External Email - Use Caution
group cc'd - thanks for the reminder.
My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid 1kl5011 -all
Is there an efficient way to handle the flipped L-R or should I mri_convert the nifti and then do recon-all?
(Assuming that I can't just switch lh_ and rh_ in the aparcstats2table)
Ellen
On 9/15/2020 6:51 PM, Fischl, Bruce wrote:
Hi Ellen
Can you cc the list so that others can respond? What was your input data? Did you not have dicoms?
Cheers Bruce
-----Original Message----- From: Ellen Ji ellen.ji@bli.uzh.ch Sent: Tuesday, September 15, 2020 12:38 PM To: Fischl, Bruce BFISCHL@mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
External Email - Use CautionHi Bruce,
Unfortunately I just found the fiducial and realised that the L-R is incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table or do I need to run mri_convert on the nifti and run recon-all from the beginning again?
Thanks,
Ellen
On 9/15/2020 5:44 PM, Fischl, Bruce wrote:
And what is your input to recon-all? If it is dicom you should be pretty confident that we will get it correct
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 10:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
How are you checking the LR orientation?
On 9/15/2020 4:10 AM, Ellen Ji wrote:
External Email - Use CautionDear experts,
I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts.
For example, in our dataset, the lateral ventricle volume is on average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical.
In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are.
Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake!
I found this website on Left-right reversal, and it seems relevant to my issue, but I'm not fully understanding what this means (how would bias occur during segmentation?) - https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
Many thanks for your input, Ellen
Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen.ji@bli.uzh.ch homanlab.github.io/ellen/
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
First we have to determine whether it is really LR flipped or not. Do you still have the dicoms? If so, can you convert to mgz using mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see if the fiducial has changed sides relative to the nifti
On 9/15/2020 12:58 PM, Ellen Ji wrote:
External Email - Use Cautiongroup cc'd - thanks for the reminder.
My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid 1kl5011 -all
Is there an efficient way to handle the flipped L-R or should I mri_convert the nifti and then do recon-all?
(Assuming that I can't just switch lh_ and rh_ in the aparcstats2table)
Ellen
On 9/15/2020 6:51 PM, Fischl, Bruce wrote:
Hi Ellen
Can you cc the list so that others can respond? What was your input data? Did you not have dicoms?
Cheers Bruce
-----Original Message----- From: Ellen Ji ellen.ji@bli.uzh.ch Sent: Tuesday, September 15, 2020 12:38 PM To: Fischl, Bruce BFISCHL@mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
External Email - Use CautionHi Bruce,
Unfortunately I just found the fiducial and realised that the L-R is incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table or do I need to run mri_convert on the nifti and run recon-all from the beginning again?
Thanks,
Ellen
On 9/15/2020 5:44 PM, Fischl, Bruce wrote:
And what is your input to recon-all? If it is dicom you should be pretty confident that we will get it correct
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 10:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
How are you checking the LR orientation?
On 9/15/2020 4:10 AM, Ellen Ji wrote:
External Email - Use CautionDear experts,
I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts.
For example, in our dataset, the lateral ventricle volume is on average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical.
In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are.
Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake!
I found this website on Left-right reversal, and it seems relevant to my issue, but I'm not fully understanding what this means (how would bias occur during segmentation?) - https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
Many thanks for your input, Ellen
Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen.ji@bli.uzh.ch homanlab.github.io/ellen/
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Douglas,
I found the dicoms and confirm that the fiducial is on the opposite side relative to the nifti. Additionally, the PI just informed me that the fiducial was placed on the right side of the head and the nifti indicates left. I will enquire as to what method was used to convert from dicom as that appears to be the issue.
I already performed recon-all and aparcstats2table on the flipped nifti. Could you please advise if there is there an efficient way to deal with this or if I should start from the beginning?
Many thanks,
Ellen
On 9/15/2020 7:19 PM, Douglas N. Greve wrote:
First we have to determine whether it is really LR flipped or not. Do you still have the dicoms? If so, can you convert to mgz using mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see if the fiducial has changed sides relative to the nifti. That is a fiducial. And do you know what side the fiducial was placed on? mri_info does not help. How did you convert from dicom?
ps. Please make sure to post to the list and not to us personally
On 9/15/2020 12:58 PM, Ellen Ji wrote:
External Email - Use Cautiongroup cc'd - thanks for the reminder.
