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Hi Lisa,

 

Can you show what your ‘base-tps’ in your base directory looks like? I think recon-all uses it to form the lta name (6008_6008_to_6008.lta).

 

Can you also send your recon-all.log for base and cross maybe?

 

Best,

 

Yujing

 

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Taylor, Lisa
Sent: Monday, June 12, 2023 3:18 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in longitudinal process step 3

 

        External Email - Use Caution        

Hi Yujing,

 

Yes, that is correct that 6008_tp1 is timepoint 1. Originally, I only had 6008_tp1,2 & 3, and when I ran step 2 the base was created. There were no errors when I ran step 2. Here's what's in the 6008/mri/transforms/ directory:

 

[ltaylor2@login-i16:/pub/ltaylor2/downs] $ls 6008/mri/transforms/

6008_to_6008_tp1.lta  

6008_tp2_to_6008.lta  

talairach.auto.xfm      

talairach.lta

6008_to_6008_tp2.lta  

6008_tp3_to_6008.lta  

talairach.auto.xfm.lta  

talairach.m3z

6008_to_6008_tp3.lta  

bak                   

talairach_avi.log       

talairach.xfm

6008_tp1_to_6008.lta  

cc_up.lta             

talairach_avi_QA.log    

talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt

 

 

Thank you again for any feedback. 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Sent: Monday, June 12, 2023 6:58 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://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 

 

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