Assuming

NIFTI files for your subjects are 1.nii, 2.nii, …, 300.nii
To name the subjects as sub1, sub2, …, sub300

In bash shell, you can do the batch submission as following at prompt:

for i in {1..300}; \

do \

echo “recon-all -all -s sub${i} -i ${i}.nii” \

recon-all -all -s sub${i} -i ${i}.nii \

done

Adjust recon-all command line options for any additional flags, and change the subject IDs for something more descriptive.

It is a good idea to submit one first to get familiar with Freesurfer recon-all output directory structure before doing the batch submission.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Dunia A Alhamad
Sent: Tuesday, November 21, 2023 12:35 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Errors in recon-all command

External Email - Use Caution

Could explain more, as I am not very expert in freesurfer

For e.g I had 300 subject and their NIFTI files are named by their number (1.nii)

How to make a script to launch, do you mean in a txt file ?

Thank you

On Tue, Nov 21, 2023 at 5:29 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

you can write a script to launch them, eg
foreach subject (your-list-of-subjects)
recon-all -s $subject -all ...
end

On 11/21/2023 12:04 PM, Dunia A Alhamad wrote:

        External Email - Use Caution

But this will take long time because I had another group with 300 patients

On Tue, Nov 21, 2023 at 5:03 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

Each subject needs to be processed separately. You will need submit 24 recon-all.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Dunia A Alhamad
Sent: Tuesday, November 21, 2023 12:00 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Errors in recon-all command

        External Email - Use Caution

What if I had 24 subjects. Should I specify the name for each one in the line ?

Dunia

On Tue, Nov 21, 2023 at 4:52 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

This is your recon-all submitted

“/Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache”

Add ‘-all’ to the line.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Dunia A Alhamad
Sent: Tuesday, November 21, 2023 11:50 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Errors in recon-all command

        External Email - Use Caution

Could you please explain more ho to specify all in recon-all command ?

Dunia

On Tue, Nov 21, 2023 at 4:48 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

It looks like you don’t have data processed. Specify ‘-all’ on recon-all on command line.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Dunia A Alhamad
Sent: Tuesday, November 21, 2023 10:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Errors in recon-all command

        External Email - Use Caution

Hello Freesurfer Developers

I'm attempting to apply preprocess and segment to my data that consist of 24 subjects by recon-all syntax, as described on the FreeSurfer wiki on macOs software

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

ERROR: cannot find /Users/duniaalhamad/Desktop/subjects/I83870_MP-RAGE_20071127095752_2/surf/lh.thickness

Darwin dyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64

1) freesurfer version: freesurfer-macOS-darwin_x86_64-7.4.1

2) platform: bash terminal

3) log file

Tue Nov 21 15:50:35 GMT 2023
cd /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3
setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects
/Applications/freesurfer/7.4.1/bin/recon-all -s I12250_MP-RAGE_20060321115220_3 -i I12250_MP-RAGE_20060321115220_3.nii -qcache

subjid I12250_MP-RAGE_20060321115220_3
setenv SUBJECTS_DIR /Users/duniaalhamad/Desktop/subjects
FREESURFER_HOME /Applications/freesurfer/7.4.1
Actual FREESURFER_HOME /Applications/freesurfer/7.4.1
build-stamp.txt: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
Darwin dyn145223.shef.ac.uk 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:31 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T8112 arm64
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8176 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
descriptors 256
memorylocked unlimited
maxproc 1333

PhysMem: 7547M used (1397M wired, 2612M compressor), 77M unused.

########################################
program versions used
7.4.1 (freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460)
7.4.1

ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: dyn145223.shef.ac.uk Platform: Darwin PlatformVersion: 23.1.0 CompilerName: Clang CompilerVersion: 12.0.0
ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.4.1 TimeStamp: 2023/11/21-15:50:36-GMT BuildTime: Jun 14 2023 00:15:19 BuildStamp: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 User: duniaalhamad Machine: