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dear Doug,

thank you very much for the hint, your procedure works in principle; however, the --vcsf option is not available in the version of mri_binarize I have, thus I tried to create 2 labels using the options --wm+vcsf (labwmcsf.nii.gz) and -gm (labgm.nii.gz), then, once mapped onto the functional space using the template.nii.gz and the register.dof6.dat (in the bold folder), I added the 2 masks (wmcsf.nii.gz and gm.nii.gz) and computed the 'and' with the original brain.nii.gz:

cp brain.nii.gz brain.orig.nii.gz

fscalc wmcsf.nii.gz add gm.nii.gz and brain.orig.nii.gz -o brain.nii.gz

this works, however, as you can see from the figure there are holes in the mask which were not expected;

I think, may be, could it be that there are issues in the anatomical reconstruction or the segmentation by recon-all?

or, another minor issue is that I would need to use the template of each run when mapping the 2 labels into the functional space, and not the template in the bold folder, is that right?

I tried also a different solution just using the commands and options of the 'standard' pipeline:

mktemplate-sess -s $subject -fsd bold -update

mkbrainmask-sess -s $subject -fsd bold -thresh 0.1 -ndilates 0 -nerodes 1 -ne3erodes 1 -update

preproc-sess -s $subject -fsd bold -i f -nomask -sliceorder siemens -fwhm 3 -per-session -update

selxavg3-sess -s $subject -analysis ${ANALYSISDEFS} -update

in this case, the final brain.nii.gz mask seems to be fine, however it seems to erode much voxels than expected at the bottom of the brain (around RAS z=-20), would this strategy theoretically work for you?

the final goal of excluding the CSF (under the skull) from the brain mask would be to get rid of some activations 'outside the brain' I observed when using the 'standard' pipeline, I think these activations are the result of BOLD signal (of soft tissues outside the skull) and crisp movements (rotations, roll) of the head during the recording, but I can be wrong;

any further hint is really appreciated

best

stefano

Il 11 ottobre 2019 alle 0.55 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> ha scritto:

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.silvoni@libero.it wrote:

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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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