External Email - Use Caution
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.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.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.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
External Email - Use CautionHi 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.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.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salah Showiheen < sshowiheen@gmail.com> *Sent:* Monday, April 6, 2020 11:49 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Error in Tracula-all -prep
External Email - Use CautionHi 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.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