When you run the following command, what do you see?
ls -l /Volumes/HD/Post_HARDI/HIRF_Research_84/18/trac_R18/mri ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salah Showiheen sshowiheen@gmail.com Sent: Monday, April 20, 2020 7:08 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Error in Tracula-all -prep
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Hi Freesurfers
I have different type of data set and when I run trac-all I faced exactly the same issue, that I had been saving last time, but this time the file mri/brain.mgz is there!!! However, I think it is unreadable as you said las time that this file is either missing or unreadable. Because it is not missing, I assume it is unreadable.
I have attached recon-all and trac-all files.
Regards, Salah
On Wed, Apr 15, 2020 at 5:42 PM Salah Showiheen <sshowiheen@gmail.commailto:sshowiheen@gmail.com> wrote: Thanks Freesurfer developer I have followed what you have suggested and it did work for me.
Thanks once again for your help.
Regards Salah
On Sat, 11 Apr 2020, 5:54 am Yendiki, Anastasia, <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: 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.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: Friday, April 10, 2020 12:33 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer