS4GVMivfLvRmcMR4Gt4lZkA%2Fhttp%2A3A%2A2F%2A2Fwww.kneu.ovgu.de%2A2Fkneu.html__%3BJSUlJQ%21%21CvMGjuU%21rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqaFxGR3sg%24 ________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Zeng, Victor (BIDMC - Keshavan - Psychiatry) vzeng@bidmc.harvard.edu Gesendet: Donnerstag, 5. Mai 2022 10:09:26 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Reversing mri_convert
External Email - Use Caution
Hi,
I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii
I now have something registered to the T1.nii and would like to move it back to Freesurfer space. How would you go about doing that? I am assuming I would do the inverse of the mri_convert, but I can't seem to find the option to write the matrix.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinf... https://secure-web.cisco.com/1T6BpWhQTkdKu7zq-OxDUp5Hr42Ce9DrbxvtnLSTOCsVL1og4vKWzzwxIaXvBoZg1lvwpgAjlFDV5FeqdofThiY5-ZuQB85e-IiayX2SAJ1GfTwDX6IcpNUZ5CZf5BMYCeS0ZKrLNZvJp3N_f-TvPnaIvfCi0M637-BLzrME4MHFoun1uB6WLIccf13ITBM_prkKKserE_BSGrk2N89A1XHVX1wVeYO8yX3rN98K65cfACxsfdQl48mzbTuDAAi0SbJm375PzAzik2CUMjMbGI2rskW9hyx6GWYZS-SQP0XOynia7OCfcZ6DE6nzW8x_OEakPYSdRhhwM9CdT7rMqiQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21CvMGjuU%21rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqZWI937sQ%24 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://urldefense.com/v3/__https://www.massgeneralbrigham.org/compliancelin... https://secure-web.cisco.com/1RT7CRR1vRLVg40kOnyzuy29C5f1lv7R0gEaJKlLW3db6qKx5hGnKXyWco_2LP_cPhOxVla45h4mkH9vdk95VMSekOyQin7xRJXJBBhN7lznbctRKYRJmzy8R6PYE_8ETkbYfC3oH3H8ybsc2Ms10eKsGn4XBc4LZkEJJSr3aY62lBu8PYKz-ySRFBg9xkOGXhE9x4c1Y59HaDUfVCrHsMlqfkQRsEUvUCOfnPi3Q4MZKM4KCD1jyXAuj1ucP1Nd-E2pJdYOMBZ3qtH37UBfv31ia9b8hZY8WeAO2CLkNUmraw9WiAwZuv4J0RqLEUw2kajGtl-4ednKAxemR566YeQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline__%3B%21%21CvMGjuU%21rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqYCZdtugA%24 <https://urldefense.com/v3/__https://www.massgeneralbrigham.org/compliancelin...
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The output for the orig.mgz is:
Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 2.6149 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 18.2086 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 4.6564
talairach xfm : /home/victor/Processing/Finished_dev2019/25570_S4131FQU_SENSE/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 130.6149 0.0000 0.0000 1.0000 -109.7914 0.0000 -1.0000 0.0000 132.6564 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 -0.0000 130.6149 -0.0000 -0.0000 -1.0000 132.6564 0.0000 1.0000 0.0000 109.7914 -0.0000 -0.0000 -0.0000 1.0000
I use mri_convert to create a .nii. I have an ASL image that is registered exactly like it. Here is the output for the asl nifti.
Volume information for test.nii.gz type: nii dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 9345.59 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9990, y_r = 0.0435, z_r = -0.0046, c_r = 1.8094 : x_a = -0.0217, y_a = -0.4021, z_a = 0.9153, c_a = -11.3674 : x_s = -0.0379, y_s = -0.9145, z_s = -0.4027, c_s = -9.1954 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -0.9990 0.0435 -0.0046 124.7114 -0.0217 -0.4021 0.9153 -74.2729 -0.0379 -0.9145 -0.4027 164.2693 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -0.9990 -0.0217 -0.0379 129.2118 0.0435 -0.4021 -0.9145 114.9404 -0.0046 0.9153 -0.4027 134.7101 -0.0000 -0.0000 -0.0000 1.0000
Transforming the test.nii.gz into a mgz loses its registration to do the orig.mgz.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, May 5, 2022 4:36 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Reversing mri_convert
What does "isn't displaying the same i/j/k ras" mean? In what tool? What is the result of running mri_info on each volume?
On 5/5/2022 4:54 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
For some reason it isn't displaying the same i/j/k ras. The T1 and the registered image (ASL) is in the same dimension/voxel sizes. The TR is different at 7ms (T1) vs ~9000ms (ASL). When I try mri_convert -tr 7 asl.nii asl.mgz, it doesn't change the incorrect i/j/k ras matrix
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de Sent: Thursday, May 5, 2022 4:17 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Reversing mri_convert
External Email - Use Caution
Hi Victor,
in case you used mri_convert like this only, there is no change in orientation or spacing between orig.mgz and T1.nii. So, whatever you registered to the T1.nii should also be in space of the orig.mgz.
Best,
Falk
...............................................
[https://secure-web.cisco.com/1XDjs35E80nuhx0jkDl27tOZTYOjO9FhJVGMFMgWDKn0ojQ... ] Universitätsklinik für Neurologie
Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg
Telefon: +49-391-6117-512
falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1THRcMxba80O0Rbk05pMgv_uOB7nlhQkC0Srsd2vyoQkE0a...https://secure-web.cisco.com/1Y1MakUHgzVS_rzUsSFtlHfyvkx8NN5A1H4v6MamyuZ72VYX2h-Sx5NvMoAuG7q5XCrRSHWBtDwFFq_CY-Vr2aitf7rNiDpm-Ox8Fltjb7xlcj-IvFr-pby9FtlFTX7OgFjqKpVZdcdtP5Ugjn9wSEPnsPEtn_2GI-8UXHvkWmAx8adj5bj-Av5FhA3PXM73vOnafxYJwVIqhu4OzmstMU4JpBIvi7Ascb9KT8jr0PzAw-dlHWUJo8Fi4N_Huiw9ZSd7ON7kTXuEQrywt9y7oUouL9zWOi7kn87WtDt5CmSgDrCYCYEB7uAGeo8Y6jRu6/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1zKilxLvUtOcslJ-NeZ-r6q6_ihlUtPUwQi5aENW7AlA2XGBDTAThmSOjDC6OEs9n2lSaPhs0XJSMBudXQxuxfLWnkcTQa2GSCmYp0osiECuFZWqhJgETRmchOqWX9A4kp8HnqoyrF_i9nqpqLv8XebTBMEWXote0H5zoAkPv5ukQp-lPH2zlsCIAmll2Wsfbu_IU8dvoLthf7o5x2pzg6KSvqv_sk9nnNH1uGPHyp5ePJPJW6Icx2cToEZRfaQUc0Fvyy2oemRECy8qdhl5V1KYHNSprV74P50X5pomOQy1rsgW-J3Ezda1aDR6Erd8maGZPNbftDq1i16TKS18kmQ%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2F*2Fsecure-web.cisco.com*2F1Ot95tcBSI8NwAu9j3-MCi-WNazHI1x3J_Wd7KLcLqqDxbYOgUclzwlyOXOLYHH412QcBGDnXDUOxzgguWCcQel8L9ZaACvmWHS4zTEdK8m4QYnGS7xdkGY5RGp0vFAppqrzydZAf5JmpYcPyBnyWZKvGyEXVs4m-zIc-l0qYdee1xdYpnuNye9cAN_EA7WpEICaRtzUMDWnXay-IFvAa1sx-CEhdTWl_sspDuOZKqHB0SYGJ-szyMlAYGZFOOg42NNc91WEMisk0SlaKG7_cgfvjHUrowbBBNtrdR_lL3mwsJ8-Tq9I_Xgwp-2hdoPYS4GVMivfLvRmcMR4Gt4lZkA*2Fhttp*2A3A*2A2F*2A2Fwww.kneu.ovgu.de*2A2Fkneu.html__*3BJSUlJQ*21*21CvMGjuU*21rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqaFxGR3sg*24__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!CvMGjuU!pUZtmg2d8JM9mwaw_QLOOo6dBRiTNqvkHVbUtnVB9LT4nQ4KjZxvkdtizpgGohLtWLbeeg$ ________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Zeng, Victor (BIDMC - Keshavan - Psychiatry) vzeng@bidmc.harvard.edumailto:vzeng@bidmc.harvard.edu Gesendet: Donnerstag, 5. Mai 2022 10:09:26 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Reversing mri_convert
External Email - Use Caution
Hi,
I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii
I now have something registered to the T1.nii and would like to move it back to Freesurfer space. How would you go about doing that? I am assuming I would do the inverse of the mri_convert, but I can't seem to find the option to write the matrix.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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The ASL has a different vox2ras transform. How did you register the ASL to the anatoical? How did you convert the ASL to the anatomical space?
