Re: [Freesurfer] Error in longitudinal process step 3

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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Sent: Tuesday, June 13, 2023 10:44 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error in longitudinal process step 3

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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: Re: [Freesurfer] Error in longitudinal process step 3

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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-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 Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Monday, June 12, 2023 2:27 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in longitudinal process step 3

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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-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: Monday, June 12, 2023 4:32 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in longitudinal process step 3

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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-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 Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Monday, June 12, 2023 1:11 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in longitudinal process step 3

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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.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: Monday, June 12, 2023 3:18 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in longitudinal process step 3

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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Sent: Monday, June 12, 2023 6:58 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error in longitudinal process step 3

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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/1AEScOI1V8JpAwJzbO6xu1ZWU3teslKx9-JIfLmgqDzWkU-...https://secure-web.cisco.com/1Nq3IZzDO2GU4j12MpN0pTK3Kxp59czmWiCxqVMuLFUsl2uKjS2KB_-9nu9syhZPpQBh-3H-01t3dA5r3pqaoi__BmTnAvykhEwVX18E0yf-EKS9r30c7IXNEr8WC-bsAkeIUYnEiBllyvwXcF0hYXYbnX_DSK_7fw7G6aZhOvUcXOolwYJd-w3w8UascwUxqQfn5CDrRrvELFl8zf22aJMfNuT7y0crnWxS279G8Pp8Lgu2nXuLREfr6NFYJnIc_F8js3HnbagI9sh9WM1azu3Rnfe3uDIho5HryEhtPwFQDtYiXpZGFGiykJo6Cilwr/https%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*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1lJw66roFegPoj49nxGd8ITrM2v7hKeiXRQ6z1nAQ93HVP1duHia-Mw0pUW87BZEimQJ5-jbAWch3A5trbTqrambrjeiaQLDpEJua7Stp6o6ijFENWmDkoQ10L9Vc0p1sO4Q0XQFRe4QKIyjS8AhkV0We_8LmFTpVEumsYlYKLq02_BGEYVU1e2wl0LeEOqnTyC3Ciw0ht-IEFhNCqwf1vkIHrBuOOwasXQYxV6QGa4YT1MND6GlA8NM9HJ3D-sAaTDMrNyYk0fmJnh3aAE4Lmq5R5L6ibE9zjaNpL8bQna_OX4lFw4I2cGdwYpH-1Rs0Whrjc3tgrF5iEXggpqvQog*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2F*2A2Fsecure-web.cisco.com*2A2F1TIJb1q28A0k0t5_QVNLyETpDrnYMAxnFOYk3NQRkhy7rN7N7te2IA5fVicd1RUaAGLpujuL7aLf-_wnTmD9GHUceyp2S2bAHUOr9SOwIcTOKbyPAptg7QUFUaasE-voVHZgjN1y5I2gqLLr93RDIsXtLl4egwkLRKsvqoayVFNHJVBXcpbr0zk3qKtM0JscUAf9flGSvZ-qPMJjQhOV_noW2b0SVBYPIld-NnRvdbeq05k-67RjgO-JSQqG8cy4A5GQSa3beAI6Cr7QurQtXQ3PrC3E90GcU9Q3SmM83Ap0K4lGg_P77XPI4fjIGaDfn*2A2Fhttps*2A2A3A*2A2A2F*2A2A2Furldefense.com*2A2A2Fv3*2A2A2F__https*2A2A3A*2A2A2F*2A2A2Fsecure-web.cisco.com*2A2A2F1Nz79iT6wwJKR4a3Ed_19kMfciGp4lXCuKWTwtt2qq3AkOn7J4P5JIheKc1ia2vB6p04gFO-Pj49AZY5AOn1_9_LjVgV14SGYin5YV5xa5PPlh-cnDO2kyUMI7tUCRWuDMWpXQHg2_ZBdVbu2n3FKbxss7v_5ZmGr7uZL1Km1njZHf2lrYhlme2dqIxxH3zhKsWB4pWWO4FH2rslkAwflH2cTxhwL4_WjAoIhBlnYOaaN93P3o_AtLe0PKeD4TSDkRJl7Sbt-t6NXKUZCtdUIEg*2A2A2Fhttps*2A2A2A3A*2A2A2A2F*2A2A2A2Fsurfer.nmr.mgh.harvard.edu*2A2A2A2Ffswiki*2A2A2A2FLongitudinalProcessing__*2A2A3BJSUlJSU*2A2A21*2A2A21OLgoXmg*2A2A21VR8jFW8nFEjSePWUh_4TBKr75EMyxK6_-wYZEWEFzaObMQZ3QBXxUJuQzTzMohG70zM82RDrCK99ucBSh0JshPK1uSg*2A2A24__*2A3BJSUlJSUlJSUlJSUlJSUlJSUlJSU*2A21*2A21OLgoXmg*2A21SS2VFXDwWe-GoBcp43-V-H2pHukekp6U6PqQK0pOzczR65ep0JCN5AGdfpF4JpQVnDRU3ec1BbbcT4SEudbBBUwBoUg*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU*21*21OLgoXmg*21Ryd3KdryIN4Kzx9TBGoa15gAQpjEFRDiPnpGAEIttBdi_3Ol2vcI_i5j2tb7zlBUrP5468MtWNcjlsPZv6ThH3VAN8o*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!OLgoXmg!QX2czVhN-JM653AWcklfBQqMoabEZsvxQfpjt6_mcCEqriaFB_5UdXfbeyONaBDi7MSI-D8ef2cM7ikukL5D5wwYGpc$

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

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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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