Hi Lisa,

I’m wondering what your naming convention is.

Here is tutorial page for longitudinal processing: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

Looking at your attached recon-all.log, I’m assuming ‘6008_tp1’ is your time point 1, and ‘6008’ is your base templateid from your recon-all -base.

What are the .lta files ouput from base process? If ‘6008’ is your base templateid, you should find them in $SUBJECTS_DIR/6008/ mri/transforms/.

How are your cross recon-all commands?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Taylor, Lisa
Sent: Thursday, June 8, 2023 5:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error in longitudinal process step 3

External Email - Use Caution

Hi,

I am trying to run the long. processing pipeline but I am having issues with step three. Here's the last lines in the recon-all log:

cp -vf /dfs8/pub/ltaylor2/downs/6008/mri/transforms/6008_6008_to_6008.lta /dfs8/pub/ltaylor2/downs/6008_tp1.long.6008/mri/transforms/6008_6008_to_6008_tp1.long.6008.lta

cp: cannot stat '/dfs8/pub/ltaylor2/downs/6008/mri/transforms/6008_6008_to_6008.lta': No such file or directory

Linux hpc3-l18-04 4.18.0-425.10.1.el8_7.x86_64 #1 SMP Thu Jan 12 16:32:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 6008_tp1.long.6008 exited with ERRORS at Mon Jun 5 10:04:45 PDT 2023

I recognize that 6008_6008_to_6008.lta is not correct, but I am not sure why it is trying to pull a file name like this instead of the following ones that are actually in 6008_tp1.long.6008/mri/transforms/ :

6008_to_6008_tp1.lta

6008_to_6008_tp3.lta

6008_tp2_to_6008.lta

bak

talairach.auto.xfm

talairach_avi.log

talairach.lta

talairach.xfm
6008_to_6008_tp2.lta

6008_tp1_to_6008.lta

6008_tp3_to_6008.lta

cc_up.lta

talairach.auto.xfm.lta

talairach_avi_QA.log

talairach.m3z

talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt

Here is an example of how the scripts are set up when using the HPC3. I have also attached the some output files. Let me know if any more information is needed.

#!/bin/bash

#SBATCH --job-name=fs_tp1_tp_long

#SBATCH -A ltaylor2

#SBATCH -p free

#SBATCH --nodes=1

#SBATCH --ntasks=1

#SBATCH --cpus-per-task=1

#SBATCH --error=slurm-%J.err

module load freesurfer/6.0.1

source ${FREESURFER_HOME}/SetUpFreeSurfer.sh

export SUBJECTS_DIR=/pub/ltaylor2/downs

#run freesurfer longitudinal workflow step 3

srun ${FREESURFER_HOME}/bin/recon-all -long 6008_tp1 6008 -all > out_fs_6008_tp1_long_output.txt

Please help! Thank you,

Lisa