Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Douglas N Greve]

Try using mri_convert to convert one set and see if that fixes it. If 
so, then never use unpack_fsl.sh again. Note that unpack_fsl.sh is not 
part of the FSL suit of tools, so don't blame them ...

On 08/17/2016 01:57 PM, Afzal, Afsana wrote:
> I opened up the functional and anatomical (original and reversed) in freeview 
> and the functional volume is better aligned with the reversed anatomical than 
> with the original anatomical. I realize this is a gross visual check that is 
> probably unreliable but I don't have any other guesses as so why the coreg is 
> failing for over 150 subjects.
>
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, August 17, 2016 1:44 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>
> what do you mean "visual inspection shows that they are actually
> reversed"? Please give details
>
> On 08/17/2016 01:31 PM, Afzal, Afsana wrote:
>> I'm trying to understand why the coregistration for a bunch of subjects are 
>> bad/failing (mincost value > 8).
>>
>> The orientation for the anatomical matches the functional (after FSL 
>> unpacking) but visual inspection shows that they are actually reversed. Then 
>> I used mri_convert to change the orientation of the anatomical but the 
>> coregistration is still failing. So I still have no idea what's causing the 
>> coreg to fail or how to fix it.
>>
>> -Afsana
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, August 16, 2016 5:51 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>>
>> I'm still not sure why you are trying to do this. If FSL did not unpack
>> the volumes with the correct orientation, then you need to switch to
>> mri_convert. If they are in the right orientation, then I don't
>> understand what you are trying to do.
>> doug
>>
>> On 08/16/2016 05:27 PM, Afzal, Afsana wrote:
>>> Hi Doug,
>>>
>>> After the coregistration failed for the majority of the subjects, I 
>>> visually inspected a handful of the subjects in freeview and it looks like 
>>> the anatomical and the functional are reversed but I could be wrong.
>>>
>>> The nifti files are unpacked from DICOMs using unpack_fsl.sh 
>>> (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you 
>>> to a specific subject directory if that would be of any help.
>>>
>>> Might be worth mentioning that the subjects who failed coreg were not 
>>> scanned using siemens scanners but Phillips and GE scanners. Don't know if 
>>> there's some sort of discrepancy between the scanner coordinate frames that 
>>> could potentially lead to this issue.
>>>
>>> Thank you very much for your help,
>>>
>>> Afsana
>>> __
>>> Afsana Afzal
>>> Clinical Research Coordinator
>>> Massachusetts General Hospital
>>> Division of Neurotherapeutics
>>> Department of Psychiatry: Neurosciences
>>> 149 13th St, Room 2612
>>> Charlestown, MA 02129
>>> Phone: 617-643-5129
>>> Fax: 617-726-4078
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, August 16, 2016 3:45 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>>>
>>> How do you know that the structural is left-right reversed? Or that the
>>> fMRI is? How did you create the nifti files?
>>>
>>>
>>> On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
>>>> Hi,
>>>>
>>>> I'm having trouble co-registering a bunch of subjects whose T1 is
>>>> left-right reve

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Afzal, Afsana]

I opened up the functional and anatomical (original and reversed) in freeview 
and the functional volume is better aligned with the reversed anatomical than 
with the original anatomical. I realize this is a gross visual check that is 
probably unreliable but I don't have any other guesses as so why the coreg is 
failing for over 150 subjects. 

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, August 17, 2016 1:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

what do you mean "visual inspection shows that they are actually
reversed"? Please give details

