[Freesurfer] Freesurfer fails

[Franklin, Crystal G]

Freesurfer,

I have been running a group of subjects through recon-all and some of the 
subjects are failing at the very beginning of the process and I am not sure  
why.   The images look fine, but I keep getting the following error:

#@# Talairach Failure Detection Fri Dec  7 10:54:57 CST 2012
/Applications/freesurfer/subjects/PHY002/mri
\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
***FAILED*** (p=0.0013, pval=0. < threshold=0.0050)
INFO: Attempting MINC mritotal to perform Talairach align

Do you know what could be causing this?

I read that you can include the command –notal –check to skip this test, but 
how will this effect my data?  If I run this command  on the subjects that 
failed and combine their results with the subjects that worked will my group 
results be effected?

Any help would be appreciated.  I have attached one of the log files for a 
subject that failed.

Thanks,
Crystal


recon-all.error
Description: recon-all.error


recon-all.log
Description: recon-all.log
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Re: [Freesurfer] Freesurfer fails

[Franklin, Crystal G]

Bruce,

I have visually checked the transforms and they do indeed seem incorrect.
The images are stretched.  I have attached the talairach.xfm for one of
the images that failed and one that worked.

Thanks for all your help,
Crystal

On 1/13/13 3:08 PM, "Bruce Fischl"  wrote:

>can you cc the list? Have you visualized the transform to see if it is
>indeed incorrect?
>
>On Sun, 13 Jan 2013, Franklin, Crystal G wrote:
>
>> I used mri_convert to create the 001.mgz file. In freeview the
>>directions appear correct.
>>
>> Thanks,
>> Crystal
>> -Original Message-
>> From: Bruce Fischl 
>> Date: Sun, 13 Jan 2013 09:02:16
>> To: Franklin, Crystal G
>> Cc: Freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Freesurfer fails
>>
>> Hi Crystal
>>
>> how did you create the 001.mgz? When you view it in freeview does
>> freeview have the correct directions in the anatomy (i.e. I/S, A/P and
>> L/R)?
>>
>> cheers
>> Bruce
>> On Sat, 12 Jan 2013, Franklin, Crystal G wrote:
>>
>>> Freesurfer,
>>>
>>> I have been running a group of subjects through recon-all and some of
>>>the
>>> subjects are failing at the very beginning of the process and I am not
>>>sure
>>>  why.   The images look fine, but I keep getting the following error:
>>>
>>> #@# Talairach Failure Detection Fri Dec  7 10:54:57 CST 2012
>>> /Applications/freesurfer/subjects/PHY002/mri
>>> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
>>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
>>> ***FAILED*** (p=0.0013, pval=0. < threshold=0.0050)
>>> INFO: Attempting MINC mritotal to perform Talairach align
>>>
>>> Do you know what could be causing this?
>>>
>>> I read that you can include the command ?notal ?check to skip this
>>>test, but how
>>> will this effect my data?  If I run this command  on the subjects that
>>> failed and combine their results with the subjects that worked will my
>>>group
>>> results be effected?
>>>
>>> Any help would be appreciated.  I have attached one of the log files
>>>for a
>>> subject that failed.
>>>
>>> Thanks,
>>> Crystal
>>>
>>>
>>
>>
>> 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.
>>
>>
>>



failed_talairach.xfm
Description: failed_talairach.xfm


talairach.xfm
Description: talairach.xfm
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[Freesurfer] FW: Freesurfer fails

[Franklin, Crystal G]

On 1/14/13 11:38 AM, "Franklin, Crystal G"  wrote:

