These are the contents of a different directory from the one I asked about. TRACULA is looking for your subject's freesurfer recon under /Volumes/HD/Post_HARDI/HIRF_Research_84/18/trac_R18 because your SUBJECTS_DIR is set to /Volumes/HD/Post_HARDI/HIRF_Research_84/18 and your subject name is trac_R18. If you want it to look elsewhere, you have to set your SUBJECTS_DIR accordingly.
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 8:56 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in Tracula-all -prep
 

        External Email - Use Caution        

Hi Anastasia,

Here is what I have within the folder DIR/mri


QUT-gonzo:/ n9800093$ cd Volumes/G_RAID/Backup_Salah/Post_HARDI/HIRF_Research_84/18/Recon_R18/mri/

QUT-gonzo:mri n9800093$ ls -l

total 98496

-rw-rw-r--   1 n9800093  staff   5616637 17 Apr 16:39 T1.mgz

-rw-rw-r--   1 n9800093  staff    413271 18 Apr 05:18 aparc+aseg.mgz

-rw-rw-r--   1 n9800093  staff    411315 18 Apr 05:33 aparc.DKTatlas+aseg.mgz

-rw-rw-r--   1 n9800093  staff    449897 18 Apr 05:25 aparc.a2009s+aseg.mgz

-rw-rw-r--   1 n9800093  staff    254587 17 Apr 22:12 aseg.auto.mgz

-rw-rw-r--   1 n9800093  staff      1544 17 Apr 20:31 aseg.auto_noCCseg.label_intensities.txt

-rw-rw-r--   1 n9800093  staff    254025 17 Apr 22:10 aseg.auto_noCCseg.mgz

-rw-rw-r--   1 n9800093  staff    357285 18 Apr 05:33 aseg.mgz

-rw-rw-r--   1 n9800093  staff    254943 18 Apr 05:11 aseg.presurf.hypos.mgz

-rw-rw-r--   1 n9800093  staff    254587 17 Apr 22:12 aseg.presurf.mgz

-rw-rw-r--   1 n9800093  staff   1463192 17 Apr 22:19 brain.finalsurfs.mgz

-rw-rw-r--   1 n9800093  staff   1496605 17 Apr 22:19 brain.mgz

-rw-rw-r--   1 n9800093  staff   1495689 17 Apr 16:59 brainmask.auto.mgz

-rw-rw-r--   1 n9800093  staff   1495689 17 Apr 16:59 brainmask.mgz

-rw-rw-r--   1 n9800093  staff    557913 17 Apr 17:17 ctrl_pts.mgz

-rw-rw-r--   1 n9800093  staff    140475 17 Apr 22:25 filled.mgz

-rw-rw-r--   1 n9800093  staff    114842 18 Apr 05:00 lh.ribbon.mgz

-rw-rw-r--   1 n9800093  staff     14275 17 Apr 16:36 mri_nu_correct.mni.log

-rw-rw-r--   1 n9800093  staff     12794 17 Apr 16:32 mri_nu_correct.mni.log.bak

-rw-rw-r--   1 n9800093  staff   1600004 17 Apr 17:17 norm.mgz

-rw-rw-r--   1 n9800093  staff   5906417 17 Apr 16:36 nu.mgz

drwxrwxr-x   3 n9800093  staff       102 17 Apr 16:28 orig

-rw-rw-r--   1 n9800093  staff   5909247 17 Apr 16:29 orig.mgz

-rw-rw-r--   1 n9800093  staff   5790997 17 Apr 16:32 orig_nu.mgz

-rw-rw-r--   1 n9800093  staff  13973314 17 Apr 16:29 rawavg.mgz

-rw-rw-r--   1 n9800093  staff    117517 18 Apr 05:00 rh.ribbon.mgz

-rw-rw-r--   1 n9800093  staff    220417 18 Apr 05:00 ribbon.mgz

-rw-rw-r--   1 n9800093  staff       121 17 Apr 22:19 segment.dat

-rw-rw-r--   1 n9800093  staff      1544 17 Apr 18:03 talairach.label_intensities.txt

-rw-rw-r--   1 n9800093  staff       214 17 Apr 17:15 talairach.log

-rw-rw-r--   1 n9800093  staff       214 17 Apr 16:58 talairach_with_skull.log

drwxrwxr-x  13 n9800093  staff       442 17 Apr 22:12 transforms

-rw-rw-r--   1 n9800093  staff    419883 17 Apr 22:24 wm.asegedit.mgz

-rw-rw-r--   1 n9800093  staff    421210 17 Apr 22:24 wm.mgz

-rw-rw-r--   1 n9800093  staff    454934 17 Apr 22:22 wm.seg.mgz

-rw-rw-r--   1 n9800093  staff    468036 18 Apr 05:43 wmparc.mgz

QUT-gonzo:mri n9800093$ 




Regards,
Salah

On Tue, Apr 21, 2020 at 5:17 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:
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.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:

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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