On 08/17/2016 01:31 PM, Afzal, Afsana wrote:
> I'm trying to understand why the coregistration for a bunch of subjects are 
> bad/failing (mincost value > 8).
>
> The orientation for the anatomical matches the functional (after FSL 
> unpacking) but visual inspection shows that they are actually reversed. Then 
> I used mri_convert to change the orientation of the anatomical but the 
> coregistration is still failing. So I still have no idea what's causing the 
> coreg to fail or how to fix it.
>
> -Afsana
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, August 16, 2016 5:51 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>
> I'm still not sure why you are trying to do this. If FSL did not unpack
> the volumes with the correct orientation, then you need to switch to
> mri_convert. If they are in the right orientation, then I don't
> understand what you are trying to do.
> doug
>
> On 08/16/2016 05:27 PM, Afzal, Afsana wrote:
>> Hi Doug,
>>
>> After the coregistration failed for the majority of the subjects, I visually 
>> inspected a handful of the subjects in freeview and it looks like the 
>> anatomical and the functional are reversed but I could be wrong.
>>
>> The nifti files are unpacked from DICOMs using unpack_fsl.sh 
>> (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to 
>> a specific subject directory if that would be of any help.
>>
>> Might be worth mentioning that the subjects who failed coreg were not 
>> scanned using siemens scanners but Phillips and GE scanners. Don't know if 
>> there's some sort of discrepancy between the scanner coordinate frames that 
>> could potentially lead to this issue.
>>
>> Thank you very much for your help,
>>
>> Afsana
>> __
>> Afsana Afzal
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>>
>> ____________
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, August 16, 2016 3:45 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>>
>> How do you know that the structural is left-right reversed? Or that the
>> fMRI is? How did you create the nifti files?
>>
>>
>> On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
>>> Hi,
>>>
>>> I'm having trouble co-registering a bunch of subjects whose T1 is
>>> left-right reversed. While the orientation of the structural file in
>>> the NIfTI header is LIA and the orientation of the functional volume
>>> is LAS, visual inspection shows that the structural is left-right
>>> reversed. I then followed the steps outlined in
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
>>> <https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal> to rerun
>>> the reconstruction and re-registered the subject but the registration
>>> mincost value is still hovering around 0.9 even with the left-right
>>> reversed structural.
>>>
>>> I've tried ru

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Douglas N Greve]

what do you mean "visual inspection shows that they are actually 
reversed"? Please give details

On 08/17/2016 01:31 PM, Afzal, Afsana wrote:
> I'm trying to understand why the coregistration for a bunch of subjects are 
> bad/failing (mincost value > 8).
>
> The orientation for the anatomical matches the functional (after FSL 
> unpacking) but visual inspection shows that they are actually reversed. Then 
> I used mri_convert to change the orientation of the anatomical but the 
> coregistration is still failing. So I still have no idea what's causing the 
> coreg to fail or how to fix it.
>
> -Afsana
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, August 16, 2016 5:51 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>
> I'm still not sure why you are trying to do this. If FSL did not unpack
> the volumes with the correct orientation, then you need to switch to
> mri_convert. If they are in the right orientation, then I don't
> understand what you are trying to do.
> doug
>
> On 08/16/2016 05:27 PM, Afzal, Afsana wrote:
>> Hi Doug,
>>
>> After the coregistration failed for the majority of the subjects, I visually 
>> inspected a handful of the subjects in freeview and it looks like the 
>> anatomical and the functional are reversed but I could be wrong.
>>
>> The nifti files are unpacked from DICOMs using unpack_fsl.sh 
>> (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to 
>> a specific subject directory if that would be of any help.
>>
>> Might be worth mentioning that the subjects who failed coreg were not 
>> scanned using siemens scanners but Phillips and GE scanners. Don't know if 
>> there's some sort of discrepancy between the scanner coordinate frames that 
>> could potentially lead to this issue.
>>
>> Thank you very much for your help,
>>
>> Afsana
>> __
>> Afsana Afzal
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>>
>> ________________
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, August 16, 2016 3:45 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>>
>> How do you know that the structural is left-right reversed? Or that the
>> fMRI is? How did you create the nifti files?
>>
>>
>> On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
>>> Hi,
>>>
>>> I'm having trouble co-registering a bunch of subjects whose T1 is
>>> left-right reversed. While the orientation of the structural file in
>>> the NIfTI header is LIA and the orientation of the functional volume
>>> is LAS, visual inspection shows that the structural is left-right
>>> reversed. I then followed the steps outlined in
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
>>> <https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal> to rerun
>>> the reconstruction and re-registered the subject but the registration
>>> mincost value is still hovering around 0.9 even with the left-right
>>> reversed structural.
>>>
>>> I've tried running registration with SPM and FSL; neither method is
>>> able to register these subjects properly.
>>>
>>> With --init-fsl I get the following:
>>> WARNING: initial G-W contrast is negative, but expecting positive.
>>> If the mov data has a T1 contrast, re-run with --T1
>>>
>>> and with --init-spm I get:
>>> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
>>>... continuing.
>>>
>>> At this point I'm out of ideas to try out. This issue is occurring for
>>> over 170 subjects (data collected outside Martinos using non-siemens
>>> scanners).
>>>
>>> Any help would be much appreciated!
>>>
>>> Thanks,
>>>
>>> Afsana
>>>
>>>
>>>
>>> __
>>> *Afsana Afzal*

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Afzal, Afsana]

I'm trying to understand why the coregistration for a bunch of subjects are 
bad/failing (mincost value > 8). 