>I put the data on your ftp site in the folder called
>crystal_failed_talairach.tar.
>
>Thanks,
>Crystal
>
>On 1/14/13 9:31 AM, "Bruce Fischl"  wrote:
>
>>Hi Crystal
>>
>>we'll need the image volume also
>>
>>cheers
>>Bruce
>>On Mon, 14 Jan 2013, Franklin, Crystal G
>>wrote:
>>
>>> Bruce,
>>>
>>> I have visually checked the transforms and they do indeed seem
>>>incorrect.
>>> The images are stretched.  I have attached the talairach.xfm for one of
>>> the images that failed and one that worked.
>>>
>>> Thanks for all your help,
>>> Crystal
>>>
>>> On 1/13/13 3:08 PM, "Bruce Fischl"  wrote:
>>>
>>>> can you cc the list? Have you visualized the transform to see if it is
>>>> indeed incorrect?
>>>>
>>>> On Sun, 13 Jan 2013, Franklin, Crystal G wrote:
>>>>
>>>>> I used mri_convert to create the 001.mgz file. In freeview the
>>>>> directions appear correct.
>>>>>
>>>>> Thanks,
>>>>> Crystal
>>>>> -Original Message-
>>>>> From: Bruce Fischl 
>>>>> Date: Sun, 13 Jan 2013 09:02:16
>>>>> To: Franklin, Crystal G
>>>>> Cc: Freesurfer@nmr.mgh.harvard.edu
>>>>> Subject: Re: [Freesurfer] Freesurfer fails
>>>>>
>>>>> Hi Crystal
>>>>>
>>>>> how did you create the 001.mgz? When you view it in freeview does
>>>>> freeview have the correct directions in the anatomy (i.e. I/S, A/P
>>>>>and
>>>>> L/R)?
>>>>>
>>>>> cheers
>>>>> Bruce
>>>>> On Sat, 12 Jan 2013, Franklin, Crystal G wrote:
>>>>>
>>>>>> Freesurfer,
>>>>>>
>>>>>> I have been running a group of subjects through recon-all and some
>>>>>>of
>>>>>> the
>>>>>> subjects are failing at the very beginning of the process and I am
>>>>>>not
>>>>>> sure
>>>>>>  why.   The images look fine, but I keep getting the following
>>>>>>error:
>>>>>>
>>>>>> #@# Talairach Failure Detection Fri Dec  7 10:54:57 CST 2012
>>>>>> /Applications/freesurfer/subjects/PHY002/mri
>>>>>> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
>>>>>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
>>>>>> ***FAILED*** (p=0.0013, pval=0. < threshold=0.0050)
>>>>>> INFO: Attempting MINC mritotal to perform Talairach align
>>>>>>
>>>>>> Do you know what could be causing this?
>>>>>>
>>>>>> I read that you can include the command ?notal ?check to skip this
>>>>>> test, but how
>>>>>> will this effect my data?  If I run this command  on the subjects
>>>>>>that
>>>>>> failed and combine their results with the subjects that worked will
>>>>>>my
>>>>>> group
>>>>>> results be effected?
>>>>>>
>>>>>> Any help would be appreciated.  I have attached one of the log files
>>>>>> for a
>>>>>> subject that failed.
>>>>>>
>>>>>> Thanks,
>>>>>> Crystal
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> 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.
>>>>>
>>>>>
>>>>>
>>>
>>>
>


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Re: [Freesurfer] FW: Freesurfer fails

[Franklin, Crystal G]

Thank you.  I will give it a try.

Crystal

On 1/14/13 1:36 PM, "Nick Schmansky"  wrote:

