As for the --preserve=timestamps error, this is a bug on osx. This will be fixed in the next 7.1 patch, but in the meantime, you can fix this manually via:

cd $FREESURFER_HOME/bin
sudo rm rca-long-tp-init
sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init -o rca-long-tp-init
sudo chmod +x rca-long-tp-init

best
Andrew


On 6/9/20, 7:36 AM, "Martin Reuter" <mreuter@nmr.mgh.harvard.edu> wrote:


    Hi Jieyin,

    a couple things I noticed:

    1) you call this:

    recon-all -long P0567/tp4 P0567/tpm -all

    this is not the way recon-all should be called. You need to specify a
    SUBJECTS_DIR under which all your time points exists usually you would
    have

    $SUBJECTS_DIR/me_tp1
    $SUBJECTS_DIR/me_tp2
    $SUBJECTS_DIR/me_tpm    # (the base or subject-template)
    $SUBJECTS_DIR/me_tp1.long.me_tpm   # (output of long stream)
    $SUBJECTS_DIR/me_tp2.long.me_tpm   # (output of long stream)
    $SUBJECTS_DIR/you_tp1
    $SUBJECTS_DIR/you_tp2
    ...


    If you want a separate directory for each subject, you would need to
    specify that dir in SUBJECTS_DIR and then the names would just be
    tp1
    tp2
    tpm
    tp1.long.tpm

    etc.

    It could be that the / in the subject name messes things up!


    2. The command that fails is:

    /Users/jif19007/Documents/PLING_dataset/MRI_raw/pilot_data/output_P0567
    /tp4.long.tpm/mri

    cp -f --preserve=timestamps
    /Users/jif19007/Documents/PLING_dataset/MRI_raw/pilot_data/output_P0567
    /tpm/mri/brainmask.mgz ./brainmask_tpm.mgz
    cp: illegal option -- -

    maybe the mac has problems with the --preserve flag? I don't know when
    this was added and whether it is really necessary. Currently I don't
    even know where this is called. Can't find it in recon-all. Maybe some
    sub-script?


    Best, Martin

    On Wed, 2020-05-20 at 19:28 -0400, Jieyin Feng wrote:
    >         External Email - Use Caution       
    > Dear FreeSurfer experts,
    >
    > I am running longitudinal processing with FreeSurfer 7.1.0 on MacOX
    > Catalina.
    > The dataset is 5 time points with T1 data. I tried to run a single
    > subject. So far it succeeded on Step 1 (recon-all at each time
    > point), and Step 2 (-base to build the template), all of them
    > reported successfully. But I failed at step3, recon-all -long, to
    > compare each timepoint with the template.
    > The log file is attached.
    > I tried to run several times with different timepoints data, all
    > reported the same stuff. My guess is at the last 9 row, reported that
    > the cp command incorrectly. But I still have no idea to fix it, or
    > maybe I need to go to freesurfer's script file? I have no idea...
    >
    > Thanks for you time and help in advance!
    > Stay safe and sound!
    >
    > Best,
    > Jieyin
    > _______________________________________________
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer