Hi Salah - You're probably running into this problem: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64575.html
You can edit the script $FREESURFER_HOME/bin/trac-preproc, search for tkregister2, change it to tkregister2_cmdl, then try again.
a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salah Showiheen sshowiheen@gmail.com Sent: Friday, April 10, 2020 12:33 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error in Tracula-all -prep
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Hi Anastasia,
It is true that this file was missing. When I added it, the processing in trac-all -intra took longer time but comes with an error :
/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.
Any hint in fixing this issue or finding if the file (brain,mgz) is unreadable? I was able to open it in freeviewer, though!!
NB: log file is attached.
Regards, Salah
On Thu, Apr 9, 2020 at 12:35 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Salah - It looks like it didn't find your subject's freesurfer recon when it was doing the pre-processing, so it skipped some steps that you need to go beyond that point. Based on your SUBJECTS_DIR and your subject name, it looked for this file: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/mri/brain.mgz
Any chance this was missing or unreadable?
a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen <sshowiheen@gmail.commailto:sshowiheen@gmail.com> Sent: Monday, April 6, 2020 11:49 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Error in Tracula-all -prep
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Hi Freesurfer community,
I have an issue that I spent ages trying to figure out and this error has been asked about back in (17/12/2016) and the title is ([Freesurfer] Tracula trac -all preprocessing error.
my error is:
ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni
There is an issue that the mini folder is empty.
Attached is the log file and the configuration file (tracula_conf.txt)
Regards, Salah _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer