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

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