>Crystal,
>
>I can replicate the failure you are seeing, and the problem is one that
>is fixed for the upcoming v5.2.  It is described here:
>
>https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1
>
>the first solution described should fix your problem.
>
>Nick
>
>
>On Mon, 2013-01-14 at 18:49 +, Franklin, Crystal G wrote:
>> 
>> On 1/14/13 11:38 AM, "Franklin, Crystal G" 
>>wrote:
>> 
>> >I put the data on your ftp site in the folder called
>> >crystal_failed_talairach.tar.
>> >
>> >Thanks,
>> >Crystal
>> >
>> >On 1/14/13 9:31 AM, "Bruce Fischl"  wrote:
>> >
>> >>Hi Crystal
>> >>
>> >>we'll need the image volume also
>> >>
>> >>cheers
>> >>Bruce
>> >>On Mon, 14 Jan 2013, Franklin, Crystal G
>> >>wrote:
>> >>
>> >>> Bruce,
>> >>>
>> >>> I have visually checked the transforms and they do indeed seem
>> >>>incorrect.
>> >>> The images are stretched.  I have attached the talairach.xfm for
>>one of
>> >>> the images that failed and one that worked.
>> >>>
>> >>> Thanks for all your help,
>> >>> Crystal
>> >>>
>> >>> On 1/13/13 3:08 PM, "Bruce Fischl" 
>>wrote:
>> >>>
>> >>>> can you cc the list? Have you visualized the transform to see if
>>it is
>> >>>> indeed incorrect?
>> >>>>
>> >>>> On Sun, 13 Jan 2013, Franklin, Crystal G wrote:
>> >>>>
>> >>>>> I used mri_convert to create the 001.mgz file. In freeview the
>> >>>>> directions appear correct.
>> >>>>>
>> >>>>> Thanks,
>> >>>>> Crystal
>> >>>>> -Original Message-
>> >>>>> From: Bruce Fischl 
>> >>>>> Date: Sun, 13 Jan 2013 09:02:16
>> >>>>> To: Franklin, Crystal G
>> >>>>> Cc: Freesurfer@nmr.mgh.harvard.edu
>> >>>>> Subject: Re: [Freesurfer] Freesurfer fails
>> >>>>>
>> >>>>> Hi Crystal
>> >>>>>
>> >>>>> how did you create the 001.mgz? When you view it in freeview does
>> >>>>> freeview have the correct directions in the anatomy (i.e. I/S, A/P
>> >>>>>and
>> >>>>> L/R)?
>> >>>>>
>> >>>>> cheers
>> >>>>> Bruce
>> >>>>> On Sat, 12 Jan 2013, Franklin, Crystal G wrote:
>> >>>>>
>> >>>>>> Freesurfer,
>> >>>>>>
>> >>>>>> I have been running a group of subjects through recon-all and
>>some
>> >>>>>>of
>> >>>>>> the
>> >>>>>> subjects are failing at the very beginning of the process and I
>>am
>> >>>>>>not
>> >>>>>> sure
>> >>>>>>  why.   The images look fine, but I keep getting the following
>> >>>>>>error:
>> >>>>>>
>> >>>>>> #@# Talairach Failure Detection Fri Dec  7 10:54:57 CST 2012
>> >>>>>> /Applications/freesurfer/subjects/PHY002/mri
>> >>>>>> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
>> >>>>>> ERROR: talairach_afd: Talairach Transform:
>>transforms/talairach.xfm
>> >>>>>> ***FAILED*** (p=0.0013, pval=0. < threshold=0.0050)
>> >>>>>> INFO: Attempting MINC mritotal to perform Talairach align
>> >>>>>>
>> >>>>>> Do you know what could be causing this?
>> >>>>>>
>> >>>>>> I read that you can include the command ?notal ?check to skip
>>this
>> >>>>>> test, but how
>> >>>>>> will this effect my data?  If I run this command  on the subjects
>> >>>>>>that
>> >>>>>> failed and combine their results with the subjects that worked
>>will
>> >>>>>>my
>> >>>>>> group
>> >>>>>> results be effected?
>> >>>>>>
>> >>>>>> Any help would be appreciated.  I have attached one of the log
>>files
>> >>>>>> for a
>> >>>>>> subject that failed.
>> >>>>>>
>> >>>>>> Thanks,
>> >>>>>> Crystal
>> >>>>>>
>> >>>>>>
>> >>>>>
>> >>>>>
>> >>>>> 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.
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>
>> >>>
>> >
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>
>


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Re: [Freesurfer] FW: Freesurfer fails

[Franklin, Crystal G]

It worked

Once again thank you,
Crystal

On 1/14/13 1:36 PM, "Nick Schmansky"  wrote:

