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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.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

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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.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 Caution

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

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