On 5/6/2022 4:47 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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/The output for the orig.mgz is: /
Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 2.6149 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 18.2086 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 4.6564
talairach xfm : /home/victor/Processing/Finished_dev2019/25570_S4131FQU_SENSE/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 130.6149 0.0000 0.0000 1.0000 -109.7914 0.0000 -1.0000 0.0000 132.6564 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 -0.0000 130.6149 -0.0000 -0.0000 -1.0000 132.6564 0.0000 1.0000 0.0000 109.7914 -0.0000 -0.0000 -0.0000 1.0000
/I use mri_convert to create a .nii. I have an ASL image that is registered exactly like it. Here is the output for the asl nifti. /
Volume information for test.nii.gz type: nii dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 9345.59 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9990, y_r = 0.0435, z_r = -0.0046, c_r = 1.8094 : x_a = -0.0217, y_a = -0.4021, z_a = 0.9153, c_a = -11.3674 : x_s = -0.0379, y_s = -0.9145, z_s = -0.4027, c_s = -9.1954 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -0.9990 0.0435 -0.0046 124.7114 -0.0217 -0.4021 0.9153 -74.2729 -0.0379 -0.9145 -0.4027 164.2693 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -0.9990 -0.0217 -0.0379 129.2118 0.0435 -0.4021 -0.9145 114.9404 -0.0046 0.9153 -0.4027 134.7101 -0.0000 -0.0000 -0.0000 1.0000
Transforming the test.nii.gz into a mgz loses its registration to do the orig.mgz.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Thursday, May 5, 2022 4:36 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] Reversing mri_convert What does "isn't displaying the same i/j/k ras" mean? In what tool? What is the result of running mri_info on each volume?
On 5/5/2022 4:54 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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For some reason it isn't displaying the same i/j/k ras. The T1 and the registered image (ASL) is in the same dimension/voxel sizes. The TR is different at 7ms (T1) vs ~9000ms (ASL). When I try mri_convert -tr 7 asl.nii asl.mgz, it doesn't change the incorrect i/j/k ras matrix
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab
--
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of falk.luesebrink@med.ovgu.de mailto:falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.de mailto:falk.luesebrink@med.ovgu.de *Sent:* Thursday, May 5, 2022 4:17 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] Reversing mri_convert External Email - Use Caution
Hi Victor,
in case you used mri_convert like this only, there is no change in orientation or spacing between orig.mgz and T1.nii. So, whatever you registered to the T1.nii should also be in space of the orig.mgz.
Best,
Falk
...............................................
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External Email - Use Caution
Hi,
I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii
I now have something registered to the T1.nii and would like to move it back to Freesurfer space. How would you go about doing that? I am assuming I would do the inverse of the mri_convert, but I can't seem to find the option to write the matrix.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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This was part of an independent ASL pipeline called ExploreASL.
I do not know 100% the details, but in short the orig.mgz was converted to a .nii through mri_convert for CAT12 and was registered to some native space, the deformation field was saved into some y_T1.nii (SPM). The ASL map was likewise registered to this native space. I used SPM to revert the ASL map to the original T1 space (which works) using the y_T1.nii. Some intermediate reslicing steps were done as well to get it to a certain dimension. I will get back to you with further details as I inquire
Is this something that has an easy fix?
