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Thanks Yujing,

I realized that was likely the issue after sending my message. Indeed, removing the -qcache option for this longitudinal processing step resolved my issue.

Thanks for the clarification.

Dan

On Mon, Mar 25, 2024 at 9:37 AM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

The recon-all ‘WM/GM Contrast’ step is skipped for longitudinal base processing. So, I’m not sure that ‘-qcache’ option can be used in base processing.

 

Best,

 

Yujing

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Dan Levitas
Sent: Thursday, March 21, 2024 11:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all mris_preproc error: Cannot find surf/lh.w-g.pct.mgh

 

        External Email - Use Caution        

Hello,

 

I have a longitudinal dataset where each participant was scanned twice over the course of 5 months. I have been following FS's Longitudinal Tutorial. 

 

For the CROSS section, each subjects' session scan successfully completed recon-all, where I used the following command:

recon-all \

-subjid sub-${sub}_ses-${ses} \
-i $raw_anat_file   \
-qcache \
-all

 

I then used the following recon-all command for the BASE section:

recon-all \
-base sub-${sub}_year-1 \
-tp $subjects_dir/$pre_sub_ses   \
-tp $subjects_dir/$post_sub_ses \
-qcache \
-all

 

This recon-all ran for several hours before failing at the following command:

mris_preproc --s sub-5009_year-1 --hemi lh --meas w-g.pct.mgh --target fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh

 

The error message is:

nsubjects = 1
ERROR: cannot find /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-5009_year-1/surf/lh.w-g.pct.mgh
Command exited with non-zero status 1
@#@FSTIME  2024:03:21:02:30:48 mris_preproc N 10 e 0.09 S 0.05 U 0.02 P 82% M 3568 F 0 R 2201 W 0 c 2 w 45 I 0 O 0 L 60.94 63.09 63.23
@#@FSLOADPOST 2024:03:21:02:30:48 mris_preproc N 10 60.94 63.09 63.23
Linux c50.quartz.uits.iu.edu 4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-5009_year-1 exited with ERRORS at Thu Mar 21 02:30:48 EDT 2024

 

I have checked the archive but can't seem to find a similar question. I'm a bit new to FreeSurfer, so I am unsure how to resolve this issue. I've attached the recon-all.log if that might help. 

 

FreeSurfer version: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460

Platform: Red Hat Enterprise Linux 8.9 Ootpa)

uname -a: Linux i48.red.uits.iu.edu 4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all log: see attached

 

Thank you.


Dan

 

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