Re: [Freesurfer] Error in longitudinal process step 3

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There should be a file named 'base-tps' in your base directory. it should contain all the -tp <> passed to your base processing, and they should agree with <tpNid> to your cross and long processing.

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Monday, June 12, 2023 9:59 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error in longitudinal process step 3

External Email - Use Caution 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://secure-web.cisco.com/1EyyhgWueEzyvjNcxxF7yEKjFB7N7uVOMoAWTuiwSL7K_YE...https://secure-web.cisco.com/1Nz79iT6wwJKR4a3Ed_19kMfciGp4lXCuKWTwtt2qq3AkOn7J4P5JIheKc1ia2vB6p04gFO-Pj49AZY5AOn1_9_LjVgV14SGYin5YV5xa5PPlh-cnDO2kyUMI7tUCRWuDMWpXQHg2_ZBdVbu2n3FKbxss7v_5ZmGr7uZL1Km1njZHf2lrYhlme2dqIxxH3zhKsWB4pWWO4FH2rslkAwflH2cTxhwL4_WjAoIhBlnYOaaN93P3o_AtLe0PKeD4TSDkRJl7Sbt-t6NXKUZCtdUIEg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Taylor, Lisa Sent: Thursday, June 8, 2023 5:08 PM To: freesurfer@nmr.mgh.harvard.edumailto: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