Re: [Freesurfer] Question re: Longitudinal processing stream transforms.

[Martin Reuter]

Hi Jamie, 

looks like your command is wrong (reverse).

Here are spaces:
tp1 original space
tp2 original space
base = tp1.long.base = tp2.long.base space

so the longitudinals and the base are in the same space  (rigidly aligned and 
resliced to that space). 

The lta files map between tp1 original and the base space. 

Your command uses as mov the tp1.long.base brain.mgz file, which is already in 
base space. No need to map it to the template=base space again. In fact 
applying that transform will move it away. If you want to go from base back to 
original tp1 space, you need to invert the transform. 

Best, Martin


> On 16. Oct 2019, at 20:10, Jamie Hanson  wrote:
> 
> Dear FS List,
> 
> My group was trying to look at the overlap between cortical labels in the 
> longitudinal processing stream and I had a question re: use of transform 
> files. In brief, we followed the commands for the longitudinal processing 
> stream, creating a "subject-specific" template for each participant 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing#WorkflowSummary
>  
> ,
>  using FS v.6.0). We processed T1w images multiple times and now, we wanted 
> to transform the time 1 and time 2 (native space) scans to their 
> subject-specific template. 
> 
> We used the following commands--
> mri_vol2vol --mov 
> $INDIVIDUAL_SCAN_TIME1_DIR/sub-BNU_25864_001.long.sub-BNU_25864_template/mri/brain.mgz
>  --o $INDIVIDUAL_SCAN_TIME1/brain_001_to_temp.mgz --lta 
> $SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/transforms/sub-BNU_25864_001_to_sub-BNU_25864_template.lta
>  --targ $SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/brain.mgz
> 
> But when we did this for time 1 and time 2 scans, they were poorly aligned. I 
> also used the lta file for template to 001, but again things were poorly 
> aligned. Should we be using m3z files? Or combining different transforms? Any 
> guidance or suggestions are deeply appreciated.
> 
> Thanks much,
> Jamie.
> 
> 
> --
> Jamie Hanson
> Assistant Professor, Psychology
> Research Scientist, Learning Research and Development Center
> University of Pittsburgh
> Personal website: jamiehanson.org 
> 
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> Freesurfer mailing list
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[Freesurfer] Question re: Longitudinal processing stream transforms.

[Jamie Hanson]

External Email - Use Caution

Dear FS List,

My group was trying to look at the overlap between cortical labels in the
longitudinal processing stream and I had a question re: use of transform
files. In brief, we followed the commands for the longitudinal
processing stream, creating a "subject-specific" template for each
participant (
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing#WorkflowSummary,
using FS v.6.0). We processed T1w images multiple times and now, we wanted
to transform the time 1 and time 2 (native space) scans to their
subject-specific template.

We used the following commands--
mri_vol2vol --mov
$INDIVIDUAL_SCAN_TIME1_DIR/sub-BNU_25864_001.long.sub-BNU_25864_template/mri/brain.mgz
--o $INDIVIDUAL_SCAN_TIME1/brain_001_to_temp.mgz --lta
$SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/transforms/sub-BNU_25864_001_to_sub-BNU_25864_template.lta
--targ $SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/brain.mgz

But when we did this for time 1 and time 2 scans, they were poorly aligned.
I also used the lta file for template to 001, but again things were poorly
aligned. Should we be using m3z files? Or combining different transforms?
Any guidance or suggestions are deeply appreciated.

Thanks much,
Jamie.


--
Jamie Hanson
Assistant Professor, Psychology
Research Scientist, Learning Research and Development Center
University of Pittsburgh
Personal website: jamiehanson.org
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