Re: [Freesurfer] left-right flip?

[Ellen Ji]

   External Email - Use Caution

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-boun...@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-boun...@nmr.mgh.harvard.edu  
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
  
<mailto:freesurfer-boun...@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  
<mailto:ellen...@bli.uzh.ch>

Sent: Tuesday, September 15, 2020 12:38 PM

To: Fischl, Bruce  
<mailto:bfis...@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 

Re: [Freesurfer] left-right flip?

[Douglas Greve]

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-boun...@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-boun...@nmr.mgh.harvard.edu  
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>  
  
<mailto:freesurfer-boun...@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  
<mailto:ellen...@bli.uzh.ch>

Sent: Tuesday, September 15, 2020 12:38 PM

To: Fischl, Bruce  
<mailto:bfis...@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-boun...@nmr.mgh.harvard.edu  
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

  
<mailto:freesurfer-boun...@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>

  

Re: [Freesurfer] left-right flip?

[Fischl, Bruce]

I think so, but I defer to Doug

From: freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@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 <mailto:ellen...@bli.uzh.ch>

Sent: Tuesday, September 15, 2020 12:38 PM

To: Fischl, Bruce <mailto:bfis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

<mailto:freesurfer-boun...@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 inver

Re: [Freesurfer] left-right flip?

[Ellen Ji]

   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-boun...@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 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 
Sent: Tuesday, September 15, 2020 12:38 PM
To: Fischl, Bruce 
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-boun...@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 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...@bli.uzh.ch
homanlab.github.io/ellen/




___
Freesurfer mailing list
Freesurfer

Re: [Freesurfer] left-right flip?

[Fischl, Bruce]

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-boun...@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 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 
>>> Sent: Tuesday, September 15, 2020 12:38 PM
>>> To: Fischl, Bruce 
>>> 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-boun...@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 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 
>>>>> orient

Re: [Freesurfer] left-right flip?

[Ellen Ji]

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 
>>> Sent: Tuesday, September 15, 2020 12:38 PM
>>> To: Fischl, Bruce 
>>> 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-boun...@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 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!
>>>>>
>>>

Re: [Freesurfer] left-right flip?

[Douglas N. Greve]

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 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 
>> Sent: Tuesday, September 15, 2020 12:38 PM
>> To: Fischl, Bruce 
>> 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-boun...@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 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...@bli.uzh.ch
>>>> homanlab.github.io/ellen/
>>>>
>>>>
>>>>
>>>>
>>>> ___
>>>> Freesurfer mailing list
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>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> ___
>>> Freesurfer mailing list
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>>>
>>> ___
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>>> 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.
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Re: [Freesurfer] left-right flip?

[Ellen Ji]

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 
> Sent: Tuesday, September 15, 2020 12:38 PM
> To: Fischl, Bruce 
> 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-boun...@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 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...@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
>>
>> ___
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>> 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, 
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Re: [Freesurfer] left-right flip?

[Douglas N. Greve]

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 11:36 AM, Ellen Ji wrote:
> External Email - Use Caution
> Hi Doug - see the screenshot attached. I believe this is the fiducial?
>
>
> On 9/15/2020 5:33 PM, Ellen Ji wrote:
>> Oh no, then I guess we have to assume a fiducial wasn't used. Is 
>> there any other way to determine which is left and right? Does the 
>> LAS/ASR/PSR from mri_info tell us that at all?
>>
>> Thanks,
>>
>> Ellen
>>
>>
>> On 9/15/2020 5:23 PM, Douglas N. Greve wrote:
>>> How do you know which side of the subject is left and right? I don't 
>>> see a fiducial.
>>> You do not need to convert the orientation to RAS.
>>>
>>> On 9/15/2020 10:29 AM, Ellen Ji wrote:
 External Email - Use Caution
 I loaded each T1 into freeview and verified that what freeview 
 thinks is left and right, and anterior and posterior, is also what 
 I see. Attached is a screenshot.

 However, when I ran "mri_info --orientation, the orientations of 
 the subjects are either LAS or ASR and PSR (i.e. not consistent and 
 not RAS). Is this going to affect the output of recon-all? Do I 
 need to convert all the orientations to RAS before running recon-all?

 Thanks,

 Ellen


 On 9/15/2020 4:17 PM, Douglas N. Greve wrote:
> 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...@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
>>>
>>> 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.

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Re: [Freesurfer] left-right flip?

[Fischl, Bruce]

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-boun...@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 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...@bli.uzh.ch
> homanlab.github.io/ellen/
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] left-right flip?

