Dear all,
When I want to run a recon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong?
Best,
Marja
Hi Marja
can you send us the command you ran and the full screen output and the recon-all.log file?
thanks Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote:
Dear all,
When I want to run a recon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong?
Best,
Marja
Hi Bruce,
I tried a lot of different commands, trying to figure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist. --- *bash-3.2$ recon-all -i L001.nii -subjid L1 -all* *ERROR: cannot find L001.nii* *Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64*
*recon-all -s exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016*
*For more details, see the log file * *To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting* *---* *bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all* *ERROR: SUBJECTS_DIR /Desktop/MRI does not exist.* *bash-3.2$ export SUBJECTS_DIR=/Documents/MRI* *bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all* *ERROR: SUBJECTS_DIR /Documents/MRI does not exist.* *bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1* *bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all* *ERROR: cannot find L001.nii.gz* *Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64*
*recon-all -s exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016*
*For more details, see the log file * *To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting* *---*
Where can I find the log? I have been looking for it, hoping to give me some insight in the problem, but I could not find it.
It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out.
Thank you!
Best,
Marja
On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Marja
can you send us the command you ran and the full screen output and the recon-all.log file?
thanks Bruce
On Wed, 19 Oct 2016, Marja Caverlé wrote:
Dear all,
When I want to run a recon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong?
Best,
Marja
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.
what directory is the file L001.nii.gz in?
cheers Bruce
On Wed, 19 Oct 2016, Marja Caverlé wrote:
Hi Bruce,
I tried a lot of different commands, trying to figure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist. ---bash-3.2$ recon-all -i L001.nii -subjid L1 -all ERROR: cannot find L001.nii Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Desktop/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Documents/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1 bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: cannot find L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Where can I find the log? I have been looking for it, hoping to give me some insight in the problem, but I could not find it.
It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out.
Thank you!
Best,
Marja
On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
can you send us the command you ran and the full screen output and the recon-all.log file? thanks Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear all, When I want to run a recon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong? Best, Marja
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.
I changed it multiple times because I thought it would solve the problem (applications, desktop, documents). Currently it is in Documents/MRI.
Marja Caverlé
On 19 Oct 2016, at 15:29, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what directory is the file L001.nii.gz in?
cheers Bruce
On Wed, 19 Oct 2016, Marja Caverlé wrote:
Hi Bruce, I tried a lot of different commands, trying to figure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist. ---bash-3.2$ recon-all -i L001.nii -subjid L1 -all ERROR: cannot find L001.nii Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Desktop/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Documents/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1 bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: cannot find L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Where can I find the log? I have been looking for it, hoping to give me some insight in the problem, but I could not find it. It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out. Thank you! Best, Marja On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
can you send us the command you ran and the full screen output and the recon-all.log file? thanks Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear all, When I want to run a recon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong? Best, Marja
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 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.
You need to provide the full path to it with the -i command. Then you can use -sd <SUBJECTS_DIR> and -s <SUBJECT ID> to specify where the output should go. Make sure that the directory <SUBJECTS_DIR> exists and is writeable by you, as recon-all will create a subtree called <SUBJECT_ID> under it
cheers Bruce
On Wed, 19 Oct 2016, Marja Caverle wrote:
I changed it multiple times because I thought it would solve the problem (applications, desktop, documents). Currently it is in Documents/MRI.
Marja Caverlé
On 19 Oct 2016, at 15:29, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what directory is the file L001.nii.gz in?
cheers Bruce
On Wed, 19 Oct 2016, Marja Caverlé wrote:
Hi Bruce, I tried a lot of different commands, trying to figure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist. ---bash-3.2$ recon-all -i L001.nii -subjid L1 -all ERROR: cannot find L001.nii Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Desktop/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Documents/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1 bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: cannot find L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Where can I find the log? I have been looking for it, hoping to give me some insight in the problem, but I could not find it. It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out. Thank you! Best, Marja On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
can you send us the command you ran and the full screen output and the recon-all.log file? thanks Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear all, When I want to run a recon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong? Best, Marja
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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce,
Thanks for your reply. I tried that, but it does not change anything (at least if I did correctly what you suggested):
bash-3.2$ recon-all -i /Documents/MRI/L001.nii.gz -sd MRI -subjid L1 -all ERROR: cannot find /Documents/MRI/L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Wed Oct 19 15:39:16 CEST 2016
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Wed, Oct 19, 2016 at 3:34 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
You need to provide the full path to it with the -i command. Then you can use -sd <SUBJECTS_DIR> and -s <SUBJECT ID> to specify where the output should go. Make sure that the directory <SUBJECTS_DIR> exists and is writeable by you, as recon-all will create a subtree called <SUBJECT_ID> under it
cheers Bruce
On Wed, 19 Oct 2016, Marja Caverle wrote:
I changed it multiple times because I thought it would solve the problem
(applications, desktop, documents). Currently it is in Documents/MRI.
