External Email - Use Caution        

Hi Yujing, sure thing. Thanks for taking a look. 

rawavg.mgz
Volume information for rawavg.mgz
          type: MGH
    dimensions: 208 x 300 x 320
   voxel sizes: 0.800001, 0.800000, 0.800000
          type: SHORT (4)
           fov: 256.000
           dof: 1
        xstart: -83.2, xend: 83.2
        ystart: -120.0, yend: 120.0
        zstart: -128.0, zend: 128.0
            TR: 2500.00 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 =   0.9972, y_r =   0.0478, z_r =   0.0572, c_r =     4.2108
              : x_a =  -0.0268, y_a =   0.9456, z_a =  -0.3241, c_a =    13.0358
              : x_s =  -0.0696, y_s =   0.3217, z_s =   0.9443, c_s =   -19.3591

talairach xfm : 
Orientation   : RAS
Primary Slice Direction: axial

voxel to ras transform:
                0.7978   0.0383   0.0457   -91.8157
               -0.0214   0.7565  -0.2593   -56.7298
               -0.0556   0.2573   0.7554  -173.0404
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant 0.512001

ras to voxel transform:
                1.2465  -0.0335  -0.0869    97.5046
                0.0598   1.1821   0.4021   142.1226
                0.0714  -0.4051   1.1804   187.8310
                0.0000   0.0000   0.0000     1.0000


orig.mgz
Volume information for rawavg.mgz
          type: MGH
    dimensions: 208 x 300 x 320
   voxel sizes: 0.800001, 0.800000, 0.800000
          type: SHORT (4)
           fov: 256.000
           dof: 1
        xstart: -83.2, xend: 83.2
        ystart: -120.0, yend: 120.0
        zstart: -128.0, zend: 128.0
            TR: 2500.00 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 =   0.9972, y_r =   0.0478, z_r =   0.0572, c_r =     4.2108
              : x_a =  -0.0268, y_a =   0.9456, z_a =  -0.3241, c_a =    13.0358
              : x_s =  -0.0696, y_s =   0.3217, z_s =   0.9443, c_s =   -19.3591

talairach xfm : 
Orientation   : RAS
Primary Slice Direction: axial

voxel to ras transform:
                0.7978   0.0383   0.0457   -91.8157
               -0.0214   0.7565  -0.2593   -56.7298
               -0.0556   0.2573   0.7554  -173.0404
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant 0.512001

ras to voxel transform:
                1.2465  -0.0335  -0.0869    97.5046
                0.0598   1.1821   0.4021   142.1226
                0.0714  -0.4051   1.1804   187.8310
                0.0000   0.0000   0.0000     1.0000


nu.mgz
Volume information for nu.mgz
          type: MGH
    dimensions: 256 x 256 x 256
   voxel sizes: 1.000000, 1.000000, 1.000000
          type: UCHAR (0)
           fov: 256.000
           dof: 1
        xstart: -128.0, xend: 128.0
        ystart: -128.0, yend: 128.0
        zstart: -128.0, zend: 128.0
            TR: 2500.00 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 =     4.2108
              : x_a =   0.0000, y_a =  -0.0000, z_a =   1.0000, c_a =    13.0358
              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =   -19.3591

talairach xfm : /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer_failed/HCA6429272_V1_MR/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.0000  -0.0000   0.0000   132.2108
                0.0000  -0.0000   1.0000  -114.9642
                0.0000  -1.0000   0.0000   108.6409
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
               -1.0000   0.0000   0.0000   132.2108
                0.0000   0.0000  -1.0000   108.6409
                0.0000   1.0000  -0.0000   114.9643
               -0.0000  -0.0000  -0.0000     1.0000

T1.mgz?
Volume information for T1.mgz
          type: MGH
    dimensions: 256 x 256 x 256
   voxel sizes: 1.000000, 1.000000, 1.000000
          type: UCHAR (0)
           fov: 256.000
           dof: 1
        xstart: -128.0, xend: 128.0
        ystart: -128.0, yend: 128.0
        zstart: -128.0, zend: 128.0
            TR: 2500.00 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 =     4.2108
              : x_a =   0.0000, y_a =  -0.0000, z_a =   1.0000, c_a =    13.0358
              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =   -19.3591

talairach xfm : /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer_failed/HCA6429272_V1_MR/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.0000  -0.0000   0.0000   132.2108
                0.0000  -0.0000   1.0000  -114.9642
                0.0000  -1.0000   0.0000   108.6409
                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:
               -1.0000   0.0000   0.0000   132.2108
                0.0000   0.0000  -1.0000   108.6409
                0.0000   1.0000  -0.0000   114.9643
               -0.0000  -0.0000  -0.0000     1.0000

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu>
Sent: Wednesday, July 12, 2023 12:16 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Freesurfer Digest, Vol 233, Issue 12
 