[Douglas N. Greve]

If you don't have a fiducial, then there is no way to know for sure; 
mri_info just gets the same info that freeview gets, which comes from 
the header. How did you convert the file from dicom?


On 9/15/2020 11:33 AM, Ellen Ji wrote:
> External Email - Use Caution
> Oh no, then I guess we have to assume a fiducial wasn't used. Is there 
> any other way to determine which is left and right? Does the 
> LAS/ASR/PSR from mri_info tell us that at all?
>
> Thanks,
>
> Ellen
>
>
> On 9/15/2020 5:23 PM, Douglas N. Greve wrote:
>> How do you know which side of the subject is left and right? I don't 
>> see a fiducial.
>> You do not need to convert the orientation to RAS.
>>
>> On 9/15/2020 10:29 AM, Ellen Ji wrote:
>>> External Email - Use Caution
>>> I loaded each T1 into freeview and verified that what freeview 
>>> thinks is left and right, and anterior and posterior, is also what I 
>>> see. Attached is a screenshot.
>>>
>>> However, when I ran "mri_info --orientation, the orientations of the 
>>> subjects are either LAS or ASR and PSR (i.e. not consistent and not 
>>> RAS). Is this going to affect the output of recon-all? Do I need to 
>>> convert all the orientations to RAS before running recon-all?
>>>
>>> Thanks,
>>>
>>> Ellen
>>>
>>>
>>> On 9/15/2020 4:17 PM, Douglas N. Greve wrote:
 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...@bli.uzh.ch
> homanlab.github.io/ellen/
>
>
>
>
> ___
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 ___
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 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.

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Re: [Freesurfer] left-right flip?

[Douglas N. Greve]

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...@bli.uzh.ch
> homanlab.github.io/ellen/
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] left-right flip?

[Ellen Ji]

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...@bli.uzh.ch
homanlab.github.io/ellen/




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Re: [Freesurfer] Left & Right flip on asymmetric MNI template

[Douglas N Greve]

sorry, we don't know anything about this template or ch2better. If you 
just want to flip the image left right, you can

mri_convert --left-right-reverse-pix input.nii output.nii



On 09/18/2017 01:42 AM, yskim wrote:
> Dear Freesurfer experts,
> I recently received manually segmentated MR data that registered to ch2better 
> MNI template.
> However, I have been informed that this data has been registered in inverted 
> form,
> and I could not simply flip left and right because ch2better MNI template was 
> asymmetric.
> To solve this problem, I first used the LeftRightReversal method of 
> freesurfer,
> but this method did not properly reflect the left-right different structure 
> of the asymmetric template.
> How can I flip registered data successfully with reflecting asymmetric MNI 
> template structure?
> Thank you for your help and information.
>
> - yskim
>
>
> *Yeong Sik Kim*
> Bio-Imaging Signal Processing Laboratory (http://bisp.kaist.ac.kr 
> )
> KAIST Dept.of Bio and Brain Engineering (http://bioeng.kaist.ac.kr 
> )
> E-mail : alley...@kaist.ac.kr 
> Mobile : 82-10-3828-8541
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[Freesurfer] Left & Right flip on asymmetric MNI template

[yskim]

 
 
  Dear Freesurfer experts,I recently received manually segmentated MR data that 
registered to ch2better MNI template.

  
  However, I have been informed that this data has been registered in inverted 
form, and I could not simply flip left and right because ch2better MNI template 
was asymmetric.To solve this problem, I first used the LeftRightReversal method 
of freesurfer, but this method did not properly reflect the left-right 
different structure of the asymmetric template.How can I flip registered data 
successfully with reflecting asymmetric MNI template structure?
  
  Thank you for your help and information.

- yskim
   
  
 
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Re: [Freesurfer] Left right flip surfaces

[Douglas N Greve]

Look at http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
if you want to compare all subjects, then you'll need to do this for all 
subjects not just the ones you want to flip

On 03/28/2016 02:30 PM, Ajay Kurani wrote:
> Hello Freesurfer Experts,
>
>I processed all of my brains through freesurfer 6.0 dev for 
> Linux and warped the surfaces to standardized space.  For a handful of 
> subjects I want to perform a left right flip of the cortical thickness 
> files (standardized space) for a group analysis.  What is the best way 
> to perform this in freesurfer? I have found a previous post 
> referencing mris_reverse but there was a mention of it being off by a 
> voxel when flipped.  I wanted to see if this is still a concern with 
> the latest version?
>
> Is there a better way to achieve this goal without rerunning all of 
> freesurfer such as a newer took, or is this the preferred method?
>
>
>
> Thanks,
> Ajay
>
>
> ___
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Left right flip surfaces

[Douglas N Greve]

You should use xhemireg. Just changing the sign of the x coordinate will 
not be meaningful.

