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 Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
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 &
[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
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
joya
Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i T1_original_joya.nii -subject joya -all &
[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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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,JasminJasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
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,JasminJasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Jasmin
if this is the first time you have run this subject (that is, the subject dir doesn't exist within $SUBJECTS_DIR), you still need to specify the input volume with -i T1_original_joya.nii
cheers Bruce
On Tue, 26 Jan 2016, Jasmin Alves wrote:
Bruce, Sorry to be a pain, but for some reason, I cannot still get recon-all to work.
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
Hi Bruce,
Could you elaborate on what you mean I need to specify the input volume?
Thanks, Jasmin
On Wed, Jan 27, 2016 at 5:48 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jasmin
if this is the first time you have run this subject (that is, the subject dir doesn't exist within $SUBJECTS_DIR), you still need to specify the input volume with -i T1_original_joya.nii
cheers Bruce
On Tue, 26 Jan 2016, Jasmin Alves wrote:
Bruce,
Sorry to be a pain, but for some reason, I cannot still get recon-all to work.
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Jasmin
oh, I take it back. It looks like the SUBJECTS_DIR you pointed it at didn't exist. Create it first with
mkdir /Desktop/Brain_Child_subs
then try rerunning. Bruce
On Wed, 27 Jan 2016, Jasmin Alves wrote:
Hi Bruce, Could you elaborate on what you mean I need to specify the input volume?
Thanks, Jasmin
On Wed, Jan 27, 2016 at 5:48 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Jasmin
if this is the first time you have run this subject (that is, the subject dir doesn't exist within $SUBJECTS_DIR), you still need to specify the input volume with -i T1_original_joya.nii cheers Bruce On Tue, 26 Jan 2016, Jasmin Alves wrote: Bruce, Sorry to be a pain, but for some reason, I cannot still get recon-all to work. Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
This directory already exists. I had already made it, which is why I am confused that it cannot be found.
On Wed, Jan 27, 2016 at 10:43 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Jasmin
oh, I take it back. It looks like the SUBJECTS_DIR you pointed it at didn't exist. Create it first with
mkdir /Desktop/Brain_Child_subs
then try rerunning. Bruce
On Wed, 27 Jan 2016, Jasmin Alves wrote:
Hi Bruce,
Could you elaborate on what you mean I need to specify the input volume?
Thanks, Jasmin
On Wed, Jan 27, 2016 at 5:48 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Jasmin
if this is the first time you have run this subject (that is, the subject dir doesn't exist within $SUBJECTS_DIR), you still need to specify the input volume with -i T1_original_joya.nii cheers Bruce On Tue, 26 Jan 2016, Jasmin Alves wrote: Bruce, Sorry to be a pain, but for some reason, I cannot still get recon-all to work. Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Jasmin Alves