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, May 12, 2022 3:38 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] [External] Re: Reversing mri_convert
The ASL has a different vox2ras transform. How did you register the ASL to the anatoical? How did you convert the ASL to the anatomical space?
On 5/6/2022 4:47 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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The output for the orig.mgz is:
Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 2.6149 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 18.2086 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 4.6564
talairach xfm : /home/victor/Processing/Finished_dev2019/25570_S4131FQU_SENSE/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 130.6149 0.0000 0.0000 1.0000 -109.7914 0.0000 -1.0000 0.0000 132.6564 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 -0.0000 130.6149 -0.0000 -0.0000 -1.0000 132.6564 0.0000 1.0000 0.0000 109.7914 -0.0000 -0.0000 -0.0000 1.0000
I use mri_convert to create a .nii. I have an ASL image that is registered exactly like it. Here is the output for the asl nifti.
Volume information for test.nii.gz type: nii dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 9345.59 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9990, y_r = 0.0435, z_r = -0.0046, c_r = 1.8094 : x_a = -0.0217, y_a = -0.4021, z_a = 0.9153, c_a = -11.3674 : x_s = -0.0379, y_s = -0.9145, z_s = -0.4027, c_s = -9.1954 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -0.9990 0.0435 -0.0046 124.7114 -0.0217 -0.4021 0.9153 -74.2729 -0.0379 -0.9145 -0.4027 164.2693 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -0.9990 -0.0217 -0.0379 129.2118 0.0435 -0.4021 -0.9145 114.9404 -0.0046 0.9153 -0.4027 134.7101 -0.0000 -0.0000 -0.0000 1.0000
Transforming the test.nii.gz into a mgz loses its registration to do the orig.mgz.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Thursday, May 5, 2022 4:36 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Reversing mri_convert
What does "isn't displaying the same i/j/k ras" mean? In what tool? What is the result of running mri_info on each volume?
On 5/5/2022 4:54 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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For some reason it isn't displaying the same i/j/k ras. The T1 and the registered image (ASL) is in the same dimension/voxel sizes. The TR is different at 7ms (T1) vs ~9000ms (ASL). When I try mri_convert -tr 7 asl.nii asl.mgz, it doesn't change the incorrect i/j/k ras matrix
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de Sent: Thursday, May 5, 2022 4:17 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Reversing mri_convert
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Hi Victor,
in case you used mri_convert like this only, there is no change in orientation or spacing between orig.mgz and T1.nii. So, whatever you registered to the T1.nii should also be in space of the orig.mgz.
Best,
Falk
...............................................
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Hi,
I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii
I now have something registered to the T1.nii and would like to move it back to Freesurfer space. How would you go about doing that? I am assuming I would do the inverse of the mri_convert, but I can't seem to find the option to write the matrix.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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I don't know. You describe a lot of steps which were hard to follow. Without digging into it, I would have a hard time recommending anything. You can always just register your ASL directly to the anatomical (bbregister) and resamploe
On 5/12/2022 4:18 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
This was part of an independent ASL pipeline called ExploreASL.
I do not know 100% the details, but in short the orig.mgz was converted to a .nii through mri_convert for CAT12 and was registered to some native space, the deformation field was saved into some y_T1.nii (SPM). The ASL map was likewise registered to this native space. I used SPM to revert the ASL map to the original T1 space (which works) using the y_T1.nii. Some intermediate reslicing steps were done as well to get it to a certain dimension. I will get back to you with further details as I inquire
Is this something that has an easy fix?
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Thursday, May 12, 2022 3:38 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] [External] Re: Reversing mri_convert The ASL has a different vox2ras transform. How did you register the ASL to the anatoical? How did you convert the ASL to the anatomical space?
