Re: [Freesurfer] [External] Re: [External] Re: Reversing mri_convert

Thu, 12 May 2022 13:23:53 -0700

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-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve 
<dgr...@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-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
<freesurfer-boun...@nmr.mgh.harvard.edu> 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas 
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@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-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
<freesurfer-boun...@nmr.mgh.harvard.edu> 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 
falk.luesebr...@med.ovgu.de <mailto:falk.luesebr...@med.ovgu.de> 
<falk.luesebr...@med.ovgu.de> <mailto:falk.luesebr...@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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________________________________

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
<freesurfer-boun...@nmr.mgh.harvard.edu> 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Zeng, 
Victor (BIDMC - Keshavan - Psychiatry) <vz...@bidmc.harvard.edu> 
<mailto:vz...@bidmc.harvard.edu>

Gesendet: Donnerstag, 5. Mai 2022 10:09:26

An: freesurfer@nmr.mgh.harvard.edu 
<mailto: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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<https://secure-web.cisco.com/18zrbL9mWC1_mLkGn-_Wn2Xp44jW7V1I0_xvSuTthz_SCTbFVs0JWN5ZUtodRHjTJ1Z6NOaV2__krPDTzkmRqMBTtt2s9tyFEGP6wG0I2as0Qw4um_byD-6jU0vZhbFlCBICSNxYH-b2hEwBxaG-CT2sEZMtiNr57YOaY98hIAEw1vxRnRkw2P7kZeFnVRH9dyMtZw-xtt0Su3gtUM_AV5TQ9x_tikL-7krD6h8PSV6U9bZT4EoTCN8r100WaU_Jc52U5pNjjdMZz3oYX_z74pjt2Hy9tMIPp6ZnKcTrE2AI4aPgQZN_IuPa8ShWOmbSu3gMEz5nm3jRJ5U8Y1hEltQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1QcZm4Lay6XZJceCVTXrc0EmUjr4IiuKqSpM5m28Qrq3sjFqX65dnLEDXFWkNABhdIMXAk1pi-rktQiqrbN9-wGuZEzyTEUOh1lT3ZJIF8NAAed0kzN1Tv7hxMJbT0m2wzSYukNhM1XuU4dv7Jgt7O7Aa182u8kpY2Lfl3yVdg47QH_egU0C0_oJKg0udHbCjHtlyQIBPUKyLZKEVh2mHjpa7HFm5Fbd_fIkhVXaBhl2TZU0iamdtxNxNsyEVJUIi1lWlTdfwmZrS24ACUro3vnTtOd1pPBClYoKBDcuB3CbYOFXlhF6mOB-9NUcv0-03%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2F%2A2Fsecure-web.cisco.com%2A2F1T6BpWhQTkdKu7zq-OxDUp5Hr42Ce9DrbxvtnLSTOCsVL1og4vKWzzwxIaXvBoZg1lvwpgAjlFDV5FeqdofThiY5-ZuQB85e-IiayX2SAJ1GfTwDX6IcpNUZ5CZf5BMYCeS0ZKrLNZvJp3N_f-TvPnaIvfCi0M637-BLzrME4MHFoun1uB6WLIccf13ITBM_prkKKserE_BSGrk2N89A1XHVX1wVeYO8yX3rN98K65cfACxsfdQl48mzbTuDAAi0SbJm375PzAzik2CUMjMbGI2rskW9hyx6GWYZS-SQP0XOynia7OCfcZ6DE6nzW8x_OEakPYSdRhhwM9CdT7rMqiQ%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Furldefense.com%2A2A2Fv3%2A2A2F__https%2A2A3A%2A2A2F%2A2A2Fmail.nmr.mgh.harvard.edu%2A2A2Fmailman%2A2A2Flistinfo%2A2A2Ffreesurfer__%2A2A3B%2A2A21%2A2A21CvMGjuU%2A2A21rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqZWI937sQ%2A2A24__%2A3BJSUlJSUlJSUlJSUlJSUlJQ%2A21%2A21CvMGjuU%2A21pUZtmg2d8JM9mwaw_QLOOo6dBRiTNqvkHVbUtnVB9LT4nQ4KjZxvkdtizpgGohLJiPgV5A%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ%21%21CvMGjuU%21svx96Ib2c330QFwERkEsUhvnuW-cpdIGoJ7nEcG-CHckmJmYryQX_IVA8MoigQh64h6F4A%24>
