External Email - Use Caution

Hi Douglas,

thanks so much for you reply. Yes, I checked the template and it looks good. The orientation was in LAS originally then I did the Left-Right Reversal by using the command "mri_convert --in_orientation RIA". Before or after the reversal, I got the same error message. Here I attached the template, could you please have a look in case of any clue? Thank you so much!

Best, Chen

----- Original Message -----

From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDU To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, 29 May, 2024 15:26:25 Subject: Re: [Freesurfer] Recon-all for a common template

sounds like something is wrong with the image. Did you look at ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a head?

On 5/28/2024 6:07 AM, Chen Yang wrote:

...

     External Email - Use Caution

Hi everyone,

I tried to run the reconstruction with the command line: recon-all -i ANTS_QS_template_MNI.nii.gz -subject CGBT -all

then I got the error message: talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux

And this is the error message in the talairach_avi.log: imgrege: no voxels in register ERROR: 'imgreg_4dfp /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305 /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted

Does anyone know how to solve this problem? Thanks so much!

Best, Chen ----- Original Message -----

...

From: "Chen Yang" yangc@cbs.mpg.de To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, 20 May, 2024 13:59:13 Subject: [Freesurfer] Recon-all for a common template

...

External Email - Use Caution

Dear Freesurfer Developers,

my data is from 50 preschoolers and I created my own group template from these kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti file (see attached). Then we'd like to process this group template in Freesurfer to reconstruct the cortical surfaces as the individual brain images. My question is, how can i do the recon-all with the template? Because I only have this template file I feel I don't have enough input files(?).

Thanks in advance!

Best regards, Chen

-- Chen Yang

PhD Student Independent Research Group 'Milestones of Early Childhood Development' Max Planck Institute for Human Cognitive and Brain Sciences

Email:yangc@cbs.mpg.de

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External Email - Use Caution

Dear Douglas,

we had checked the template and compared it to the standard template (MNI152_T1_1mm_brain.nii.gz). Our template looks normal on orientation and we don't see anything unusual (please see screenshot). The only difference is our head is smaller (probably because it's children data).

Therefore, I have two questions: 1. Do you think that the head size could be the reason for the reconstruction failure? I don't think it should be, because the reconstruction of individual data has been going very well. 2. After creating our template, we also used the commands below to fill holes and normalize. The data type of output file is float, but we find that the standard template has a data type of short. Do you think the data type might influence the reconstruction? In fact, we also tried to change the datatype to 'short', but there were obvious problems with the output image.

# Fill holes and normalize fslmaths ANTS_43Kids_template_rigid2MNI.nii.gz -bin -fillh -mul ANTS_43Kids_template_rigid2MNI.nii.gz -div $(fslstats ANTS_43Kids_template_rigid2MNI.nii.gz -P 100) -range ANTS_QS_template_MNIS.nii.gz -odt float

Thank you so much!

Best regards, Chen

----- Original Message -----

From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDU To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, 3 June, 2024 18:42:14 Subject: Re: [Freesurfer] Recon-all for a common template

Why did you do an lr reversal if it looked good? And when you say it looks good, what do you mean. One thing to double check is that the orientation looks ok. Load it in freeview. Up at the top you will see little brain images in coronal, sagital, and axial. When you click on one of those, the brain in the main image should become coronal, sag, or axial. If this does not happen, then something is wrong.

On 5/29/2024 10:47 AM, Chen Yang wrote:

...

     External Email - Use Caution

Hi Douglas,

thanks so much for you reply. Yes, I checked the template and it looks good. The orientation was in LAS originally then I did the Left-Right Reversal by using the command "mri_convert --in_orientation RIA". Before or after the reversal, I got the same error message. Here I attached the template, could you please have a look in case of any clue? Thank you so much!

Best, Chen

----- Original Message -----

...

From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDU To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, 29 May, 2024 15:26:25 Subject: Re: [Freesurfer] Recon-all for a common template sounds like something is wrong with the image. Did you look at ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a head?

On 5/28/2024 6:07 AM, Chen Yang wrote:

...

      External Email - Use Caution

Hi everyone,

I tried to run the reconstruction with the command line: recon-all -i ANTS_QS_template_MNI.nii.gz -subject CGBT -all

then I got the error message: talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux

And this is the error message in the talairach_avi.log: imgrege: no voxels in register ERROR: 'imgreg_4dfp /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305 /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted

Does anyone know how to solve this problem? Thanks so much!

Best, Chen ----- Original Message -----

...

From: "Chen Yang" yangc@cbs.mpg.de To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, 20 May, 2024 13:59:13 Subject: [Freesurfer] Recon-all for a common template External Email - Use Caution

Dear Freesurfer Developers,

my data is from 50 preschoolers and I created my own group template from these kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti file (see attached). Then we'd like to process this group template in Freesurfer to reconstruct the cortical surfaces as the individual brain images. My question is, how can i do the recon-all with the template? Because I only have this template file I feel I don't have enough input files(?).

Thanks in advance!

Best regards, Chen

-- Chen Yang

PhD Student Independent Research Group 'Milestones of Early Childhood Development' Max Planck Institute for Human Cognitive and Brain Sciences

Email:yangc@cbs.mpg.de

---

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And also don't expect the cortical surface to be very good once you get ont

On 6/24/2024 8:08 AM, Chen Yang wrote:

     External Email - Use Caution

Dear Douglas,

we had checked the template and compared it to the standard template (MNI152_T1_1mm_brain.nii.gz). Our template looks normal on orientation and we don't see anything unusual (please see screenshot). The only difference is our head is smaller (probably because it's children data).

Therefore, I have two questions:

1. Do you think that the head size could be the reason for the reconstruction failure? I don't think it should be, because the reconstruction of individual data has been going very well.
2. After creating our template, we also used the commands below to fill holes and normalize. The data type of output file is float, but we find that the standard template has a data type of short. Do you think the data type might influence the reconstruction? In fact, we also tried to change the datatype to 'short', but there were obvious problems with the output image.

# Fill holes and normalize fslmaths ANTS_43Kids_template_rigid2MNI.nii.gz -bin -fillh -mul ANTS_43Kids_template_rigid2MNI.nii.gz -div $(fslstats ANTS_43Kids_template_rigid2MNI.nii.gz -P 100) -range ANTS_QS_template_MNIS.nii.gz -odt float

Thank you so much!

Best regards, Chen

----- Original Message -----

...

From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDU To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, 3 June, 2024 18:42:14 Subject: Re: [Freesurfer] Recon-all for a common template Why did you do an lr reversal if it looked good? And when you say it looks good, what do you mean. One thing to double check is that the orientation looks ok. Load it in freeview. Up at the top you will see little brain images in coronal, sagital, and axial. When you click on one of those, the brain in the main image should become coronal, sag, or axial. If this does not happen, then something is wrong.

On 5/29/2024 10:47 AM, Chen Yang wrote:

...

      External Email - Use Caution

Hi Douglas,

thanks so much for you reply. Yes, I checked the template and it looks good. The orientation was in LAS originally then I did the Left-Right Reversal by using the command "mri_convert --in_orientation RIA". Before or after the reversal, I got the same error message. Here I attached the template, could you please have a look in case of any clue? Thank you so much!

Best, Chen

----- Original Message -----

...

From: "Douglas N. Greve" dgreve@MGH.HARVARD.EDU To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, 29 May, 2024 15:26:25 Subject: Re: [Freesurfer] Recon-all for a common template sounds like something is wrong with the image. Did you look at ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a head?

On 5/28/2024 6:07 AM, Chen Yang wrote:

...

       External Email - Use Caution

Hi everyone,

I tried to run the reconstruction with the command line: recon-all -i ANTS_QS_template_MNI.nii.gz -subject CGBT -all

then I got the error message: talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 GNU/Linux

And this is the error message in the talairach_avi.log: imgrege: no voxels in register ERROR: 'imgreg_4dfp /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305 /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted

Does anyone know how to solve this problem? Thanks so much!

Best, Chen ----- Original Message -----

...

From: "Chen Yang" yangc@cbs.mpg.de To: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Monday, 20 May, 2024 13:59:13 Subject: [Freesurfer] Recon-all for a common template External Email - Use Caution

Dear Freesurfer Developers,

my data is from 50 preschoolers and I created my own group template from these kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti file (see attached). Then we'd like to process this group template in Freesurfer to reconstruct the cortical surfaces as the individual brain images. My question is, how can i do the recon-all with the template? Because I only have this template file I feel I don't have enough input files(?).

Thanks in advance!

Best regards, Chen

-- Chen Yang

PhD Student Independent Research Group 'Milestones of Early Childhood Development' Max Planck Institute for Human Cognitive and Brain Sciences

Email:yangc@cbs.mpg.de

---

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