Re: [Freesurfer] recon -all errors

Bruce,

Sorry to be a pain, but for some reason, I cannot still get recon-all to work.

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya -all &

[1] 14655

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: SUBJECTS_DIR /Desktop/Brain_Child_subs does not exist.

Thanks,

Jasmin

On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Jasmin

you need a '-' sign first. It should be:

recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject \ joya -all &

cheers Bruce

On Mon, 25 Jan 2016, Jasmin Alves wrote:

Hi Bruce,

...

Thanks for the reply, I attempted to direct Subjects_dir to the folder with my data but I received the following error.

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ export SUBJECTS_DIR=/Desktop/Brain_Child_subs

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all &

[1] 13867

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: Flag all unrecognized.

-sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all

Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

recon-all -s joya exited with ERRORS at Mon Jan 25 21:12:58 PST 2016

Thanks so much,

Jasmin

On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu

...

wrote: Hi Jasmin

  you  need to create a directory where you have write permission
  and room for the subject reconstruction to be written to, then
  set the SUBJECTS_DIR environment variable to point to it. At the
  moment you are trying to use the subject directory we
  distribute, which is in some system (and read-only) location.
  You can do this on the command line of recon-all via:

  recon-all -sd <path to directory> ...

  cheers
  Bruce


  On Sun, 24 Jan 2016, Jasmin Alves wrote:

  Hello Freesurfer,

  I am trying to learn freesurfer and ran into the following
  issues below
  running the recon -all command.

  FREESURFER_HOME: /Applications/freesurfer

  Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

  Kernel info: Darwin 14.5.0 x86_64

    1)

  joya

   2)

   Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i
  T1_original_joya.nii
  -subject joya -all &


  3)

  [1] 12300

  Jasmins-MacBook-Pro:subjects jasminalves$ mkdir:
  /Applications/freesurfer/subjects/joya: Permission denied

  mkdir: /Applications/freesurfer/subjects/joya/scripts:
  Permission denied

  mkdir: /Applications/freesurfer/subjects/joya/scripts:
  Permission denied

  cp:
  /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
  No such
  file or directory

  cat:
  /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
  No such
  file or directory

  INFO: FreeSurfer build stamps do not match

  Subject Stamp:

  Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

  INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects

  Actual FREESURFER_HOME /Applications/freesurfer

  /Applications/freesurfer/subjects/joya: No such file or
  directory.


  [1]+  Exit 1                  recon-all -i
  T1_original_joya.nii -subject
  joya -a

  Thank you,Jasmin

Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu

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-- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu

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