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Hi Lisa,
The first line of 'base-tps' is causing the error - 'cp: cannot stat
'/dfs8/pub/ltaylor2/downs/6008/mri/transforms/6008_6008_to_6008.lta': No such
file or directory'.
Did you pass 6008_6008 as one of the time points for recon-all base processing?
Attached is the long processing. Can you attach recon.log for base processing?
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Taylor, Lisa
Sent: Monday, June 12, 2023 4:32 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,
I've attached the base recon-all.log for review. Not sure which directory would
be considered cross?
There is a file name 'base-tps', and I am not sure why it populates a 6008_6008?
[ltaylor2@login-i16:/pub/ltaylor2/downs/6008] $cat base-tps
6008_6008
6008_tp1
6008_tp2
6008_tp3
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: Monday, June 12, 2023 1:11 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Error in longitudinal process step 3
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: Monday, June 12, 2023 6:58 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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/16cO30x2aZuOwjC4AQNI_H_2uZ7mzJOWqDiuC3lZsbLiATGzay-0OvFzD6mZyrcJpBQwfobVLfJx0P5nuW7txouPOfyjuefx-kT47trA1wHPgpYKMPHvSUp-MOxESV2I4EVVek7h_Z10dhNCbtNNYyeMq6PTjtbHuCySeHkrVIJsD8enzFOGVKOW7D4BeVZP3rVFIKo7RPu3mvEtz-S0ltVP3SZubAhU-Y1EuMBFSDw15quRp48Su8fARLkztwq-7ipmHnMSdWNJciOj9YfK_Ow/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing<https://secure-web.cisco.com/1lJw66roFegPoj49nxGd8ITrM2v7hKeiXRQ6z1nAQ93HVP1duHia-Mw0pUW87BZEimQJ5-jbAWch3A5trbTqrambrjeiaQLDpEJua7Stp6o6ijFENWmDkoQ10L9Vc0p1sO4Q0XQFRe4QKIyjS8AhkV0We_8LmFTpVEumsYlYKLq02_BGEYVU1e2wl0LeEOqnTyC3Ciw0ht-IEFhNCqwf1vkIHrBuOOwasXQYxV6QGa4YT1MND6GlA8NM9HJ3D-sAaTDMrNyYk0fmJnh3aAE4Lmq5R5L6ibE9zjaNpL8bQna_OX4lFw4I2cGdwYpH-1Rs0Whrjc3tgrF5iEXggpqvQog/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1TIJb1q28A0k0t5_QVNLyETpDrnYMAxnFOYk3NQRkhy7rN7N7te2IA5fVicd1RUaAGLpujuL7aLf-_wnTmD9GHUceyp2S2bAHUOr9SOwIcTOKbyPAptg7QUFUaasE-voVHZgjN1y5I2gqLLr93RDIsXtLl4egwkLRKsvqoayVFNHJVBXcpbr0zk3qKtM0JscUAf9flGSvZ-qPMJjQhOV_noW2b0SVBYPIld-NnRvdbeq05k-67RjgO-JSQqG8cy4A5GQSa3beAI6Cr7QurQtXQ3PrC3E90GcU9Q3SmM83Ap0K4lGg_P77XPI4fjIGaDfn%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2F%2A2Fsecure-web.cisco.com%2A2F1Nz79iT6wwJKR4a3Ed_19kMfciGp4lXCuKWTwtt2qq3AkOn7J4P5JIheKc1ia2vB6p04gFO-Pj49AZY5AOn1_9_LjVgV14SGYin5YV5xa5PPlh-cnDO2kyUMI7tUCRWuDMWpXQHg2_ZBdVbu2n3FKbxss7v_5ZmGr7uZL1Km1njZHf2lrYhlme2dqIxxH3zhKsWB4pWWO4FH2rslkAwflH2cTxhwL4_WjAoIhBlnYOaaN93P3o_AtLe0PKeD4TSDkRJl7Sbt-t6NXKUZCtdUIEg%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Fsurfer.nmr.mgh.harvard.edu%2A2A2Ffswiki%2A2A2FLongitudinalProcessing__%2A3BJSUlJSU%2A21%2A21OLgoXmg%2A21VR8jFW8nFEjSePWUh_4TBKr75EMyxK6_-wYZEWEFzaObMQZ3QBXxUJuQzTzMohG70zM82RDrCK99ucBSh0JshPK1uSg%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSU%21%21OLgoXmg%21SS2VFXDwWe-GoBcp43-V-H2pHukekp6U6PqQK0pOzczR65ep0JCN5AGdfpF4JpQVnDRU3ec1BbbcT4SEudbBBUwBoUg%24>
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Taylor, Lisa
Sent: Thursday, June 8, 2023 5:08 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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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