The output L_parahipp_seed.surf.lh/L_parahipp/sig.nii.gz is already on
the surface.
if you need the output as text, you can run mri_convert sig.nii.gz
output.txt --ascii
or use --ascii+crsf
--ascii
save output as ascii. This will be a data file with a
single
column of data. The fastest dimension will be col, then
row,then slice, then frame.
--ascii+crsf
same as --ascii but includes col row slice and frame
On 06/30/2016 05:42 PM, Taha Abdullah wrote:
> Good Afternoon Freesurfers,
>
> I am running a seed-based connectivity for one individual subject. The
> seed is in the L_parahippocampus. I have followed the steps outlined
> in FSFast walkthrough. Below is a list of my commands. Mind you that I
> was trying to keep my analysis as simple as possible before delving
> deeper into it. I have a question on the sig.nii.gz output. Please see
> at the end.
>
> preproc-sess -s taha_brain -fwhm 0 -surface self lhrh -mni305-2mm -fsd
> resting_scans -per-run
>
> fcseed-config -segid 1016 -fcname L_parahipp -fsd resting_scans -mean
> -cfg mean.L_parahipp.config -overwrite -fillthresh 1
>
> fcseed-sess -s taha_brain -cfg mean.L_parahipp.config
>
> mkanalysis-sess -analysis L_parahipp_seed.surf.lh -surface self lh
> -fwhm 0 -notask -taskreg L_parahipp 1 -fsd resting_scans -TR 0.555
> -mcextreg -polyfit 2 -per-run
>
> selxavg3-sess -s taha_brain -a L_parahipp_seed.surf.lh
>
> Output files
> /home/tabdullah/Project/Sess01/fsd/L_parahipp_seed.surf.lh/L_parahipp/sig.nii.gz
> amongst others
>
> *Is there a way to convert the volume to a surface and then extract
> per vertex the sig value?* I used tmri_vol2surf see below:
>
> mri_vol2surf --mov ./sig.nii.gz --reg
> /home/tabdullah/resting_state_1/taha_brain/resting_scans/001/register.dof6.dat
>
> --trgsubject taha_brain --interp nearest --projfrac 0.5 --hemi lh --o
> /home/tabdullah/sig.mgh --noreshape --cortex
>
> I tried using mris_convert -c
>
> mris_convert -c ./sig.mgh
> /usr/local/freesurfer/subjects/taha_brain/surf/lh.white sig.asc
>
> The last column is all zeros. I am not entirely sure what I am doing
> wrong here, it is probably somewhere in the last two commands.
> Possibly using mri_segstats or mri_read.m? Any help would be greatly
> appreciated. Apologize in advance for the long email.
>
>
> --
> Taha Abdullah
> Department of Physiology
> Northwestern University Feinberg School of Medicine
> Masters of Science Physiology and Biophysics, Georgetown University 2015
> Work: (312)-503-0413
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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