External Email - Use Caution Okay! Thank you for that. I will change the script and run the process. Prob won't have results for some time and will check back in.
Thank you!! ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <yhuan...@mgh.harvard.edu> Sent: Tuesday, June 13, 2023 12:19 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in longitudinal process step 3 External Email - Use Caution In your script, this line selects all 4 directories (6008, 6008_tp1, 6008_tp2, 6008_tp3) timepoints=`ls -d1 ${subid}* | cut -d'_' -f2` change it to timepoints=`ls -d1 ${subid} _tp* | cut -d'_' -f2` From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Taylor, Lisa Sent: Tuesday, June 13, 2023 2:58 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, The recon-all.logs I sent previously were the recon-all was done for each individual time point before longitudinal process. I wonder if there is something in the step 2 script I have that is adding the additional file. I have also attached the recon-all.log file for 6008/scripts/recon-all.log. Here's the script that I run for step 2: [ltaylor2@login-i16:/pub/ltaylor2/downs] $cat freesurfer_longitudinal_step2.sh #!/bin/sh # NOTE, basic freesurfer recon-all should already be run on subjects before this longitudinal processing step # see freesurfer_prep.sh script for details wd=$(pwd) #dirs=`ls -d1 ${wd}/* | awk -F/ '/'_tp'?[0-9]/ { print $NF } '` subids=`ls -d1 ${wd}/* | awk -F/ '/'_tp'?[0-9]$/ { print $NF } ' | sed s/'_tp'[0-9]//g | uniq` echo $subids if [[ $# -lt 2 ]] ; then echo 'Usage: sh freesurfer_longitudinal_step2.sh [queue] [account_to_charge]' echo '[queue] = free | standard' echo '[account_to_charge] = DBKEATOR | DBKEATOR_LAB | UMAR_LAB' echo 'PLEASE ONLY USE THE FREE QUEUE UNLESS OTHERWISE INSTRUCTED' exit 0 fi for subid in ${subids}; do #get list of timepoints from directory names timepoints=`ls -d1 ${subid}* | cut -d'_' -f2` len=`echo "${timepoints}" | wc -l` if [ ${len} -gt 1 ] then printf '#!/bin/bash\n' > freesurfer_${subid}_long_s2.sub printf '#SBATCH --job-name=fs_%s_tp%s_long\n' ${subjid} ${time} >> freesurfer_${subid}_long_s2.sub printf '#SBATCH -A %s\n' ${2} >> freesurfer_${subid}_long_s2.sub printf '#SBATCH -p %s\n' ${1} >> freesurfer_${subid}_long_s2.sub printf '#SBATCH --nodes=1\n' >> freesurfer_${subid}_long_s2.sub printf '#SBATCH --ntasks=1\n' >> freesurfer_${subid}_long_s2.sub printf '#SBATCH --cpus-per-task=1\n' >> freesurfer_${subid}_long_s2.sub printf '#SBATCH --error=slurm-%%J.err\n' >> freesurfer_${subid}_long_s2.sub printf 'module load freesurfer/6.0.1\n' >> freesurfer_${subid}_long_s2.sub printf 'source ${FREESURFER_HOME}/SetUpFreeSurfer.sh\n' >> freesurfer_${subid}_long_s2.sub printf 'export SUBJECTS_DIR=%s\n' ${wd} >> freesurfer_${subid}_long_s2.sub printf '#run freesurfer longitudinal workflow step 2\n' >> freesurfer_${subid}_long_s2.sub printf 'srun ${FREESURFER_HOME}/bin/recon-all -base %s' ${subid} >> freesurfer_${subid}_long_s2.sub for time in ${timepoints}; do printf " -tp %s_%s" ${subid} ${time} >> freesurfer_${subid}_long_s2.sub done printf " -all\n" >> freesurfer_${subid}_long_s2.sub fi sbatch freesurfer_${subid}_long_s2.sub done Just to clarify, just in case it's important, that there are 3 