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When replying, please edit your Subject line so it is more specific
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Today's Topics:

   1. Re: FreeSurfer 6 Error On Macbook M2 (fsbuild)
   2. Issue with FS7.4.1 (Ruifeng Dong)
   3. Matrix setup to examine group effect between three groups,
      one covariate (age) as nuisance variable (Gavette, Levi William)
   4. Re: Matrix setup to examine group effect between three
      groups, one covariate (age) as nuisance variable (Huang, Yujing)
   5. Re: Issue with FS7.4.1 (Huang, Yujing)
   6. Re: Indices out of bounds error during mri_watershed
      (Huang, Yujing)


----------------------------------------------------------------------

Message: 1
Date: Wed, 12 Jul 2023 15:57:21 +0200
From: fsbuild <fsbuild@contbay.com>
Subject: Re: [Freesurfer] FreeSurfer 6 Error On Macbook M2
To: freesurfer@nmr.mgh.harvard.edu
Cc: thuvaragan.prathifkumar@sri.utoronto.ca
Message-ID: <c47171311e8871740213347438567e50@trashmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       



The graphics packages used in Freeview have changed since the Freesurfer
 6 release, and also how they and the other Intel binaries are compiled for current
versions of MacOS. &nbsp; So a run time error, e.g., segfault, could occur when running under Rosetta on a silicon Mac.

Please try one of the current MacOS Freesurfer 7 releases from the download page,
  surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads
 
- R.




On 7/12/23 08:35, Prathifkumar, Thuvaragan (thuvaragan.prathifkumar@sri.utoronto.ca) wrote:







  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;

 
Hello,



I recently installed Free Surfer 6, and was following this guide:&nbsp;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1NRP4tsM45lW3UFB3Jf_X6qXB5GUcDVNjcJDXPLcS2Shw2L-nOknee2bklELFhm3yl9E7Rg_e1a6Z_SQ2ZfTnwuQEKG5-KnkPaZcBauyjIwEOwRPMYqb8HYwMLBSgrsvfhb0GZp7WdPb75RgJdnnym7zlQQfS4S3YzdfJ0fgVTeHKHrhxNgPSaGawnn6Sh52Pg1ABE8N_OPg4P_vFqD7hjK-RxKVLT8Jib-xqRRcD3Jidq9IG95oj8STTmA080TSMeRYUyj01iX_iV4yIxwEinr-eAfaM7UrQ73Zw4byptTk6RqKYMulRZOkN3PhQvrcEfKaxS0YgIqgq9Tojw-7x5A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel6downloads



I got till Example 3, and Example 3 works perfectly. As attached as an image in this email.&nbsp;



For some reason, in Example 4, to open the GUI (freeview) based on the&nbsp;fully
 recon-ed subject bert in Example 3, I get an error and I'm not sure
why. Why does that happen? Is it due to compatibility issues with the
apple silicon chip? The error message
 is attached as an image in this email as well.



Any help is appreciated. Thank you.
 

  This
e-mail is intended only for the named recipient(s) and may contain
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------------------------------

Message: 2
Date: Wed, 12 Jul 2023 11:19:05 -0400
From: Ruifeng Dong <ruifeng14@gmail.com>
Subject: [Freesurfer] Issue with FS7.4.1
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CACPKmtm7rfa=ZVKmcdAVvmGBJ5Rp+GoMN13D1dX2DQz0AwbuPQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi Freesurfers,

I am running the new Freesurfer 7.4.1 on Ubuntu 22.04, but ran into the
following error. I tested the same data using FS 6.0.0 and it worked fine.
The command I am using is recon-all -3T -all. Thanks.

mri_label2vol --defects
/qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/surf/lh.orig.nofix
/qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/surf/lh.defect_labels
/qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/mri/orig.mgz
1000 0
/qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/mri/surface.defects.mgz
/qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/label/lh.nofix.cortex.label
*** buffer overflow detected ***: terminated
Abort (core dumped)
ERROR:
Command exited with non-zero status 1
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------------------------------

Message: 3
Date: Wed, 12 Jul 2023 15:21:07 +0000
From: "Gavette, Levi William" <LGAVETTE@mgh.harvard.edu>
Subject: [Freesurfer] Matrix setup to examine group effect between
        three groups, one covariate (age) as nuisance variable
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BYAPR04MB4182D75D9D22BE39FA718D5D8A36A@BYAPR04MB4182.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="windows-1252"

        External Email - Use Caution       

Hello FreeSurfer community,

I am looking to perform a GLM between three groups with the single covariate of age as the nuisance variable. I am wondering how to set up my matrix design so that the output will be the group difference with age removed? Any help is really appreciated.

