Hi Doug, this is indeed an fsfast analysis. I used the fsaverage subject
included with the 5.1 distribution. Here is the code that I used to produce
the registration matrix for one subject. Note that I did use mri_convert to
change the .mgz files into .nii.gz
The use of flirt (below) is more of an ad-hoc solution to register each
subject's anatomical image to fsaverage. I'm not wedded to this method if
there's a better alternative.
bet ${SUBJECTS_DIR}/${SUBJECT}/mri/nu.nii.gz \
${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet.nii.gz \
-f 0.3 -g 0
flirt -in ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet.nii.gz \
-ref ${SUBJECTS_DIR}/fsaverage/mri/brain.nii.gz \
-out ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet_reg.nii.gz \
-omat ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet_reg.mat \
-bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 \
-searchrz -90 90 -dof 12 -interp trilinear
cd $SUBJECTS_DIR
tkregister2 --targ $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.nii.gz \
--mov $SUBJECTS_DIR/fsaverage/mri/brain.nii.gz \
--fsl $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.mat \
--reg $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.dat \
--noedit
-----Original Message-----
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, July 18, 2011 3:11 PM
To: John Richey
Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] Problem registering labels to native space
How did you create it? What is the actual "fsaverage space"? Is this an
FSFAST analysis?
doug
John Richey wrote:
> Hi Doug, the .dat file that I mention below had already been converted
into
> a fs matrix using tkregister2.
>
> -----Original Message-----
> From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Monday, July 18, 2011 12:38 PM
> To: John Richey
> Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.edu'
> Subject: Re: [Freesurfer] Problem registering labels to native space
>
> You can't use a flirt matrix with mri_label2label. You can convert a
> flirt matrix to the proper format with tkregister2 using the --fsl
> option (this will allow you to check the reg as well).
>
> doug
>
> John Richey wrote:
>
>> Hi Bruce,
>>
>> The labels that I have fsaverage space are 3D/volume-based and not
>> surface-based labels.
>>
>>
>> -----Original Message-----
>> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, July 18, 2011 12:00 PM
>> To: John Richey
>> Cc: 'freesurfer@nmr.mgh.harvard.edu'
>> Subject: RE: [Freesurfer] Problem registering labels to native space
>>
>> Hi John
>>
>> why are you using an affine volume registration for fsaverage? Why
>> not use surface registration?
>>
>> Bruce
>>
>>
>> On Mon, 18 Jul 2011, John Richey wrote:
>>
>>
>>
>>> Hi Bruce - thanks for the reply.
>>>
>>> Here is my command line:
>>>
>>> mri_label2label --srcsubject fsaverage \ --trgsubject ${SUBJECT}
>>> --srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} \
>>> --trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} \
>>> --regmethod volume \ --reg $SUBJECTS_DIR/$SUBJECT/mri/brain_reg.dat
>>>
>>> Where "brain_reg.dat" is the subject-specific matrix I created
>>> through FLIRT. However, as I mentioned, disincluding this matrix
>>> does not seem to change the result much.
>>>
>>> One other problem I encounter... Occasionally when I view the label
>>> in native space, the label itself seems to be eroded on a voxel-wise
>>>
>>>
>> basis.
>>
>>
>>> That is, the label essentially appears as a series of non-contiguous
>>> dots (which if dialated would become contiguous).
>>>
>>>
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
>>> Sent: Monday, July 18, 2011 11:20 AM
>>> To: John Richey
>>> Cc: 'freesurfer@nmr.mgh.harvard.edu'
>>> Subject: Re: [Freesurfer] Problem registering labels to native space
>>>
>>> Hi John
>>>
>>> can you email us your label2label cmdline?
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 18 Jul 2011, John Richey
>>> wrote:
>>>
>>>
>>>
>>>> Dear freesurfer experts,
>>>>
>>>> I have a series of labels corresponding to clusters of significant
>>>> activation in fsaverage space.
>>>>
>>>> I want to map these back to native space using mri_label2label,
>>>> however when I view the individual (native) labels, the
>>>> registration is way off and the labels do not map into plausible space.
>>>>
>>>> I have tried using talairach space as an intemediary (by omitting
>>>> the --reg flag in mri_label2label), as well as using fsl tools
>>>> (FLIRT) to create a registration matrix but unfortunately I cannot
>>>> seem to get the label into the right space to query my ces maps in
>>>>
> funcroi-sess.
>
>>>> Have others encountered this problem? And how might I create a more
>>>> robust registration between fsaverage and native space to
>>>> facilitate the spatial transformation of my labels?
>>>>
>>>> Thanks very much in advance,
>>>> John
>>>> _______________________________________________
>>>> 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
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>>>
> e-mail.
>
>>>
>>>
>>>
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>>
>>
>>
>>
>
> --
> 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
>
>
>
--
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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