directories before running step 2, and after step 2 there is the main directory that is created. So initially, after running recon-all individually for each timepoint, there are just the timepoint directories (6008_tp1, 6008_tp2, 6008_tp3) and then after step 2 completes there are 4 directories (6008, 6008_tp1, 6008_tp2, 6008_tp3) Thank you again! Lisa ________________________________ 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: Tuesday, June 13, 2023 10:44 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 sorry that I didn’t make it clear. From what I understand, your longitudinal processing should look like the following: In step 1 (cross), you should have processed each of your time points separately, in your case, <tpNid> = 6008_tp1, 6008_tp2, 6008_tp3 recon-all -all -s <tpNid> -i path_to_tpN_dcm In step 2 (base), recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all You used 6008 for <templateid>, so your recon-all command should look like ‘recon-all -base 6008 -tp 6008_tp1 -tp 6008_tp2 -tp 6008_tp3 -all’. I’m wondering if ‘-tp 6008_6008’ was passed to your ‘recon-all -base’ command. I was hoping to take a look of recon-all.log in your base directory - /dfs8/pub/ltaylor2/downs/6008/scripts/recon-all.log. In step 3 (long), ‘recon-all -long <tpNid> <templateid> -all’. It should output in directory <tpNid>.long.<templateid>. 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: Tuesday, June 13, 2023 12:55 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, I have attached recon-all.log for all 3 time points for this participant (is this what you mean?). Before running step2 of the long. processing, I have the setup the following directories for this participant: 6008_tp1 6008_tp2 6008_tp3 After step two, it creates the 6008/ directory and I am assuming the 6008_6008 to 6008.lta file, but I am not sure why because I don't originally have a 6008_6008 directory just the three above and the one that is created after step 2 (6008/). Is there something in my step 2 script creating this erroneous file? Thank you again, Yujing, for helping try to solve this. Lisa ________________________________ 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 2:27 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, 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<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 4:32 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, 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/1M4CNCtBdhgc57v4KqHnVJjzyLLm3op_FhpCQOcu1XGzgzbrTR-OmZlCcI7sc4MYCFDawt5Borcb3-nDf0c39S2XLxjVrved_rzQvH8Xpj72wIqEL-WKM9NMDw1VlWNtVnMEpyW8C0yTfUaywV6SjxhFPvWjIyC3mMCn8AhC84puEL4iEoOA3eGoE52BAgHEzu2765D7JZ94zKRZShJ2ZHPVDEmPGnTNTDmQZUKhYOhRIIdL3OutbJXgjY7u1wmFfvVdJrikh07zWtFLa6wXLawbak5E5nOltYzlqqbxEvSgMTA5va8MzGy2-q3uGLFbveHD8fxVUPlfkkFgumYrcmA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing<https://secure-web.cisco.com/1WYxVDrGm5HgcN1Ghlgxxyec1paTUn5q2_CeIyStuDlOIP3sn0-zMlxI2t5mZLvZIYlqpf8OFoaaqhh6UVhzs7yF-L9B6aleoXZieRVnAM0cGMQR9SjcGyI4cT0zOU0ifMQk_MlV3gYdxN65FgHqsvspWlcaKRchA8GQtJvPimFyRPO2a6F2Xlre6iOhyu0WymDxIWI3i3JJEyfCFTygCWgY-8HZ_it-uca_8PmkpBh3AHWLfClU7eynDQAurdqDsPcY5ED5FVKmHi6kPOQ-AbNEyH0HbRR063pDMZWkc8s9bDdIBIJSsoIxFq3hRhiwBzaSjlMzjq_3iEGrG0FWwoQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1yhaicAQC5j8RdRx00QzR-1H_ecghoMsYC8ElYlh5_rGafe6zKHA4F_QaN_oQtHDyLPXXx27utv_P8c94CsT33UD6CVSnRxKMHqarmqsjE63-tKJ344uXriFHIE9R_H8xPZJ6kjSCGgtMsCkGfzBywEclFFJ0oh96XqV3arvj_zgzYLkPG3O81wqX_vJOxHvy-Rp52n6B9CikCM3VTmxzV8w_ZwM9-VEsqkZLFbd-y_yQC3H2XfJwdSXFU1ROYg8U69TkBPr9gGcrcUWWo1LD6w%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1P_IdYRZXS6sGbfTKULpF0ng0TCZTD7hE3K-GTcgRIaTkPHAXuG2kJeOORizpSrthPf_Jg6Wxp3ReHFCE2gUaOdMlX6yLG_N3DEF8132yjdHc9d-uuJe455IDd0C9Z34GRJNYN6IINNU_LJR1EXfjJn9bcW_FDRL4B9gptzjmrH842C1PuVUT0pPWBL8KMIFp08Q5MohvlktVBNh3L1XPgBCF_AWP-1U2SrvWK5XFvCebttk3hbm0lSYQSd7F29pddiyue34G-7xRA3zoxfuEXA*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2F*2A2Fsecure-web.cisco.com*2A2F1lJw66roFegPoj49nxGd8ITrM2v7hKeiXRQ6z1nAQ93HVP1duHia-Mw0pUW87BZEimQJ5-jbAWch3A5trbTqrambrjeiaQLDpEJua7Stp6o6ijFENWmDkoQ10L9Vc0p1sO4Q0XQFRe4QKIyjS8AhkV0We_8LmFTpVEumsYlYKLq02_BGEYVU1e2wl0LeEOqnTyC3Ciw0ht-IEFhNCqwf1vkIHrBuOOwasXQYxV6QGa4YT1MND6GlA8NM9HJ3D-sAaTDMrNyYk0fmJnh3aAE4Lmq5R5L6ibE9zjaNpL8bQna_OX4lFw4I2cGdwYpH-1Rs0Whrjc3tgrF5iEXggpqvQog*2A2Fhttps*2A2A3A*2A2A2F*2A2A2Furldefense.com*2A2A2Fv3*2A2A2F__https*2A2A3A*2A2A2F*2A2A2Fsecure-web.cisco.com*2A2A2F1TIJb1q28A0k0t5_QVNLyETpDrnYMAxnFOYk3NQRkhy7rN7N7te2IA5fVicd1RUaAGLpujuL7aLf-_wnTmD9GHUceyp2S2bAHUOr9SOwIcTOKbyPAptg7QUFUaasE-voVHZgjN1y5I2gqLLr93RDIsXtLl4egwkLRKsvqoayVFNHJVBXcpbr0zk3qKtM0JscUAf9flGSvZ-qPMJjQhOV_noW2b0SVBYPIld-NnRvdbeq05k-67RjgO-JSQqG8cy4A5GQSa3beAI6Cr7QurQtXQ3PrC3E90GcU9Q3SmM83Ap0K4lGg_P77XPI4fjIGaDfn*2A2A2Fhttps*2A2A2A3A*2A2A2A2F*2A2A2A2Furldefense.com*2A2A2A2Fv3*2A2A2A2F__https*2A2A2A3A*2A2A2A2F*2A2A2A2Fsecure-web.cisco.com*2A2A2A2F1Nz79iT6wwJKR4a3Ed_19kMfciGp4lXCuKWTwtt2qq3AkOn7J4P5JIheKc1ia2vB6p04gFO-Pj49AZY5AOn1_9_LjVgV14SGYin5YV5xa5PPlh-cnDO2kyUMI7tUCRWuDMWpXQHg2_ZBdVbu2n3FKbxss7v_5ZmGr7uZL1Km1njZHf2lrYhlme2dqIxxH3zhKsWB4pWWO4FH2rslkAwflH2cTxhwL4_WjAoIhBlnYOaaN93P3o_AtLe0PKeD4TSDkRJl7Sbt-t6NXKUZCtdUIEg*2A2A2A2Fhttps*2A2A2A2A3A*2A2A2A2A2F*2A2A2A2A2Fsurfer.nmr.mgh.harvard.edu*2A2A2A2A2Ffswiki*2A2A2A2A2FLongitudinalProcessing__*2A2A2A3BJSUlJSU*2A2A2A21*2A2A2A21OLgoXmg*2A2A2A21VR8jFW8nFEjSePWUh_4TBKr75EMyxK6_-wYZEWEFzaObMQZ3QBXxUJuQzTzMohG70zM82RDrCK99ucBSh0JshPK1uSg*2A2A2A24__*2A2A3BJSUlJSUlJSUlJSUlJSUlJSUlJSU*2A2A21*2A2A21OLgoXmg*2A2A21SS2VFXDwWe-GoBcp43-V-H2pHukekp6U6PqQK0pOzczR65ep0JCN5AGdfpF4JpQVnDRU3ec1BbbcT4SEudbBBUwBoUg*2A2A24__*2A3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU*2A21*2A21OLgoXmg*2A21Ryd3KdryIN4Kzx9TBGoa15gAQpjEFRDiPnpGAEIttBdi_3Ol2vcI_i5j2tb7zlBUrP5468MtWNcjlsPZv6ThH3VAN8o*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU*21*21OLgoXmg*21QX2czVhN-JM653AWcklfBQqMoabEZsvxQfpjt6_mcCEqriaFB_5UdXfbeyONaBDi7MSI-D8ef2cM7ikukL5D5wwYGpc*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!OLgoXmg!R3C97a8haN8Uii_8FJBEaw-PKzP6Wf0hhGqX5-LTPRMMljFYDd78hC4buHJ6CukOwZqUylU1jNBCu6JB7sFdlIeQAyk$> 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 . WARNING - This email originated from outside of the UCI Health email system. Do not click any links and do not open attachments unless you can confirm the sender. PLEASE FORWARD SUSPICIOUS EMAILS TO: secur...@hs.uci.edu<mailto:secur...@hs.uci.edu> .
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