On 03/29/2016 12:49 PM, Ajay Kurani wrote:
> Hi Doug,
>I used the caudate surface I created as an example as I was testing 
> the command out.  I do not plan to use this command for the caudate.  
> It just happened to show the same issue as the earlier post 
> (https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22\[Freesurfer\]+R+L+flipping%22=newest=1
>  
> )
>  
> and so I thought it would be the clearest way of showing you the issue 
> I was referring to.
>
>  I want to flip the lh.thickness.fwhm10.fsaverage.gii files to the 
> right hemisphere for certain subjects and I was worried about having a 
> similar voxel shift if I used mris_reverse.  I found posts using 
> xhemireg and surfreg along with mris_reverse, and so I am trying to 
> figure out what is the best way to flip these thickness files to the 
> opposite hemisphere (files already warped to symmetric space)
>
> Thanks,
> Ajay
>
> On Mon, Mar 28, 2016 at 5:05 PM, Ajay Kurani  > wrote:
>
> Hi Doug,
>I attached a .png file to show an example.  The Yellow outline
> is the right and left caudate surface. The right surface (yellow)
> was created by using 3dLRflip (Afni program) to symmetrically flip
> the volumetric ROI so that I can create the right caudate surface
> from scratch again.  The blue outline is the same right caudate
> surface created when I used mris_reverse on the left hemisphere
> surface.  As you can see the blue surface outline is not exactly
> symmetrical, but rather it is shifted to the left by one voxel. 
> This was noted in some earlier posts regarding mris_reverse from
> 2004 as an issue
> 
> (https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22\[Freesurfer\]+R+L+flipping%22=newest=1
> 
> ).
>
>
> I was curious to see if xhemireg or the surfreg methods alleviate
> this issue, or if there is another set of preferred commands to
> symmetrically L-R flip the brain?
>
> Thanks,
> Ajay
>
> On Mon, Mar 28, 2016 at 3:03 PM, Ajay Kurani
> > wrote:
>
> Hi Freesurfer Experts,
>In testing mris_reverse, there seems to be a voxel shift. 
> In looking up other freesurfer utitlites I came across
> xhemireg and surfreg.
>
> 
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-September/040573.html
>
> Does xhemireg or surfreg call out mris_reverse, causing the
> same pixel shift issue???
>
> Based on what I can find is it best to run the following:
>
> surfreg --s sub001 --t fsaverage_sym --lh --xhemi
> Would this flip my lh.thickness.fwhm10.fsaverage_sym.mgh file to the 
> other hemisphere?
>
> Thanks,
>
> Ajay
>
>
> On Mon, Mar 28, 2016 at 1:30 PM, Ajay Kurani
> >
> wrote:
>
> Hello Freesurfer Experts,
>
>I processed all of my brains through freesurfer 6.0 dev
> for Linux and warped the surfaces to standardized space. 
> For a handful of subjects I want to perform a left right
> flip of the cortical thickness files (standardized space)
> for a group analysis.  What is the best way to perform
> this in freesurfer?  I have found a previous post
> referencing mris_reverse but there was a mention of it
> being off by a voxel when flipped.  I wanted to see if
> this is still a concern with the latest version?
>
> Is there a better way to achieve this goal without
> rerunning all of freesurfer such as a newer took, or is
> this the preferred method?
>
>
>
> Thanks,
> Ajay
>
>
>
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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The information in 

Re: [Freesurfer] Left right flip surfaces

[Ajay Kurani]

Hi Doug,
   I used the caudate surface I created as an example as I was testing the
command out.  I do not plan to use this command for the caudate.  It just
happened to show the same issue as the earlier post (
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22\[Freesurfer\]+R+L+flipping%22=newest=1
)
and so I thought it would be the clearest way of showing you the issue I
was referring to.