On 5/6/2022 4:47 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
/The output for the orig.mgz is: /
Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 7.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 2.6149 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 18.2086 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 4.6564
talairach xfm : /home/victor/Processing/Finished_dev2019/25570_S4131FQU_SENSE/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 130.6149 0.0000 0.0000 1.0000 -109.7914 0.0000 -1.0000 0.0000 132.6564 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 -0.0000 130.6149 -0.0000 -0.0000 -1.0000 132.6564 0.0000 1.0000 0.0000 109.7914 -0.0000 -0.0000 -0.0000 1.0000
/I use mri_convert to create a .nii. I have an ASL image that is registered exactly like it. Here is the output for the asl nifti. /
Volume information for test.nii.gz type: nii dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 9345.59 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -0.9990, y_r = 0.0435, z_r = -0.0046, c_r = 1.8094 : x_a = -0.0217, y_a = -0.4021, z_a = 0.9153, c_a = -11.3674 : x_s = -0.0379, y_s = -0.9145, z_s = -0.4027, c_s = -9.1954 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -0.9990 0.0435 -0.0046 124.7114 -0.0217 -0.4021 0.9153 -74.2729 -0.0379 -0.9145 -0.4027 164.2693 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -0.9990 -0.0217 -0.0379 129.2118 0.0435 -0.4021 -0.9145 114.9404 -0.0046 0.9153 -0.4027 134.7101 -0.0000 -0.0000 -0.0000 1.0000
Transforming the test.nii.gz into a mgz loses its registration to do the orig.mgz.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Thursday, May 5, 2022 4:36 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] Reversing mri_convert What does "isn't displaying the same i/j/k ras" mean? In what tool? What is the result of running mri_info on each volume?
On 5/5/2022 4:54 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
For some reason it isn't displaying the same i/j/k ras. The T1 and the registered image (ASL) is in the same dimension/voxel sizes. The TR is different at 7ms (T1) vs ~9000ms (ASL). When I try mri_convert -tr 7 asl.nii asl.mgz, it doesn't change the incorrect i/j/k ras matrix
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab
--
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of falk.luesebrink@med.ovgu.de mailto:falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.de mailto:falk.luesebrink@med.ovgu.de *Sent:* Thursday, May 5, 2022 4:17 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] Reversing mri_convert External Email - Use Caution
Hi Victor,
in case you used mri_convert like this only, there is no change in orientation or spacing between orig.mgz and T1.nii. So, whatever you registered to the T1.nii should also be in space of the orig.mgz.
Best,
Falk
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External Email - Use Caution
Hi,
I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii
I now have something registered to the T1.nii and would like to move it back to Freesurfer space. How would you go about doing that? I am assuming I would do the inverse of the mri_convert, but I can't seem to find the option to write the matrix.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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If you have 2 volumes that share an RAS coordinate system but have different voxel geometry you can use the -rl ("reslice like") option:
mri_convert -rl template.mgz vol_to_convert.nii vol_like_template.mgz
cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Zeng, Victor (BIDMC - Keshavan - Psychiatry) Sent: Thursday, May 5, 2022 4:09 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Reversing mri_convert
External Email - Use Caution Hi,
I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii
I now have something registered to the T1.nii and would like to move it back to Freesurfer space. How would you go about doing that? I am assuming I would do the inverse of the mri_convert, but I can't seem to find the option to write the matrix.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
External Email - Use Caution
Can I send three images so that you could debug? It is not seeming to work
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If you have 2 volumes that share an RAS coordinate system but have different voxel geometry you can use the -rl (“reslice like”) option:
mri_convert -rl template.mgz vol_to_convert.nii vol_like_template.mgz
cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Zeng, Victor (BIDMC - Keshavan - Psychiatry) Sent: Thursday, May 5, 2022 4:09 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Reversing mri_convert
External Email - Use Caution
Hi,
I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii
I now have something registered to the T1.nii and would like to move it back to Freesurfer space. How would you go about doing that? I am assuming I would do the inverse of the mri_convert, but I can't seem to find the option to write the matrix.
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
falk.luesebrink＠med.ovgu.de -
Fischl, Bruce -
Zeng, Victor (BIDMC - Keshavan - Psychiatry)