The orientation for the anatomical matches the functional (after FSL unpacking) 
but visual inspection shows that they are actually reversed. Then I used 
mri_convert to change the orientation of the anatomical but the coregistration 
is still failing. So I still have no idea what's causing the coreg to fail or 
how to fix it. 

-Afsana


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, August 16, 2016 5:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

I'm still not sure why you are trying to do this. If FSL did not unpack
the volumes with the correct orientation, then you need to switch to
mri_convert. If they are in the right orientation, then I don't
understand what you are trying to do.
doug

On 08/16/2016 05:27 PM, Afzal, Afsana wrote:
> Hi Doug,
>
> After the coregistration failed for the majority of the subjects, I visually 
> inspected a handful of the subjects in freeview and it looks like the 
> anatomical and the functional are reversed but I could be wrong.
>
> The nifti files are unpacked from DICOMs using unpack_fsl.sh 
> (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to 
> a specific subject directory if that would be of any help.
>
> Might be worth mentioning that the subjects who failed coreg were not scanned 
> using siemens scanners but Phillips and GE scanners. Don't know if there's 
> some sort of discrepancy between the scanner coordinate frames that could 
> potentially lead to this issue.
>
> Thank you very much for your help,
>
> Afsana
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, August 16, 2016 3:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>
> How do you know that the structural is left-right reversed? Or that the
> fMRI is? How did you create the nifti files?
>
>
> On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
>> Hi,
>>
>> I'm having trouble co-registering a bunch of subjects whose T1 is
>> left-right reversed. While the orientation of the structural file in
>> the NIfTI header is LIA and the orientation of the functional volume
>> is LAS, visual inspection shows that the structural is left-right
>> reversed. I then followed the steps outlined in
>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
>> <https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal> to rerun
>> the reconstruction and re-registered the subject but the registration
>> mincost value is still hovering around 0.9 even with the left-right
>> reversed structural.
>>
>> I've tried running registration with SPM and FSL; neither method is
>> able to register these subjects properly.
>>
>> With --init-fsl I get the following:
>> WARNING: initial G-W contrast is negative, but expecting positive.
>> If the mov data has a T1 contrast, re-run with --T1
>>
>> and with --init-spm I get:
>> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
>>   ... continuing.
>>
>> At this point I'm out of ideas to try out. This issue is occurring for
>> over 170 subjects (data collected outside Martinos using non-siemens
>> scanners).
>>
>> Any help would be much appreciated!
>>
>> Thanks,
>>
>> Afsana
>>
>>
>>
>> __
>> *Afsana Afzal*
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NM

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Douglas N Greve]

I'm still not sure why you are trying to do this. If FSL did not unpack 
the volumes with the correct orientation, then you need to switch to 
mri_convert. If they are in the right orientation, then I don't 
understand what you are trying to do.
doug

On 08/16/2016 05:27 PM, Afzal, Afsana wrote:
> Hi Doug,
>
> After the coregistration failed for the majority of the subjects, I visually 
> inspected a handful of the subjects in freeview and it looks like the 
> anatomical and the functional are reversed but I could be wrong.
>
> The nifti files are unpacked from DICOMs using unpack_fsl.sh 
> (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to 
> a specific subject directory if that would be of any help.
>
> Might be worth mentioning that the subjects who failed coreg were not scanned 
> using siemens scanners but Phillips and GE scanners. Don't know if there's 
> some sort of discrepancy between the scanner coordinate frames that could 
> potentially lead to this issue.
>
> Thank you very much for your help,
>
> Afsana
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, August 16, 2016 3:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>
> How do you know that the structural is left-right reversed? Or that the
> fMRI is? How did you create the nifti files?
>
>
> On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
>> Hi,
>>
>> I'm having trouble co-registering a bunch of subjects whose T1 is
>> left-right reversed. While the orientation of the structural file in
>> the NIfTI header is LIA and the orientation of the functional volume
>> is LAS, visual inspection shows that the structural is left-right
>> reversed. I then followed the steps outlined in
>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
>> <https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal> to rerun
>> the reconstruction and re-registered the subject but the registration
>> mincost value is still hovering around 0.9 even with the left-right
>> reversed structural.
>>
>> I've tried running registration with SPM and FSL; neither method is
>> able to register these subjects properly.
>>
>> With --init-fsl I get the following:
>> WARNING: initial G-W contrast is negative, but expecting positive.
>> If the mov data has a T1 contrast, re-run with --T1
>>
>> and with --init-spm I get:
>> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
>>   ... continuing.
>>
>> At this point I'm out of ideas to try out. This issue is occurring for
>> over 170 subjects (data collected outside Martinos using non-siemens
>> scanners).
>>
>> Any help would be much appreciated!
>>
>> Thanks,
>>
>> Afsana
>>
>>
>>
>> __
>> *Afsana Afzal*
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>>
>>
>> ___
>> 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
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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
>
>

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

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Afzal, Afsana]

Hi Doug, 

After the coregistration failed for the majority of the subjects, I visually 
inspected a handful of the subjects in freeview and it looks like the 
anatomical and the functional are reversed but I could be wrong. 

