You need to run the data through all three steps of the longitudinal pipeline. The *.long.* directories are created in the last step (recon_all -long ... ). See also the wiki ( Google longitudinal processing freesurfer )

On Oct 8, 2016 21:19, Katherine Damme <katherine.damme@gmail.com> wrote:

Hello everyone,

I am running qdec for longitudinal data for the first time and although I have a file that matches the guide on the wiki, the script is looking in a non-exsistant file location (see below). While there is a 1001 file and a 1001_MR1, I am not sure where it is getting the 1001_MR1.long.1001 dir. Any ideas?

"long_mris_slopes --qdec long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-stack --do-label --time years --qcache fsaverage --sd /home/adapt/Cortical_Thickness_Data

Parsing the qdec table: long.qdec.table.dat

Working in SUBJECTS_DIR: /home/adapt/Cortical_Thickness_Data

Working on hemi: lh

Subject-Template: 1001

INFO: 2 TPs in 1001 , mean age: 0.487704918

===============================================================================
SUBJECT 1001 Intersecting Within-Subject Cortex Label

ERROR: /home/adapt/Cortical_Thickness_Data/1001_MR1.long.1001/label/lh.cortex.label does not exist!"