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the Mass General Brigham Compliance HelpLine at *MailScanner has 
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claiming to be* 
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<https://secure-web.cisco.com/1d6saDf4ia-Zxu5LD0HU3-sbBV85mg2qigELxkgvVW15RlPXYxKGonkXLOKqXxj5bxoHPLz49duuvIPZbzXKsmyWeamdMLdJXVjtkvmBzJSLvMx4_sW3Z0luzcJZ8wyBwliyV8ZPSqXdrQQ5gvHRCeppOkWcXzgsvyXNA1zxA71Jneb5MqiPgBlkMHbfpS13yQXkBqRbmBJ7j6k38qRHlLUF_6i7FoFd3dY4XqGpQXrXlcA2Lzy3JE1zyM80TkYlgbU65Vb5_8qBKw4gGylk5j2aKvQtsaHtV0BNOXe9vTZTz-B4FxgDr-bMS7gtL8towig_p7F8dTAy5UEcEE6320Q/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1uSTNTdi__IOuTQ5YiW18AYRUvgb9uXABEEurhuk-fpsVG9T9HIziHWPMLCYqyGtRzzn8qwwD-qhwp9HVV6XNDdIHscp_P3U-bMvzKIcK_a8lvX04OMJ9IPj3QvG2A_idwm73NJmdo35W3YX1SWiyFmr31Alq1vmvS0bkAX2Y62iKEMA8XktEgWMCPz8J0QSVT7ByJIrYBwavbXzEFhL-ygwyJhSwbaOXMWTBOYFxvWs-1eE_EZrLbQFt9XeZybX9r2OJA5JUmUXcnw-L0ggDmxaDnNYbAyUeyU0o80EpiErOOiYVuOQjDElMRFvrWLfH%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2F%2A2Fsecure-web.cisco.com%2A2F1RT7CRR1vRLVg40kOnyzuy29C5f1lv7R0gEaJKlLW3db6qKx5hGnKXyWco_2LP_cPhOxVla45h4mkH9vdk95VMSekOyQin7xRJXJBBhN7lznbctRKYRJmzy8R6PYE_8ETkbYfC3oH3H8ybsc2Ms10eKsGn4XBc4LZkEJJSr3aY62lBu8PYKz-ySRFBg9xkOGXhE9x4c1Y59HaDUfVCrHsMlqfkQRsEUvUCOfnPi3Q4MZKM4KCD1jyXAuj1ucP1Nd-E2pJdYOMBZ3qtH37UBfv31ia9b8hZY8WeAO2CLkNUmraw9WiAwZuv4J0RqLEUw2kajGtl-4ednKAxemR566YeQ%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Furldefense.com%2A2A2Fv3%2A2A2F__https%2A2A3A%2A2A2F%2A2A2Fwww.massgeneralbrigham.org%2A2A2Fcomplianceline__%2A2A3B%2A2A21%2A2A21CvMGjuU%2A2A21rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqYCZdtugA%2A2A24__%2A3BJSUlJSUlJSUlJSUlJSU%2A21%2A21CvMGjuU%2A21pUZtmg2d8JM9mwaw_QLOOo6dBRiTNqvkHVbUtnVB9LT4nQ4KjZxvkdtizpgGohI9sYZ5nw%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU%21%21CvMGjuU%21svx96Ib2c330QFwERkEsUhvnuW-cpdIGoJ7nEcG-CHckmJmYryQX_IVA8MoigQg_FsouwA%24> 
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
<https://urldefense.com/v3/__https://www.massgeneralbrigham.org/complianceline__;!!CvMGjuU!rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqYCZdtugA$ 
> 
<https://secure-web.cisco.com/1rIcET-y6elcz6GdTIdGkFxImLrPetM1yhDjVG-biaRg-5pKJQgKrtCJGP5mTcgOYxjHz5PNya6PoZFeAuPU53c60bBIr3KRe8PwwcvikL9QInDhN6h7gEXS1js8TMLfnzZmkkUn76DdogYGoOoeLMsznKXCnKtDxFtC1P_4XyPNwmfUOc0_spm-imQ_qYPZ016Aeqs-MtazTJ2VJAtQB4q_cccNSYpIvpwUDUsqzdMRNiSME80-yEiExSqj8nJX0NzUl3SSNnncgvwK-rmeWTn1vd_zIhACu1J3luDXuD9WQ2ZMxvI8obUe8eJBizqdqwMkIT0GpSsjhGhUBaQwurg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1GA3zH3QmXaNJCAJ-8tDMdkTLQJnja-770ejmdWiTKwVPTexTcj09fBYGYjoNlCVLH7wVcuzhp-F3ZX0Shui8MmbiPgzUDQPq7J0rfnx2pIrE18lgBwT3x_OQoOY6ne3CzeuBAY5ZrLHsY02lEaZswNg7hkFDevWFs9rG1OWiVaIiUgQGkONky8UdkFIM3ICOQJkf1zP5oXCoU2sqwoYpXhjsfgQ1dQsLa4ftPLHFBLYJT80hRDeqsrsl0vkgt-s00hrWoINkwQjY_CiS7j5RbiUlSCWPP2qEMGsCPOf76AM9U3AnZM9TAMQibpaLJc0d%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2F%2A2Fwww.massgeneralbrigham.org%2A2Fcomplianceline__%2A3B%2A21%2A21CvMGjuU%2A21rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqYCZdtugA%2A24__%3BJSUlJSUlJSUlJSUlJSU%21%21CvMGjuU%21svx96Ib2c330QFwERkEsUhvnuW-cpdIGoJ7nEcG-CHckmJmYryQX_IVA8MoigQi51SaV1w%24> 
.