My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid 1kl5011 -all
Is there an efficient way to handle the flipped L-R or should I mri_convert the nifti and then do recon-all?
(Assuming that I can't just switch lh_ and rh_ in the aparcstats2table)
Ellen
On 9/15/2020 6:51 PM, Fischl, Bruce wrote:
Hi Ellen
Can you cc the list so that others can respond? What was your input data? Did you not have dicoms?
Cheers Bruce
-----Original Message----- From: Ellen Ji ellen.ji@bli.uzh.ch Sent: Tuesday, September 15, 2020 12:38 PM To: Fischl, Bruce BFISCHL@mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
External Email - Use CautionHi Bruce,
Unfortunately I just found the fiducial and realised that the L-R is incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table or do I need to run mri_convert on the nifti and run recon-all from the beginning again?
Thanks,
Ellen
On 9/15/2020 5:44 PM, Fischl, Bruce wrote:
And what is your input to recon-all? If it is dicom you should be pretty confident that we will get it correct
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 10:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
How are you checking the LR orientation?
On 9/15/2020 4:10 AM, Ellen Ji wrote:
External Email - Use CautionDear experts,
I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts.
For example, in our dataset, the lateral ventricle volume is on average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical.
In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are.
Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake!
I found this website on Left-right reversal, and it seems relevant to my issue, but I'm not fully understanding what this means (how would bias occur during segmentation?) - https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
Many thanks for your input, Ellen
Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen.ji@bli.uzh.ch homanlab.github.io/ellen/
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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
Hi Ellen
Sorry to say it, but you really should start over. Not everything in the brain is bilaterally symmetric so processing and flipping won't be the same as flipping then processing.
Cheers Bruce
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ellen Ji Sent: Wednesday, September 16, 2020 3:41 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
External Email - Use Caution
Hi Douglas,
I found the dicoms and confirm that the fiducial is on the opposite side relative to the nifti. Additionally, the PI just informed me that the fiducial was placed on the right side of the head and the nifti indicates left. I will enquire as to what method was used to convert from dicom as that appears to be the issue.
I already performed recon-all and aparcstats2table on the flipped nifti. Could you please advise if there is there an efficient way to deal with this or if I should start from the beginning?
Many thanks,
Ellen
On 9/15/2020 7:19 PM, Douglas N. Greve wrote:
First we have to determine whether it is really LR flipped or not. Do you still have the dicoms? If so, can you convert to mgz using mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see if the fiducial has changed sides relative to the nifti. That is a fiducial. And do you know what side the fiducial was placed on? mri_info does not help. How did you convert from dicom?
ps. Please make sure to post to the list and not to us personally
On 9/15/2020 12:58 PM, Ellen Ji wrote:
External Email - Use Cautiongroup cc'd - thanks for the reminder.
My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid 1kl5011 -all
Is there an efficient way to handle the flipped L-R or should I mri_convert the nifti and then do recon-all?
(Assuming that I can't just switch lh_ and rh_ in the aparcstats2table)
Ellen
On 9/15/2020 6:51 PM, Fischl, Bruce wrote:
Hi Ellen
Can you cc the list so that others can respond? What was your input data? Did you not have dicoms?
Cheers Bruce
-----Original Message----- From: Ellen Ji ellen.ji@bli.uzh.ch Sent: Tuesday, September 15, 2020 12:38 PM To: Fischl, Bruce BFISCHL@mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
External Email - Use CautionHi Bruce,
Unfortunately I just found the fiducial and realised that the L-R is incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table or do I need to run mri_convert on the nifti and run recon-all from the beginning again?
Thanks,
Ellen
On 9/15/2020 5:44 PM, Fischl, Bruce wrote:
And what is your input to recon-all? If it is dicom you should be pretty confident that we will get it correct
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 10:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
How are you checking the LR orientation?
On 9/15/2020 4:10 AM, Ellen Ji wrote:
External Email - Use CautionDear experts,
I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts.
