Re: [Freesurfer] Errors in recon-all command

21 Nov 2023

      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
        <https://secure-web.cisco.com/1sL0UR9IcjyzN-iiFPRBpUbos_zcdbT2W0RQcJ-3jMPXPBbG7t5-6HgMR60s4YWqde4tZa0XWjtkT0aWl3XybyhjThRfDIZmH8oNIZTQHT3KJDNpBj1DUZ6PKEZrrygdbT1DPTNtfO_zUn04IsLpbI6O57RcgvpVsXEx8ujYU-9-eFN0mWsVDj6gaP-ZccrPky_ruv3wCEiKCyGbSpPLpWXig3WAycCHA4_N_rPef9kRpg4gEFbLVjmjTPA3yx66OOHSaNacYpeFWBHZKyZbf4aKwJBcw2IPYCBLyjn1TOfQIc4V1h7skqAUUfgGHtlo3I_FNzpbevSUMMmOhMJUuzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all>

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

        Darwin dyn145223.shef.ac.uk
        <http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk>
        23.1.0 Darwin Kernel Version 23.1.0: Mon Oct9 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:
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        <http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.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.

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         Platform: Darwin  PlatformVersion: 23.1.0  CompilerName:
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         TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14
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         Platform: Darwin  PlatformVersion: 23.1.0  CompilerName:
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        ProgramName: mris_volmask  ProgramArguments: mris_volmask
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         BuildStamp:
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         Platform: Darwin  PlatformVersion: 23.1.0  CompilerName:
        Clang  CompilerVersion: 12.0.0
        ProgramName: mri_tessellate  ProgramArguments:
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         TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14
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         Platform: Darwin  PlatformVersion: 23.1.0  CompilerName:
        Clang  CompilerVersion: 12.0.0
        ProgramName: mri_vol2surf  ProgramArguments: mri_vol2surf
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         Platform: Darwin  PlatformVersion: 23.1.0  CompilerName:
        Clang  CompilerVersion: 12.0.0
        ProgramName: mri_vol2vol  ProgramArguments: mri_vol2vol
        -all-info  ProgramVersion: 7.4.1  TimeStamp:
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         BuildStamp:
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         Platform: Darwin  PlatformVersion: 23.1.0  CompilerName:
        Clang  CompilerVersion: 12.0.0
        ProgramName: mri_voldiff  ProgramArguments: mri_voldiff
        -all-info  ProgramVersion: 7.4.1  TimeStamp:
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         BuildStamp:
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         User: duniaalhamad  Machine: dyn145223.shef.ac.uk
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         Platform: Darwin  PlatformVersion: 23.1.0  CompilerName:
        Clang  CompilerVersion: 12.0.0
        ProgramName: mri_watershed  ProgramArguments:
        mri_watershed -all-info  ProgramVersion: 7.4.1  TimeStamp:
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         BuildStamp:
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         User: duniaalhamad  Machine: dyn145223.shef.ac.uk
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         Platform: Darwin  PlatformVersion: 23.1.0  CompilerName:
        Clang  CompilerVersion: 12.0.0
        ProgramName: tkregister2  ProgramArguments:
        tkregister2_cmdl -all-info  ProgramVersion: 7.4.1
         TimeStamp: 2023/11/21-15:50:37-GMT  BuildTime: Jun 14
        2023 00:15:19  BuildStamp:
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         User: duniaalhamad  Machine: dyn145223.shef.ac.uk
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         Platform: Darwin  PlatformVersion: 23.1.0  CompilerName:
        Clang  CompilerVersion: 12.0.0
        mri_motion_correct.fsl 7.4.1
        mri_convert -all-info
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         BuildStamp:
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         User: duniaalhamad  Machine: dyn145223.shef.ac.uk
        <http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.shef.ac.uk>
         Platform: Darwin  PlatformVersion: 23.1.0  CompilerName:
        Clang  CompilerVersion: 12.0.0
        Program nu_correct, built from:
        Package MNI N3, version 1.12.0, compiled by
        nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2)
        on 2015-06-19 at 15:37:08
        #######################################
        GCADIR /Applications/freesurfer/7.4.1/average
        GCA RB_all_2020-01-02.gca
        GCASkull RB_all_withskull_2020_01_02.gca
        AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
        GCSDIR /Applications/freesurfer/7.4.1/average
        GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
        #######################################
        /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3
        \n mri_convert
        /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii
        /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz
        \n
        mri_convert
        /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii
        /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz

        reading from
        /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3.nii...
        TR=8.98, TE=0.00, TI=0.00, flip angle=0.00
        i_ras = (1, 0, 0)
        j_ras = (0, 1, 0)
        k_ras = (0, 0, 1)
        writing to
        /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/mri/orig/001.mgz...
        #--------------------------------------------
        #@# Qdec Cache preproc lh thickness fsaverage Tue Nov 21
        15:50:39 GMT 2023
        /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/surf
        \n mris_preproc --s I12250_MP-RAGE_20060321115220_3 --hemi
        lh --meas thickness --target fsaverage --out
        lh.thickness.fsaverage.mgh \n
        nsubjects = 1
        ERROR: cannot find
        /Users/duniaalhamad/Desktop/subjects/I12250_MP-RAGE_20060321115220_3/surf/lh.thickness
        Darwin dyn145223.shef.ac.uk
        <http://secure-web.cisco.com/17ssZVEmpLNHt-CxwXxe9utDZsBI2l_rJnTwKTg_6x0x-K6FKabQXiCAiOpJJ3jXRp7-Q4ZXIaOAjfwriBhG0_AJuohS3d_EghKyRbyUGq0Bea09MEYuszpRjdEVKFsZyp3h5e2t9K_SQci1CBIuW-awzsKbzuOwx9I_VWm8erPdUnQ5xndc2NI2S8FRk77pB9IGhsG-Q8d1uX-bbUhQ33MDOTgaou2GKHocaMySmZQ-y3hTFZg27Wbe--2ykviYsq8ryJ1M0qSInI05pH-bYMypcAgqH4UQw3pKon2pNOsJF5o_ghlyvZzNdNZDIPk-xpvllr1akdqDcrMm7X8OpEg/http%3A%2F%2Fdyn145223.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

        recon-all -s I12250_MP-RAGE_20060321115220_3 exited with
        ERRORS at Tue Nov 21 15:50:39 GMT 2023

        To report a problem, see *MailScanner has detected a
        possible fraud attempt from "secure-web.cisco.com"
        claiming to be*
        http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
        <http://secure-web.cisco.com/1kSmtgzR_pxmyG0Pcf2UmG3i7fQr9HeDya5uym7dX6z6tGZdMuhAr9QAO3NNFaL7EqiWYP3ahWxhaiiv5tbGWQ0AXo2G1smogNP5-5iWwGZQWXQhiA2kHfRzjeDr53nNN6jkHQNUbqwyTgQdhhGsviPdSNnu0IedSruBqCCVVn9tD9qqb-1l_dvLt_VKy-LeuPLheMwTDPkd7Y8D00QuxSFTVFN1eWjVMh4owHpADK6tRvs0RmLF2aXjKlrBm99PPU-qagrrset7G1i0yJVWYxTfUJnFzWssLyDDZQ4YFTCn7qQANuztgiuY8CrrxJWePWp9PbtaLrFxBsRYiJV9G_g/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>

        Thank you

        -- 

        *Dunia Ahmad Al-Hamad*

        PhD Student

        Sheffield Institute of Translational Neuroscience (SiTraN)

        The University of Sheffield

        385a Glossop Road

        Sheffield

        S10 2HQ

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Re: [Freesurfer] Errors in recon-all command