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



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