For example, in our dataset, the lateral ventricle volume is on average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical.
In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are.
Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake!
I found this website on Left-right reversal, and it seems relevant to my issue, but I'm not fully understanding what this means (how would bias occur during segmentation?) - https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
Many thanks for your input, Ellen
Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen.ji@bli.uzh.ch homanlab.github.io/ellen/
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks for your reply Bruce. Could you confirm if I can run mri_convert on the incorrectly flipped niftis to appropriately correct them? (https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal)
Something like:
mri_convert --in_orientation LIA subject1.nii subject1_corrected.nii
best,
Ellen
On 9/16/2020 4:47 PM, Fischl, Bruce wrote:
Hi Ellen
Sorry to say it, but you really should start over. Not everything in the brain is bilaterally symmetric so processing and flipping won't be the same as flipping then processing.
Cheers Bruce
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ellen Ji Sent: Wednesday, September 16, 2020 3:41 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
External Email - Use CautionHi Douglas,
I found the dicoms and confirm that the fiducial is on the opposite side relative to the nifti. Additionally, the PI just informed me that the fiducial was placed on the right side of the head and the nifti indicates left. I will enquire as to what method was used to convert from dicom as that appears to be the issue.
I already performed recon-all and aparcstats2table on the flipped nifti. Could you please advise if there is there an efficient way to deal with this or if I should start from the beginning?
Many thanks,
Ellen
On 9/15/2020 7:19 PM, Douglas N. Greve wrote:
First we have to determine whether it is really LR flipped or not. Do you still have the dicoms? If so, can you convert to mgz using mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see if the fiducial has changed sides relative to the nifti. That is a fiducial. And do you know what side the fiducial was placed on? mri_info does not help. How did you convert from dicom?
ps. Please make sure to post to the list and not to us personally
On 9/15/2020 12:58 PM, Ellen Ji wrote:
External Email - Use Cautiongroup cc'd - thanks for the reminder.
My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid 1kl5011 -all
Is there an efficient way to handle the flipped L-R or should I mri_convert the nifti and then do recon-all?
(Assuming that I can't just switch lh_ and rh_ in the aparcstats2table)
Ellen
On 9/15/2020 6:51 PM, Fischl, Bruce wrote:
Hi Ellen
Can you cc the list so that others can respond? What was your input data? Did you not have dicoms?
Cheers Bruce
-----Original Message----- From: Ellen Ji ellen.ji@bli.uzh.ch Sent: Tuesday, September 15, 2020 12:38 PM To: Fischl, Bruce BFISCHL@mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
External Email - Use CautionHi Bruce,
Unfortunately I just found the fiducial and realised that the L-R is incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table or do I need to run mri_convert on the nifti and run recon-all from the beginning again?
Thanks,
Ellen
On 9/15/2020 5:44 PM, Fischl, Bruce wrote:
And what is your input to recon-all? If it is dicom you should be pretty confident that we will get it correct
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 10:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
How are you checking the LR orientation?
On 9/15/2020 4:10 AM, Ellen Ji wrote:
External Email - Use CautionDear experts,
I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts.
For example, in our dataset, the lateral ventricle volume is on average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical.
In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are.
Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake!
I found this website on Left-right reversal, and it seems relevant to my issue, but I'm not fully understanding what this means (how would bias occur during segmentation?) - https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
Many thanks for your input, Ellen
Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen.ji@bli.uzh.ch homanlab.github.io/ellen/
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 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
I think so, but I defer to Doug
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Ellen Ji Sent: Wednesday, September 16, 2020 11:05 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip?
External Email - Use Caution
Thanks for your reply Bruce. Could you confirm if I can run mri_convert on the incorrectly flipped niftis to appropriately correct them? (https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal)
Something like:
mri_convert --in_orientation LIA subject1.nii subject1_corrected.nii
best,
Ellen
On 9/16/2020 4:47 PM, Fischl, Bruce wrote:
Hi Ellen
Sorry to say it, but you really should start over. Not everything in the brain is bilaterally symmetric so processing and flipping won't be the same as flipping then processing.
Cheers
Bruce
-----Original Message-----
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 Ellen Ji
Sent: Wednesday, September 16, 2020 3:41 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] left-right flip?
External Email - Use Caution
Hi Douglas,
I found the dicoms and confirm that the fiducial is on the opposite side relative to the nifti. Additionally, the PI just informed me that the fiducial was placed on the right side of the head and the nifti indicates left. I will enquire as to what method was used to convert from dicom as that appears to be the issue.
I already performed recon-all and aparcstats2table on the flipped nifti.
Could you please advise if there is there an efficient way to deal with this or if I should start from the beginning?
Many thanks,
Ellen
On 9/15/2020 7:19 PM, Douglas N. Greve wrote:
First we have to determine whether it is really LR flipped or not. Do
you still have the dicoms? If so, can you convert to mgz using
mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see
if the fiducial has changed sides relative to the nifti.
That is a fiducial. And do you know what side the fiducial was placed
on? mri_info does not help. How did you convert from dicom?
ps. Please make sure to post to the list and not to us personally
On 9/15/2020 12:58 PM, Ellen Ji wrote:
External Email - Use Caution
group cc'd - thanks for the reminder.
My input data was the niftis. Example: recon-all -i 1kl5011.nii
-subjid
1kl5011 -all
Is there an efficient way to handle the flipped L-R or should I
mri_convert the nifti and then do recon-all?
(Assuming that I can't just switch lh_ and rh_ in the
aparcstats2table)
Ellen
On 9/15/2020 6:51 PM, Fischl, Bruce wrote:
Hi Ellen
Can you cc the list so that others can respond? What was your input data? Did you not have dicoms?
Cheers
Bruce
-----Original Message-----
From: Ellen Ji ellen.ji@bli.uzh.chmailto:ellen.ji@bli.uzh.ch
Sent: Tuesday, September 15, 2020 12:38 PM
To: Fischl, Bruce BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu
Subject: Re: [Freesurfer] left-right flip?
External Email - Use Caution
Hi Bruce,
Unfortunately I just found the fiducial and realised that the L-R is incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table or do I need to run mri_convert on the nifti and run recon-all from the beginning again?
Thanks,
Ellen
On 9/15/2020 5:44 PM, Fischl, Bruce wrote:
And what is your input to recon-all? If it is dicom you should be
pretty confident that we will get it correct
-----Original Message-----
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
Sent: Tuesday, September 15, 2020 10:17 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] left-right flip?
How are you checking the LR orientation?
On 9/15/2020 4:10 AM, Ellen Ji wrote:
External Email - Use Caution
Dear experts,
I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts.
For example, in our dataset, the lateral ventricle volume is on
average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical.
In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are.
Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake!
I found this website on Left-right reversal, and it seems relevant
to my issue, but I'm not fully understanding what this means (how
would bias occur during segmentation?) -
https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
Many thanks for your input,
Ellen
---
Ellen Ji, PhD
Postdoctoral Research Fellow
Psychiatric University Hospital
University of Zürich
ellen.ji@bli.uzh.chmailto:ellen.ji@bli.uzh.ch
homanlab.github.io/ellen/
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I'm sorry to hear it, but at least you figured it out. You're best option is just to convert directly from the dicoms if you have them using mri_convert, dcmunpack, or just passing a dicom file directly to recon-all as input. If you don't have access to the dicoms, you can run mri_convert inputfile.nii.gz --left-right-reverse-pix outputfile.nii.gz
On 9/16/20 12:03 PM, Fischl, Bruce wrote:
I think so, but I defer to Doug
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Ellen Ji *Sent:* Wednesday, September 16, 2020 11:05 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] left-right flip?