>Crystal,
>
>I can replicate the failure you are seeing, and the problem is one that
>is fixed for the upcoming v5.2.  It is described here:
>
>https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1
>
>the first solution described should fix your problem.
>
>Nick
>
>
>On Mon, 2013-01-14 at 18:49 +, Franklin, Crystal G wrote:
>> 
>> On 1/14/13 11:38 AM, "Franklin, Crystal G" 
>>wrote:
>> 
>> >I put the data on your ftp site in the folder called
>> >crystal_failed_talairach.tar.
>> >
>> >Thanks,
>> >Crystal
>> >
>> >On 1/14/13 9:31 AM, "Bruce Fischl"  wrote:
>> >
>> >>Hi Crystal
>> >>
>> >>we'll need the image volume also
>> >>
>> >>cheers
>> >>Bruce
>> >>On Mon, 14 Jan 2013, Franklin, Crystal G
>> >>wrote:
>> >>
>> >>> Bruce,
>> >>>
>> >>> I have visually checked the transforms and they do indeed seem
>> >>>incorrect.
>> >>> The images are stretched.  I have attached the talairach.xfm for
>>one of
>> >>> the images that failed and one that worked.
>> >>>
>> >>> Thanks for all your help,
>> >>> Crystal
>> >>>
>> >>> On 1/13/13 3:08 PM, "Bruce Fischl" 
>>wrote:
>> >>>
>> >>>> can you cc the list? Have you visualized the transform to see if
>>it is
>> >>>> indeed incorrect?
>> >>>>
>> >>>> On Sun, 13 Jan 2013, Franklin, Crystal G wrote:
>> >>>>
>> >>>>> I used mri_convert to create the 001.mgz file. In freeview the
>> >>>>> directions appear correct.
>> >>>>>
>> >>>>> Thanks,
>> >>>>> Crystal
>> >>>>> -Original Message-
>> >>>>> From: Bruce Fischl 
>> >>>>> Date: Sun, 13 Jan 2013 09:02:16
>> >>>>> To: Franklin, Crystal G
>> >>>>> Cc: Freesurfer@nmr.mgh.harvard.edu
>> >>>>> Subject: Re: [Freesurfer] Freesurfer fails
>> >>>>>
>> >>>>> Hi Crystal
>> >>>>>
>> >>>>> how did you create the 001.mgz? When you view it in freeview does
>> >>>>> freeview have the correct directions in the anatomy (i.e. I/S, A/P
>> >>>>>and
>> >>>>> L/R)?
>> >>>>>
>> >>>>> cheers
>> >>>>> Bruce
>> >>>>> On Sat, 12 Jan 2013, Franklin, Crystal G wrote:
>> >>>>>
>> >>>>>> Freesurfer,
>> >>>>>>
>> >>>>>> I have been running a group of subjects through recon-all and
>>some
>> >>>>>>of
>> >>>>>> the
>> >>>>>> subjects are failing at the very beginning of the process and I
>>am
>> >>>>>>not
>> >>>>>> sure
>> >>>>>>  why.   The images look fine, but I keep getting the following
>> >>>>>>error:
>> >>>>>>
>> >>>>>> #@# Talairach Failure Detection Fri Dec  7 10:54:57 CST 2012
>> >>>>>> /Applications/freesurfer/subjects/PHY002/mri
>> >>>>>> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n
>> >>>>>> ERROR: talairach_afd: Talairach Transform:
>>transforms/talairach.xfm
>> >>>>>> ***FAILED*** (p=0.0013, pval=0. < threshold=0.0050)
>> >>>>>> INFO: Attempting MINC mritotal to perform Talairach align
>> >>>>>>
>> >>>>>> Do you know what could be causing this?
>> >>>>>>
>> >>>>>> I read that you can include the command ?notal ?check to skip
>>this
>> >>>>>> test, but how
>> >>>>>> will this effect my data?  If I run this command  on the subjects
>> >>>>>>that
>> >>>>>> failed and combine their results with the subjects that worked
>>will
>> >>>>>>my
>> >>>>>> group
>> >>>>>> results be effected?
>> >>>>>>
>> >>>>>> Any help would be appreciated.  I have attached one of the log
>>files
>> >>>>>> for a
>> >>>>>> subject that failed.
>> >>>>>>
>> >>>>>> Thanks,
>> >>>>>> Crystal
>> >>>>>>
>> >>>>>>
>> >>>>>
>> >>>>>
>> >>>>> 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.
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>
>> >>>
>> >
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
>
>


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[Freesurfer] Qdec

[Franklin, Crystal G]

Freesurfer,

I ran a group comparison using qdec and got my results showing the differences 
in the thickness between the groups.  I want to take these results I see in the 
viewer and convert them to nifti format so I can use them in another software 
called MANGO.  Which files do I need to convert that shows the contrast 
differences?