The nifti files are unpacked from DICOMs using unpack_fsl.sh 
(/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to a 
specific subject directory if that would be of any help. 

Might be worth mentioning that the subjects who failed coreg were not scanned 
using siemens scanners but Phillips and GE scanners. Don't know if there's some 
sort of discrepancy between the scanner coordinate frames that could 
potentially lead to this issue.

Thank you very much for your help, 

Afsana
__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, August 16, 2016 3:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

How do you know that the structural is left-right reversed? Or that the
fMRI is? How did you create the nifti files?


On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
> Hi,
>
> I'm having trouble co-registering a bunch of subjects whose T1 is
> left-right reversed. While the orientation of the structural file in
> the NIfTI header is LIA and the orientation of the functional volume
> is LAS, visual inspection shows that the structural is left-right
> reversed. I then followed the steps outlined in
> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
> <https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal> to rerun
> the reconstruction and re-registered the subject but the registration
> mincost value is still hovering around 0.9 even with the left-right
> reversed structural.
>
> I've tried running registration with SPM and FSL; neither method is
> able to register these subjects properly.
>
> With --init-fsl I get the following:
> WARNING: initial G-W contrast is negative, but expecting positive.
> If the mov data has a T1 contrast, re-run with --T1
>
> and with --init-spm I get:
> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
>  ... continuing.
>
> At this point I'm out of ideas to try out. This issue is occurring for
> over 170 subjects (data collected outside Martinos using non-siemens
> scanners).
>
> Any help would be much appreciated!
>
> Thanks,
>
> Afsana
>
>
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
> ___
> 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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Douglas N Greve]

How do you know that the structural is left-right reversed? Or that the 
fMRI is? How did you create the nifti files?


On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
> Hi,
>
> I'm having trouble co-registering a bunch of subjects whose T1 is 
> left-right reversed. While the orientation of the structural file in 
> the NIfTI header is LIA and the orientation of the functional volume 
> is LAS, visual inspection shows that the structural is left-right 
> reversed. I then followed the steps outlined in 
> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal 
>  to rerun 
> the reconstruction and re-registered the subject but the registration 
> mincost value is still hovering around 0.9 even with the left-right 
> reversed structural.
>
> I've tried running registration with SPM and FSL; neither method is 
> able to register these subjects properly.
>
> With --init-fsl I get the following:
> WARNING: initial G-W contrast is negative, but expecting positive.
> If the mov data has a T1 contrast, re-run with --T1
>
> and with --init-spm I get:
> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
>  ... continuing.
>
> At this point I'm out of ideas to try out. This issue is occurring for 
> over 170 subjects (data collected outside Martinos using non-siemens 
> scanners).
>
> Any help would be much appreciated!
>
> Thanks,
>
> Afsana
>
>
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
> ___
> 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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Bad Coregistration - Left-Right Reversed

[Afzal, Afsana]

Hi,

I'm having trouble co-registering a bunch of subjects whose T1 is left-right 
reversed. While the orientation of the structural file in the NIfTI header is 
LIA and the orientation of the functional volume is LAS, visual inspection 
shows that the structural is left-right reversed. I then followed the steps 
outlined in https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal to 
rerun the reconstruction and re-registered the subject but the registration 
mincost value is still hovering around 0.9 even with the left-right reversed 
structural.

I've tried running registration with SPM and FSL; neither method is able to 
register these subjects properly.

With --init-fsl I get the following:
WARNING: initial G-W contrast is negative, but expecting positive.
If the mov data has a T1 contrast, re-run with --T1

and with --init-spm I get:
WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
 ... continuing.

At this point I'm out of ideas to try out. This issue is occurring for over 170 
subjects (data collected outside Martinos using non-siemens scanners).

Any help would be much appreciated!

Thanks,

Afsana



__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078
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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 Partners Compliance HelpLine at
http://www.partners.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.