* External Email - Use Caution *
Thanks for your reply Bruce. Could you confirm if I can run mri_convert on the incorrectly flipped niftis to appropriately correct them? (https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal)
Something like:
mri_convert --in_orientation LIA subject1.nii subject1_corrected.nii
best,
Ellen
On 9/16/2020 4:47 PM, Fischl, Bruce wrote:
Hi Ellen Sorry to say it, but you really should start over. Not everything in the brain is bilaterally symmetric so processing and flipping won't be the same as flipping then processing. Cheers Bruce -----Original Message----- 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 Ellen Ji Sent: Wednesday, September 16, 2020 3:41 AM To:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] left-right flip? External Email - Use Caution Hi Douglas, I found the dicoms and confirm that the fiducial is on the opposite side relative to the nifti. Additionally, the PI just informed me that the fiducial was placed on the right side of the head and the nifti indicates left. I will enquire as to what method was used to convert from dicom as that appears to be the issue. I already performed recon-all and aparcstats2table on the flipped nifti. Could you please advise if there is there an efficient way to deal with this or if I should start from the beginning? Many thanks, Ellen On 9/15/2020 7:19 PM, Douglas N. Greve wrote: First we have to determine whether it is really LR flipped or not. Do you still have the dicoms? If so, can you convert to mgz using mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see if the fiducial has changed sides relative to the nifti. That is a fiducial. And do you know what side the fiducial was placed on? mri_info does not help. How did you convert from dicom? ps. Please make sure to post to the list and not to us personally On 9/15/2020 12:58 PM, Ellen Ji wrote: External Email - Use Caution group cc'd - thanks for the reminder. My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid 1kl5011 -all Is there an efficient way to handle the flipped L-R or should I mri_convert the nifti and then do recon-all? (Assuming that I can't just switch lh_ and rh_ in the aparcstats2table) Ellen On 9/15/2020 6:51 PM, Fischl, Bruce wrote: Hi Ellen Can you cc the list so that others can respond? What was your input data? Did you not have dicoms? Cheers Bruce -----Original Message----- From: Ellen Ji<ellen.ji@bli.uzh.ch> <mailto:ellen.ji@bli.uzh.ch> Sent: Tuesday, September 15, 2020 12:38 PM To: Fischl, Bruce<BFISCHL@mgh.harvard.edu> <mailto:BFISCHL@mgh.harvard.edu> Subject: Re: [Freesurfer] left-right flip? External Email - Use Caution Hi Bruce, Unfortunately I just found the fiducial and realised that the L-R is incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table or do I need to run mri_convert on the nifti and run recon-all from the beginning again? Thanks, Ellen On 9/15/2020 5:44 PM, Fischl, Bruce wrote: And what is your input to recon-all? If it is dicom you should be pretty confident that we will get it correct -----Original Message----- 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 Sent: Tuesday, September 15, 2020 10:17 AM To:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] left-right flip? How are you checking the LR orientation? On 9/15/2020 4:10 AM, Ellen Ji wrote: External Email - Use Caution Dear experts, I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts. For example, in our dataset, the lateral ventricle volume is on average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical. In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are. Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake! I found this website on Left-right reversal, and it seems relevant to my issue, but I'm not fully understanding what this means (how would bias occur during segmentation?) - https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal Many thanks for your input, Ellen --- Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen.ji@bli.uzh.ch <mailto:ellen.ji@bli.uzh.ch> homanlab.github.io/ellen/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 athttp://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks for your reply Doug. Yes, I'm thankful I figured it out with your help!
In the meantime I already tried to run mri_convert based on the mri_info --orientation information.
For instance, if mri_info --orientation yielded "LAS" for the nifti, I performed mri_convert --in_orientation RAS inputfile.nii outputfile.nii.
Would this also yield the same output as the --left-right-reverse-pix option you proposed?
Best,
Ellen
On 9/18/2020 4:54 PM, Douglas Greve wrote:
I'm sorry to hear it, but at least you figured it out. You're best option is just to convert directly from the dicoms if you have them using mri_convert, dcmunpack, or just passing a dicom file directly to recon-all as input. If you don't have access to the dicoms, you can run mri_convert inputfile.nii.gz --left-right-reverse-pix outputfile.nii.gz
On 9/16/20 12:03 PM, Fischl, Bruce wrote:
I think so, but I defer to Doug
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Ellen Ji *Sent:* Wednesday, September 16, 2020 11:05 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] left-right flip?