Thank you,
Crystal
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Re: [Freesurfer] Qdec

[Franklin, Crystal G]

Which options should I use when running mri_surf2vol?

Crystal

On 2/1/13 1:08 PM, "Douglas N Greve"  wrote:

>
>QDEC will create an output folder. In that folder, there will be a
>folder for each contrast. In the contrast folder, there will be a
>sig.mgh file. this has the -log10(p) significance values. You can
>convert this to nifti with mri_convert, but it will still be on the
>surface. If you need it in a volume, you can use mri_surf2vol
>doug
>
>On 02/01/2013 09:34 AM, Franklin, Crystal G wrote:
>> Freesurfer,
>>
>> I ran a group comparison using qdec and got my results showing the
>> differences in the thickness between the groups.  I want to take these
>> results I see in the viewer and convert them to nifti format so I can
>> use them in another software called MANGO.  Which files do I need to
>> convert that shows the contrast differences?
>>
>> Thank you,
>> Crystal
>>
>>
>> ___
>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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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.
>


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Re: [Freesurfer] Qdec

[Franklin, Crystal G]

So I ran mri_surf2vol --help and I am still a little confused on what to
run.  Where do I actually give the sig.mgh file?  All the options seem to
ask for an individual subjects file.

Thanks,
Crystal

On 2/1/13 5:57 PM, "Douglas N Greve"  wrote:

>You can run it with --help to get more info, let me know if you have
>questions after that
>On 02/01/2013 05:08 PM, Franklin, Crystal G wrote:
>> Which options should I use when running mri_surf2vol?
>>
>> Crystal
>>
>> On 2/1/13 1:08 PM, "Douglas N Greve"  wrote:
>>
>>> QDEC will create an output folder. In that folder, there will be a
>>> folder for each contrast. In the contrast folder, there will be a
>>> sig.mgh file. this has the -log10(p) significance values. You can
>>> convert this to nifti with mri_convert, but it will still be on the
>>> surface. If you need it in a volume, you can use mri_surf2vol
>>> doug
>>>
>>> On 02/01/2013 09:34 AM, Franklin, Crystal G wrote:
>>>> Freesurfer,
>>>>
>>>> I ran a group comparison using qdec and got my results showing the
>>>> differences in the thickness between the groups.  I want to take these
>>>> results I see in the viewer and convert them to nifti format so I can
>>>> use them in another software called MANGO.  Which files do I need to
>>>> convert that shows the contrast differences?
>>>>
>>>> Thank you,
>>>> Crystal
>>>>
>>>>
>>>> ___
>>>> 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: 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
>>>
>>>
>>> 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.
>>>
>>
>>
>
>-- 
>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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Qdec

[Franklin, Crystal G]

I never received a reply, so I am reposting my message below.  Any help
would be greatly appreciated.

Thanks in advance,
Crystal

On 2/4/13 10:35 AM, "Franklin, Crystal G"  wrote:

>So I ran mri_surf2vol --help and I am still a little confused on what to
>run.  Where do I actually give the sig.mgh file?  All the options seem to
>ask for an individual subjects file.
>
>Thanks,
>Crystal
>
>On 2/1/13 5:57 PM, "Douglas N Greve"  wrote:
>
>>You can run it with --help to get more info, let me know if you have
>>questions after that
>>On 02/01/2013 05:08 PM, Franklin, Crystal G wrote:
>>> Which options should I use when running mri_surf2vol?
>>>
>>> Crystal
>>>
>>> On 2/1/13 1:08 PM, "Douglas N Greve"  wrote:
>>>
>>>> QDEC will create an output folder. In that folder, there will be a
>>>> folder for each contrast. In the contrast folder, there will be a
>>>> sig.mgh file. this has the -log10(p) significance values. You can
>>>> convert this to nifti with mri_convert, but it will still be on the
>>>> surface. If you need it in a volume, you can use mri_surf2vol
>>>> doug
>>>>
>>>> On 02/01/2013 09:34 AM, Franklin, Crystal G wrote:
>>>>> Freesurfer,
>>>>>
>>>>> I ran a group comparison using qdec and got my results showing the
>>>>> differences in the thickness between the groups.  I want to take
>>>>>these
>>>>> results I see in the viewer and convert them to nifti format so I can
>>>>> use them in another software called MANGO.  Which files do I need to
>>>>> convert that shows the contrast differences?
>>>>>
>>>>> Thank you,
>>>>> Crystal
>>>>>
>>>>>
>>>>> ___
>>>>> 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: 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
>>>>
>>>>
>>>> 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.
>>>>
>>>
>>>
>>
>>-- 
>>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: 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] QDEC

