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... -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