* External Email - Use Caution *
Thanks for your reply Bruce. Could you confirm if I can run mri_convert on the incorrectly flipped niftis to appropriately correct them? (https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal)
Something like:
mri_convert --in_orientation LIA subject1.nii subject1_corrected.nii
best,
Ellen
On 9/16/2020 4:47 PM, Fischl, Bruce wrote:
Hi Ellen Sorry to say it, but you really should start over. Not everything in the brain is bilaterally symmetric so processing and flipping won't be the same as flipping then processing. Cheers Bruce -----Original Message----- 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 Ellen Ji Sent: Wednesday, September 16, 2020 3:41 AM To:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] left-right flip? External Email - Use Caution Hi Douglas, I found the dicoms and confirm that the fiducial is on the opposite side relative to the nifti. Additionally, the PI just informed me that the fiducial was placed on the right side of the head and the nifti indicates left. I will enquire as to what method was used to convert from dicom as that appears to be the issue. I already performed recon-all and aparcstats2table on the flipped nifti. Could you please advise if there is there an efficient way to deal with this or if I should start from the beginning? Many thanks, Ellen On 9/15/2020 7:19 PM, Douglas N. Greve wrote: First we have to determine whether it is really LR flipped or not. Do you still have the dicoms? If so, can you convert to mgz using mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see if the fiducial has changed sides relative to the nifti. That is a fiducial. And do you know what side the fiducial was placed on? mri_info does not help. How did you convert from dicom? ps. Please make sure to post to the list and not to us personally On 9/15/2020 12:58 PM, Ellen Ji wrote: External Email - Use Caution group cc'd - thanks for the reminder. My input data was the niftis. Example: recon-all -i 1kl5011.nii -subjid 1kl5011 -all Is there an efficient way to handle the flipped L-R or should I mri_convert the nifti and then do recon-all? (Assuming that I can't just switch lh_ and rh_ in the aparcstats2table) Ellen On 9/15/2020 6:51 PM, Fischl, Bruce wrote: Hi Ellen Can you cc the list so that others can respond? What was your input data? Did you not have dicoms? Cheers Bruce -----Original Message----- From: Ellen Ji<ellen.ji@bli.uzh.ch> <mailto:ellen.ji@bli.uzh.ch> Sent: Tuesday, September 15, 2020 12:38 PM To: Fischl, Bruce<BFISCHL@mgh.harvard.edu> <mailto:BFISCHL@mgh.harvard.edu> Subject: Re: [Freesurfer] left-right flip? External Email - Use Caution Hi Bruce, Unfortunately I just found the fiducial and realised that the L-R is incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table or do I need to run mri_convert on the nifti and run recon-all from the beginning again? Thanks, Ellen On 9/15/2020 5:44 PM, Fischl, Bruce wrote: And what is your input to recon-all? If it is dicom you should be pretty confident that we will get it correct -----Original Message----- 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 Sent: Tuesday, September 15, 2020 10:17 AM To:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] left-right flip? How are you checking the LR orientation? On 9/15/2020 4:10 AM, Ellen Ji wrote: External Email - Use Caution Dear experts, I recently performed recon-all on a set of subjects and the output (aparcstats2table and asegstats2table) will be part of a meta-analysis of other labs' cohorts. When assessing the asymmetry index direction (relative size of left vs right hemisphere across multiple rois), our dataset shows an inversion of the mean asymmetry index in several structures compared to the other cohorts. For example, in our dataset, the lateral ventricle volume is on average larger in the right hemisphere compared to the left, while the opposite is true for all other cohorts. The same inversion of asymmetry is visible in other structures that in general are more asymmetrical. In order to check this, I went through each T1 to make sure the orientation was correct and indeed they are. Is there any possible way that there was a left-right inversion somewhere during the recon-all pipeline? I want to make sure I did everything correctly on our end and that the results are due to the biology and not a technical mistake! I found this website on Left-right reversal, and it seems relevant to my issue, but I'm not fully understanding what this means (how would bias occur during segmentation?) - https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal Many thanks for your input, Ellen --- Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen.ji@bli.uzh.ch <mailto:ellen.ji@bli.uzh.ch> homanlab.github.io/ellen/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 athttp://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Douglas Greve -
Douglas N. Greve
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Ellen Ji -
Fischl, Bruce