Thanks,
? Levi
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------------------------------

Message: 4
Date: Wed, 12 Jul 2023 15:48:55 +0000
From: "Huang, Yujing" <YHUANG43@mgh.harvard.edu>
Subject: Re: [Freesurfer] Matrix setup to examine group effect between
        three groups, one covariate (age) as nuisance variable
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <MN2PR04MB5982A61240CDB429FFC62A349D36A@MN2PR04MB5982.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

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Hi Levi,

Here are examples of FreeSurfer Group Descriptor (FSGD) files and contrasts for testing various hypotheses
https://secure-web.cisco.com/1VPM48Rx8n-O3pwPy_s2hzAZX2WUWqjFwuTdIGDmxPsyOhDswK-1YgYN4BVCDfqODZwxD2r6VS0aanhyDE2HgETFvzBc0RNbUJSVdjf_ft7sxdgQAsSsfPizaJUCtY1Yud59Z7Hm2rn7-H_QiMgi-SpyZKZriX7cJfAzcLmBfNOxZsIOEEnaXjxDUooiub2Xp7tKr3jqfsdeVrWkQixhGLed2uitNYpilHDzWPoE9PKIrtTkHtkjK0lROJ4-5-nSsPwIXZgwAhgf3DeDBknRm0w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Gavette, Levi William
Sent: Wednesday, July 12, 2023 11:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Matrix setup to examine group effect between three groups, one covariate (age) as nuisance variable


        External Email - Use Caution
Hello FreeSurfer community,

I am looking to perform a GLM between three groups with the single covariate of age as the nuisance variable. I am wondering how to set up my matrix design so that the output will be the group difference with age removed? Any help is really appreciated.

Thanks,
- Levi
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------------------------------

Message: 5
Date: Wed, 12 Jul 2023 15:54:12 +0000
From: "Huang, Yujing" <YHUANG43@mgh.harvard.edu>
Subject: Re: [Freesurfer] Issue with FS7.4.1
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <MN2PR04MB59821A68AA733D479670506D9D36A@MN2PR04MB5982.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Can you attach your recon-all.log from both FS 6.0.0 and FS 7.4.1?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ruifeng Dong
Sent: Wednesday, July 12, 2023 11:19 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Issue with FS7.4.1


        External Email - Use Caution
Hi Freesurfers,

I am running the new Freesurfer 7.4.1 on Ubuntu 22.04, but ran into the following error. I tested the same data using FS 6.0.0 and it worked fine. The command I am using is recon-all -3T -all. Thanks.

mri_label2vol --defects /qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/surf/lh.orig.nofix /qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/surf/lh.defect_labels /qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/mri/orig.mgz 1000 0 /qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/mri/surface.defects.mgz /qmi08_raid/ruifeng/work_with_project_data_T1/clinical_3dresampled-2-RAI/alltogether/
 uncompressed/testSub_10_0_h/00_test_dicom/cont_10_0_PRISMA_dicom/rerun_FS741/mriconvert2nii_ASR2PSR_reorientimage3d/label/lh.nofix.cortex.label
*** buffer overflow detected ***: terminated
Abort (core dumped)
ERROR:
Command exited with non-zero status 1
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Message: 6
Date: Wed, 12 Jul 2023 16:16:03 +0000
From: "Huang, Yujing" <YHUANG43@mgh.harvard.edu>
Subject: Re: [Freesurfer] Indices out of bounds error during
        mri_watershed
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <MN2PR04MB5982D64D8D0020E7178C4F559D36A@MN2PR04MB5982.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="utf-8"

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Hi John,

I don?t know what went wrong. But can you run mri_info for the following images in your subject mri/ directory ? rawavg.mgz, orig.mgz, nu.mgz, T1.mgz?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Jacoby, John
Sent: Tuesday, July 11, 2023 11:36 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Indices out of bounds error during mri_watershed


        External Email - Use Caution
Hi all, I am running into an error running recon-all and I can't figure out what's going on just from the error messages. I'm hoping someone here can help.

I'm using FreeSurfer 7.2 and this is the command I'm trying to run: recon-all -subjid HCA6429272_V1_MR -i /autofs/space/yoda_002/users/datasets/HCA/data/as_downloaded/HCA6429272_V1_MR/scans/110-T1w/resources/NIFTI/files/HCA6429272_V1_MR_T1w_MPR_vNav_4e_RMS.nii.gz -all

build stamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b

operating system:
?cat /etc/centos-release
Rocky Linux release 8.8 (Green Obsidian)

I've run about 1200 recons in the last few weeks from the same dataset using analogous commands for the other T1s, but this is the only one that failed. The T1 isn't great quality, but not terrible either (screenshot below). The error happens during the watershed step: "mri_watershed Error: indices out of bounds". I've attached the log and error file from the recon.

Thanks for any help you can provide.

Best,
John

Screenshot of the input T1:
[cid:image001.png@01D9B4BA.A01A3890]
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End of Freesurfer Digest, Vol 233, Issue 12
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