[Franklin, Crystal G]

Freesurfer,

I want to make sure I am setting up my group analysis correctly.  I have 2 
groups, one a control population and the other a patient population , that I am 
wanting to see where there are differences controlling for age.  I set the 
group as the fixed factor and I demeaned the ages and used them as the nuisance 
factor.  Is it necessary to demean the ages before running QDEC?

Thanks,
Crystal
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Re: [Freesurfer] QDEC

[Franklin, Crystal G]

Thank you Doug. I did compute the mean from all the ages.

Crystal 

On 10/22/13 9:51 AM, "Douglas N Greve"  wrote:

>
>Hi Crystal, that is ok. When you demean the ages, make sure you compute
>the mean from all the ages, not separate means for each group
>
>doug
>
>
>
>
>On 10/21/2013 05:30 PM, Franklin, Crystal G wrote:
>> Freesurfer,
>>
>> I want to make sure I am setting up my group analysis correctly.  I
>> have 2 groups, one a control population and the other a patient
>> population , that I am wanting to see where there are differences
>> controlling for age.  I set the group as the fixed factor and I
>> demeaned the ages and used them as the nuisance factor.  Is it
>> necessary to demean the ages before running QDEC?
>>
>> Thanks,
>> Crystal
>>
>>
>> ___
>> 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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>
>
>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.
>


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[Freesurfer] Trac-all Error

[Franklin, Crystal G]

Freesurfer,

I am trying to run trac-all –prep and trac-preproc keeps exiting with errors.  
It keeps saying the unwrappedphasemaps must contain at least two volumes.  My 
data only contains one phase image and 2 magnitude images.  Do you know what 
could be causing this error or how to get around it?

Thanks in advance,
Crystal
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Re: [Freesurfer] brain mask without CSF ...

[Franklin, Crystal G]

External Email - Use Caution

3


 Original message 
From: "Greve, Douglas N.,Ph.D." 
Date: 10/10/19 5:56 PM (GMT-06:00)
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] brain mask without CSF ...

You will have to do it manually. You can create a binary CSF mask from the 
aseg.mgz using mri_binarize. Don't use 702 and 703 -- those refer to "FSL-FAST" 
not "FS-FAST". Try using the --vcsf flag to mri_binarize (ventricular csf). 
Then use mri_label2vol to map it into the functional space. Once there,  mask 
the brain.nii.gz files (found in fsd/masks and fsd/RRR/masks where RRR is each 
run) using
cp brain.nii.gz brain.orig.nii.gz
fscalc yourmask.nii.gz not and brain.orig.nii.gz -o brain.nii.gz
The rerun selxavg3-sess. It should automatically update from the brain mask 
point in the pipeline

On 10/8/2019 12:56 PM, 
stefano.silv...@libero.it wrote:

External Email - Use Caution

Dear FreeSurfer Experts,

I am running a functional analysis of subcortical structures using FS-FAST 
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) and I would use a 
brain mask excluding CSF; would it be possible using some option/flag in 
'preproc-sess'?

or should I do it manually? maybe using a command like that?


mri_binarize --i $sbjdir/mri/aparc.a2009s+aseg.mgz --match 702 703 --o 
$sbjdir/mri/GM-WM_mask.mgz


because I saw in FreeSurferColorLUT.txt the following definitions:

702 GrayMatter-FSL-FAST 205 62 78 0
703 WhiteMatter-FSL-FAST 0 225 0 0

or is there another strategy?

thanks in advance
best
stefano silvoni



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