[Freesurfer] overlay activation map on flattened surface

[Atena Akbari]

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Hello Freesurfer team,

I have flattened the occipital patch using "mris_flatten -w 10
subj04/surf/lh.occip.patch.3d subj04/surf/lh.occip.flattened" and it worked
without any error and I can load the flattened patch in freeview. However, I
have difficulty overlaying the activation map onto the flattened surface.
Is the following command correct for this purpose?
(mri_vol2surf --mov   spmT_0001.nii --out  subj04/surf/lh.bold.flat.mgz
 --reg  fsl_reg.dat.lta   --surf occip.flattened  --hemi   lh)

Many thanks,

Atena
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[Freesurfer] creating a cortical label using a 3D image ROI and calculating its volume and average thickness

[Yakupov, Renat /DZNE]

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Dear Freesurfer users,


I would like to do the following:

- there is an ROI mask image file in the same space as the T1-weighted image

- I would like to use that mask to define the borders of a cortical area

- and then calculate volume and average thickness of the above defined cortical 
area


I know that I can get a rough estimate of the volume by applying the ROI mask 
to the the aparc* file and calculating the number of voxels, but what I would 
really like to do is use the ROI mask to constrain the WM and pial surfaces to 
the volume inside the ROI and then calculate statistics using the surfaces 
approach.


I also know that I can combine existing labels, but unfortunately this custom 
ROI contains parts of various cortical regions, not whole regions.


Any advice would be appreciated!


Best wishes,

Renat.
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[Freesurfer] Creating a custom registration template with FreeSurfer template

[Asuka Toyofuku]

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Dear Freesurfer experts,


I have issues with creating a custom registration template. (I'm following this 
instruction: 
https://secure-web.cisco.com/1_qfYxT5WNAR-lGRNh895Kl4pqE513hIRdGqZt0w-oDRR8NwLSUh8ataurmByizdN5-6NPpWldetuOVhBt0OSuQVw_fTGTUnlfnRy5cZOC8gQ6xkn-I0sETntn5X7pssvIBMvxipctrdnnR0sdsJ_SEe-szwdE6WbG2z6qSW6mRoR1O_TSBtVJN6id4aZVTo30KwQes1T6AeGXG7volizYQI0te7HhF9DiqFp19oym11wqmrG8OvtY5FBou3V7ihQabCPQZdP81Qr6NFvLvkDT-D9iLBlRl7VIvT9MFviOs55EDcMS1LivQnETY_fTpuV_tnuLQHAkyphGLkrH_xwYA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSurfaceRegAndTemplates
 )


According to the instructions, we need to

1) Create an average subject (Creates $SUBJECTS_DIR/newtemplate)

2) Register each subject to the new template (do for both lh and rh), resulting 
in lh.sphere.reg.newtemplate and rh.sphere.reg.newtemplate
3) Get thickness values in the newtemplate space for GLM analysis
4) Create another average template based on the previous one: (Creates 
$SUBJECTS_DIR/newnewtemplate)

I'm stuck with the 3) command.
Instruction suggests:
mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ...

and this is my code:
for d in Teen*
do mris_preproc --surfreg sphere.reg.teenheart_average_template --s $d --hemi 
lh --out lh.surfreg.teenheart_average_template.thickness --meas thickness
done


( I specified hemi and output because, without it, I got ERROR: no source hemi 
specified)

My command led to an error saying:

ERROR: format for lh.surfreg.teenheart_average_template.thickness not recognized

So my questions are:

a) what does it mean that "format for lh.surfreg.average_template.thickness not 
recognised"? Any ideas on how to fix this?

b) Does this mris_preproc --surfreg command produce different smoothing mgh 
files? (e.g., fwhm10, fwhm15, fwhm20...?)

Because standard mris_preproc before GLM 
analysis(https://secure-web.cisco.com/1lH2n5girv1pSO3WmL3I9nDeL07oFU0ViiAmz_tUClrPQjFwGxFIj8Uw-HpRNXN4_ADUrXeK8GQcI91O76PQUoilqcBBTuz_cbBfg2BUYMoPChwgcqvL5jiL3mJuCIhROFLqmz6Ay1m-Mt3VqQfQiArWs7KPRzGvA7altNpSDzxPE8sB-_TlC3JKVV06-mzVggUwD3kS7BkRaXe1z174NmNbHyzHlcoUEX12pXebgZgGEv6bLiKxH2Wrka404J_vPCmOb8me-0QbLp1HJJdw_vbklt9SSNhdXnR2XCQ-vZeRZep_w5lp7gvo-TBU4Fdow4MtnGe-Oy6yM7OBUf0230w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis)
 are done with previously qcashed data (e.g., need thickness.fwhm10.fsaverage 
to run mris_preproc), but at this point, I don't have any of these thickness 
files with different smoothing levels.

c ) If this mris_preproc --surfreg command does not generate a set of thickness 
maps in **newtemplate space** at different smoothing levels, what kind of 
command should I run?


Any input is appreciated!


Best regards,

Asuka
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[Freesurfer] How to write rh.w-g.pct from recon-all stats output into a table

[ERNEST KISSI]

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I processed several items of data. And I have rh.w-g.pct file in my stats

folders.


How can I get process this file to get table reading file? I tried to use

 asegstats2table and aparcstats2table but it didn’t work.


Could you provide me with necessary information about getting of stats from

rh.w-g.pct to table file like asegstats2table?


Thank you.
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