 I want to flip the lh.thickness.fwhm10.fsaverage.gii files to the right
hemisphere for certain subjects and I was worried about having a similar
voxel shift if I used mris_reverse.  I  found posts using xhemireg and
surfreg along with mris_reverse, and so I am trying to figure out what is
the best way to flip these thickness files to the opposite hemisphere
(files already warped to symmetric space)

Thanks,
Ajay

On Mon, Mar 28, 2016 at 5:05 PM, Ajay Kurani 
wrote:

> Hi Doug,
>I attached a .png file to show an example.  The Yellow outline is the
> right and left caudate surface.  The right surface (yellow) was created by
> using 3dLRflip (Afni program) to symmetrically flip the volumetric ROI so
> that I can create the right caudate surface from scratch again.  The blue
> outline is the same right caudate surface created when I used mris_reverse
> on the left hemisphere surface.  As you can see the blue surface outline is
> not exactly symmetrical, but rather it is shifted to the left by one
> voxel.  This was noted in some earlier posts regarding mris_reverse from
> 2004 as an issue (
> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22\[Freesurfer\]+R+L+flipping%22=newest=1
> ).
>
>
> I was curious to see if xhemireg or the surfreg methods alleviate this
> issue, or if there is another set of preferred commands to symmetrically
> L-R flip the brain?
>
> Thanks,
> Ajay
>
> On Mon, Mar 28, 2016 at 3:03 PM, Ajay Kurani 
> wrote:
>
>> Hi Freesurfer Experts,
>>In testing mris_reverse, there seems to be a voxel shift.  In looking
>> up other freesurfer utitlites I came across xhemireg and surfreg.
>>
>>
>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-September/040573.html
>>
>> Does xhemireg or surfreg call out mris_reverse, causing the same pixel
>> shift issue???
>>
>> Based on what I can find is it best to run the following:
>>
>> surfreg --s sub001 --t fsaverage_sym --lh --xhemi
>> Would this flip my lh.thickness.fwhm10.fsaverage_sym.mgh file to the other 
>> hemisphere?
>>
>> Thanks,
>>
>> Ajay
>>
>>
>> On Mon, Mar 28, 2016 at 1:30 PM, Ajay Kurani 
>> wrote:
>>
>>> Hello Freesurfer Experts,
>>>
>>>I processed all of my brains through freesurfer 6.0 dev for Linux and
>>> warped the surfaces to standardized space.  For a handful of subjects I
>>> want to perform a left right flip of the cortical thickness files
>>> (standardized space) for a group analysis.  What is the best way to perform
>>> this in freesurfer?  I have found a previous post referencing mris_reverse
>>> but there was a mention of it being off by a voxel when flipped.  I wanted
>>> to see if this is still a concern with the latest version?
>>>
>>> Is there a better way to achieve this goal without rerunning all of
>>> freesurfer such as a newer took, or is this the preferred method?
>>>
>>>
>>>
>>> Thanks,
>>> Ajay
>>>
>>
>>
>
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Re: [Freesurfer] Left right flip surfaces

[Douglas N Greve]

hmmm, we don't have a caudate surface. How did you make it? mris_reverse 
just changes the sign on the x coordinate. This might not show up 
"properly" in freeview; it does not surprise me that it could appear to 
be 1 voxel off. This was not the intended use of this program. xhemireg 
will not help. what are you trying to do?

On 03/28/2016 06:05 PM, Ajay Kurani wrote:
> Hi Doug,
>I attached a .png file to show an example.  The Yellow outline is 
> the right and left caudate surface.  The right surface (yellow) was 
> created by using 3dLRflip (Afni program) to symmetrically flip the 
> volumetric ROI so that I can create the right caudate surface from 
> scratch again. The blue outline is the same right caudate surface 
> created when I used mris_reverse on the left hemisphere surface.  As 
> you can see the blue surface outline is not exactly symmetrical, but 
> rather it is shifted to the left by one voxel.  This was noted in some 
> earlier posts regarding mris_reverse from 2004 as an issue 
> (https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22\[Freesurfer\]+R+L+flipping%22=newest=1
>  
> ).
>  
>
>
> I was curious to see if xhemireg or the surfreg methods alleviate this 
> issue, or if there is another set of preferred commands to 
> symmetrically L-R flip the brain?
>
> Thanks,
> Ajay
>
> On Mon, Mar 28, 2016 at 3:03 PM, Ajay Kurani  > wrote:
>
> Hi Freesurfer Experts,
>In testing mris_reverse, there seems to be a voxel shift.  In
> looking up other freesurfer utitlites I came across xhemireg and
> surfreg.
>
> 
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-September/040573.html
>
> Does xhemireg or surfreg call out mris_reverse, causing the same
> pixel shift issue???
>
> Based on what I can find is it best to run the following:
>
> surfreg --s sub001 --t fsaverage_sym --lh --xhemi
> Would this flip my lh.thickness.fwhm10.fsaverage_sym.mgh file to the 
> other hemisphere?
>
> Thanks,
>
> Ajay
>
>
> On Mon, Mar 28, 2016 at 1:30 PM, Ajay Kurani
> > wrote:
>
> Hello Freesurfer Experts,
>
>I processed all of my brains through freesurfer 6.0 dev for
> Linux and warped the surfaces to standardized space.  For a
> handful of subjects I want to perform a left right flip of the
> cortical thickness files (standardized space) for a group
> analysis.  What is the best way to perform this in
> freesurfer?  I have found a previous post referencing
> mris_reverse but there was a mention of it being off by a
> voxel when flipped.  I wanted to see if this is still a
> concern with the latest version?
>
> Is there a better way to achieve this goal without rerunning
> all of freesurfer such as a newer took, or is this the
> preferred method?
>
>
>
> Thanks,
> Ajay
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Left right flip surfaces

