Hi all,
I am new to Freesurfer and have run my participants’ data through the longitudinal preprocessing stream and am now trying to assemble my data so that they can be put into a linear mixed effect model analysis. While the longitudinal tutorial with cortical thickness data is very helpful, I am interested in GM volume (specific ROIs in aseg. + the lh and rh aparc. files) and have run into a few problems. 1) Problem with mris_preproc command/with QDEC file: a) I have made a Longitudinal QDEC file (attached in this comment as an excel file and .dat file) and I made sure to export to my Subjects dir, and then put in the following command: mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi lh --meas volume --out lh.volume.mgh When I run this command, it only runs for my first participant (which it takes from the Longitudinal QDEC file, such that if I take out the first row of the QDEC file, it starts with the next participant) I do not receive any sort of error message or anything, it just doesn’t keep running. Furthermore, I cannot find the output file (lh.volume.mgh) anywhere in my subjects directory. b) I am also wondering whether I need to make separate QDEC files for 1) aseg data 2) lh.aparc and 3) rh.aparc. Right now, my QDEC file has all of the information of interest in one place. c) I made the QDEC file in excel, and saved it as tab delimited (when I try to save it as space delimited (.prn--which I rename as .dat) and re-open it, it loses many of my headers and data). Does it have to be space delimited, and if so, is there another way of formatting it as space delimited? If not, then is there something else wrong with my QDEC format? 2) I do not know whether I am supposed to smooth the volume stack. According to my understanding of the Longitudinal tutorial, we should first run mris_preproc to concatenate our files and resample volume data to a common subject. Next, we should smooth the stacked/concatenated file. Should I use the following command: mri_vol2surf --src input file --hemi hemisphere --fwhm 10 --out outpufile Thank you for taking the time to read this email, I sincerely appreciate it. Best, Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University
long.qdec.table.xlsx
Description: MS-Excel 2007 spreadsheet
long.qdec.table.dat
Description: Binary data
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