Hi Martin, Thank you for your help and clarifications. I did run the *_to_table commands and now my LME analyses are running smoothly.
Best, Jennifer Legault On Mon, Mar 9, 2015 at 11:35 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > Hi Jennifer, > > if you are interested in volumes from the stats file, you need to use > aseg_stats_to_table and aparc_stats… to stack those data across subjects and > time points into a single table that you then analyze with the LME tools. > mris_preproc is only for stacking surface maps. > > The longitudinal QDEC file can be the same, you only need it to tell > aseg_stats_2_table etc how to create the file names for the individual > *.long.* directories. So that file only needs 2 columns (fsid, fsid-base ) > for that. And maybe you want to pass other covariates (e.g. time from > baseline, average age, gender etc) into LME via that same qdec table. The FS > stats (e.g. either thickness maps, or stats tables) will be read separately. > > If you still have difficulties with the long QDEC file, try using space > separated instead of tab! > > You don’t smooth the volume data. Look at the *_to_table commands to > generate the tables. > > Best, Martin > > > On Mar 6, 2015, at 5:09 PM, Jennifer Legault <jlegaul...@gmail.com> wrote: > > 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><long.qdec.table.dat>_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