[Douglas N Greve]

what do you mean by a voxel shift?

On 03/28/2016 04:03 PM, Ajay Kurani wrote:
> Hi Freesurfer Experts,
>In testing mris_reverse, there seems to be a voxel shift. In 
> looking up other freesurfer utitlites I came across xhemireg and surfreg.
>
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-September/040573.html
>
> Does xhemireg or surfreg call out mris_reverse, causing the same pixel 
> shift issue???
>
> Based on what I can find is it best to run the following:
> surfreg --s sub001 --t fsaverage_sym --lh --xhemi
> Would this flip my lh.thickness.fwhm10.fsaverage_sym.mgh file to the other 
> hemisphere?
>
> Thanks,
> Ajay
>
> On Mon, Mar 28, 2016 at 1:30 PM, Ajay Kurani  > wrote:
>
> Hello Freesurfer Experts,
>
>I processed all of my brains through freesurfer 6.0 dev for
> Linux and warped the surfaces to standardized space.  For a
> handful of subjects I want to perform a left right flip of the
> cortical thickness files (standardized space) for a group
> analysis.  What is the best way to perform this in freesurfer?  I
> have found a previous post referencing mris_reverse but there was
> a mention of it being off by a voxel when flipped.  I wanted to
> see if this is still a concern with the latest version?
>
> Is there a better way to achieve this goal without rerunning all
> of freesurfer such as a newer took, or is this the preferred method?
>
>
>
> Thanks,
> Ajay
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Left right flip surfaces

[Ajay Kurani]

Hi Freesurfer Experts,
   In testing mris_reverse, there seems to be a voxel shift.  In looking up
other freesurfer utitlites I came across xhemireg and surfreg.

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-September/040573.html

Does xhemireg or surfreg call out mris_reverse, causing the same pixel
shift issue???

Based on what I can find is it best to run the following:

surfreg --s sub001 --t fsaverage_sym --lh --xhemi
Would this flip my lh.thickness.fwhm10.fsaverage_sym.mgh file to the
other hemisphere?

Thanks,

Ajay


On Mon, Mar 28, 2016 at 1:30 PM, Ajay Kurani 
wrote:

> Hello Freesurfer Experts,
>
>I processed all of my brains through freesurfer 6.0 dev for Linux and
> warped the surfaces to standardized space.  For a handful of subjects I
> want to perform a left right flip of the cortical thickness files
> (standardized space) for a group analysis.  What is the best way to perform
> this in freesurfer?  I have found a previous post referencing mris_reverse
> but there was a mention of it being off by a voxel when flipped.  I wanted
> to see if this is still a concern with the latest version?
>
> Is there a better way to achieve this goal without rerunning all of
> freesurfer such as a newer took, or is this the preferred method?
>
>
>
> Thanks,
> Ajay
>
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[Freesurfer] Left right flip surfaces

[Ajay Kurani]

Hello Freesurfer Experts,

   I processed all of my brains through freesurfer 6.0 dev for Linux and
warped the surfaces to standardized space.  For a handful of subjects I
want to perform a left right flip of the cortical thickness files
(standardized space) for a group analysis.  What is the best way to perform
this in freesurfer?  I have found a previous post referencing mris_reverse
but there was a mention of it being off by a voxel when flipped.  I wanted
to see if this is still a concern with the latest version?

Is there a better way to achieve this goal without rerunning all of
freesurfer such as a newer took, or is this the preferred method?



Thanks,
Ajay
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