Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[M del Mar Velasco]

Thanks you anyway, Douglas
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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[Mehta, Chintan]

Thank you for the insight; that is very interesting. I'm performing tests of 
continuous independent variables over a single sample of normally developing 
children (ages uniformly distributed from 8 to 15 along with 50/50 gender 
split). The IV is, for example, age-normed cognitive scores falling in a normal 
distribution. Since there is only one group, I suppose creating my own template 
from all samples could introduce significant bias; especially if there are 
hidden sources of heterogeneity I'm unaware of.

Thank you.

Best,
Chintan


On 11/09/2017 07:07 AM, Greve, Douglas wrote:



> It might capture specific anatomical features that are unique to your
> data set. It can be tricky though as you need to make sure to include an
> equal mix of all your groups. Eg, if you have 20 ADs and 10 controls,
> you'd need to make an atlas with 10 ADs and 10 controls.


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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[Douglas N Greve]

It might capture specific anatomical features that are unique to your 
data set. It can be tricky though as you need to make sure to include an 
equal mix of all your groups. Eg, if you have 20 ADs and 10 controls, 
you'd need to make an atlas with 10 ADs and 10 controls.


On 11/08/2017 03:57 PM, Mehta, Chintan wrote:
> Dear Doug,
> Are there reasons why registering to my_subject_average 
> (template defined from, say, average in a cross-sectional sample) can 
> be better than registering to fsaverage?
> Thank you.
> Best,
> Chintan
>
>
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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[Douglas N Greve]

no, sorry


On 11/09/2017 03:50 AM, M del Mar Velasco wrote:
>
> Thanks you for your reply.
>
> I have used surfreg script and now it runs correctly. However, my 
> subject list is very long, I have 100 subjects and running surfreg 
> with all subject takes 13 hours (using all my cpus in a parallel way). 
> Is there any option to reduce this long time? Any cuda file?
>
>
> Thanks in advance,
>
>
> M del Mar
>
>
>
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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

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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[M del Mar Velasco]

Thanks you for your reply.

I have used surfreg script and now it runs correctly. However, my subject list 
is very long, I have 100 subjects and running surfreg with all subject takes 13 
hours (using all my cpus in a parallel way). Is there any option to reduce this 
long time? Any cuda file?


Thanks in advance,


M del Mar
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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[Mehta, Chintan]

Dear Doug,
Are there reasons why registering to my_subject_average (template defined from, 
say, average in a cross-sectional sample) can be better than registering to 
fsaverage?
Thank you.
Best,
Chintan
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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[Douglas Greve]

The way that mris_preproc used to work was confusing. It made it look 
like you were actually sampling to my_subject_average. In reality, it 
was only using my_subject_average to perform smoothing -- the entire 
analysis was done in fsaverage space. To clarify this, I required that 
there by a new surface registration file when something other than 
fsaverage is specified as the target. If you want to perform the 
analysis in my_subject_average, then run the surfreg script for each 
subject targeting my_subject_average. If you want to do it as before, 
then use fsaverage. You can visualize the results on my_subject_average.




On 11/7/17 8:02 AM, M del Mar Velasco wrote:


Dear FreeSurfer experts,


I am using /mris_preproc/ command with following options:


/mris_preproc --s s_001 --s s_002 --s s_003 --target 
my_subject_average --hemi lh --meas my_input_surf.mgh --out 
/my_output_path/output_file/



I observe/mris_preproc/ uses /mri_surf2surf/. My question is related 
to Freesurfer version. Using FreeSurfer 5.3, /mri_surf2surf/ takes 
/sphere.reg/ as /srcsurfreg/, while with Freesurfer 6 script 
/mri_surf2surf/ has changed. It takes /my_subject_average.sphere.reg 
/(target of /mris_preproc/) as /s//rcsurfreg/. I get an error because 
/my_subject_average.sphere.reg/ file doesn't exist inside s_001 folder.



Why Freesurfer 6 changes /srcsurfreg/ to /$target.sphere.reg/? What 
can I do in order to be coherent with my script which was designed 
using Freesurfer 5.3?



Thanks in advance,


M del Mar




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[Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[M del Mar Velasco]

Dear FreeSurfer experts,


I am using mris_preproc command with following options:


 mris_preproc --s s_001 --s s_002 --s s_003 --target my_subject_average 
--hemi lh --meas my_input_surf.mgh --out /my_output_path/output_file


I observe mris_preproc uses mri_surf2surf. My question is related to Freesurfer 
version. Using FreeSurfer 5.3, mri_surf2surf takes sphere.reg as srcsurfreg, 
while with Freesurfer 6 script mri_surf2surf has changed. It takes 
my_subject_average.sphere.reg (target of mris_preproc) as srcsurfreg. I get an 
error because my_subject_average.sphere.reg file doesn't exist inside s_001 
folder.


Why Freesurfer 6 changes srcsurfreg to $target.sphere.reg? What can I do in 
order to be coherent with my script which was designed using Freesurfer 5.3?


Thanks in advance,


M del Mar



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