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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  <https://secure-web.cisco.com/1Hl2OQ1TnkhUfQeNDJbZrNtYv2aKIlDm_KbiYjf5iFquh-cSZGLXw5uIkFfqyMWdwCTIFrboMKoG5TDhWSzTLB32Qkvriy5tYDqiRAu41Pg8wzDljwMNiLi1Bq_yyOWufPFs6jpCPggcFYDi2W4jw4PfKFcxJYH7giVcXYWDgACV7OnanLUBAZh-sy7t1FdPqBB5A7oYVm9tNB5Eq1sBNvxNvbajR1nJFx3IX6vEuM-DYpPffJ67XIIs4PjNJ1UJj_14uLatJvKimi-foTJYeRj7zDhxE_Op_B0GEvLCOFveGmjrN5_xV4pZAS0ouhVs_AqNkwi6kRSSJLfihWofNyw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1DtsOLrfHgs9pfoB1LA-ucKBR0aGaYAyMKLJjaa85w86y5sEPlZtnVX1EIlHpXDQc2uvEuQGrKxZOSy081WkjTkKvZg86NqXXg7Muw6EhgsY78oPlfKD9nJyfLPdkG7ZCp3Fl2MmePGOU-epDW51Yu1YR98-UElC_rq1vsVzsv2UzvyoEq01KmfOK_y_Tv7XTRK3dnohRKyB9YMvNXMhWKFZCsrwsK2v-W3i1hIhUPNGXG-PNo2zh4uR2nu7YfrJ6xrb6qHCHcxdhKt1tx4IIJqln-0eNprVkLN0CNIt8zNLcgfjMoHsFVO0eaXVVuZVR%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2F%2A2Fmail.nmr.mgh.harvard.edu%2A2Fmailman%2A2Flistinfo%2A2Ffreesurfer__%2A3B%2A21%2A21CvMGjuU%2A21pUZtmg2d8JM9mwaw_QLOOo6dBRiTNqvkHVbUtnVB9LT4nQ4KjZxvkdtizpgGohJGqdztqA%2A24__%3BJSUlJSUlJSUlJSUlJSUlJQ%21%21CvMGjuU%21svx96Ib2c330QFwERkEsUhvnuW-cpdIGoJ7nEcG-CHckmJmYryQX_IVA8MoigQiFFQTc7A%24>



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