Marja Caverlé
On 19 Oct 2016, at 15:29, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
what directory is the file L001.nii.gz in?
cheers Bruce
On Wed, 19 Oct 2016, Marja Caverlé wrote:
Hi Bruce, I tried a lot of different commands, trying to figure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist. ---bash-3.2$ recon-all -i L001.nii -subjid L1 -all ERROR: cannot find L001.nii Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting
bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Desktop/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Documents/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1 bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: cannot find L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting
Where can I find the log? I have been looking for it, hoping to give me some insight in the problem, but I could not find it. It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out. Thank you! Best, Marja On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Marja
can you send us the command you ran and the full screen output andthe recon-all.log file?
thanks Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear all, When I want to run a recon-all -all, I keep getting theerror saying that the input file cannot be found. Any idea what is going wrong?
Best, Marja
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 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 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
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.
what does:
ls -l /Documents/MRI/L001.nii.gz
show?
On Wed, 19 Oct 2016, Marja Caverlé wrote:
Dear Bruce,
Thanks for your reply. I tried that, but it does not change anything (at least if I did correctly what you suggested):
bash-3.2$ recon-all -i /Documents/MRI/L001.nii.gz -sd MRI -subjid L1 -all ERROR: cannot find /Documents/MRI/L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Wed Oct 19 15:39:16 CEST 2016
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Wed, Oct 19, 2016 at 3:34 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
You need to provide the full path to it with the -i command. Then you can use -sd <SUBJECTS_DIR> and -s <SUBJECT ID> to specify where the output should go. Make sure that the directory <SUBJECTS_DIR> exists and is writeable by you, as recon-all will create a subtree called <SUBJECT_ID> under it cheers Bruce On Wed, 19 Oct 2016, Marja Caverle wrote: I changed it multiple times because I thought it would solve the problem (applications, desktop, documents). Currently it is in Documents/MRI. Marja Caverlé On 19 Oct 2016, at 15:29, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: what directory is the file L001.nii.gz in? cheers Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Hi Bruce, I tried a lot of different commands, trying to figure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist. ---bash-3.2$ recon-all -i L001.nii -subjid L1 -all ERROR: cannot find L001.nii Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --- bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Desktop/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Documents/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1 bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: cannot find L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --- Where can I find the log? I have been looking for it, hoping to give me some insight in the problem, but I could not find it. It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out. Thank you! Best, Marja On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja can you send us the command you ran and the full screen output and the recon-all.log file? thanks Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear all, When I want to run a recon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong? Best, Marja _______________________________________________ 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 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 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
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 Bruce,
that command also says there is no file or directory:
bash-3.2$ ls -l /Documents/MRI/L001.nii.gz ls: /Documents/MRI/L001.nii.gz: No such file or directory bash-3.2$ ls -l /Desktop/MRI/L001.nii.gz ls: /Desktop/MRI/L001.nii.gz: No such file or directory
Even though, the niftis are really there.
Best,
Marja
On Wed, Oct 19, 2016 at 3:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what does:
ls -l /Documents/MRI/L001.nii.gz
show?
On Wed, 19 Oct 2016, Marja Caverlé wrote:
Dear Bruce,
Thanks for your reply. I tried that, but it does not change anything (at least if I did correctly what you suggested):
bash-3.2$ recon-all -i /Documents/MRI/L001.nii.gz -sd MRI -subjid L1 -all ERROR: cannot find /Documents/MRI/L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Wed Oct 19 15:39:16 CEST 2016
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting
On Wed, Oct 19, 2016 at 3:34 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
You need to provide the full path to it with the -i command. Thenyou can use -sd <SUBJECTS_DIR> and -s <SUBJECT ID> to specify where the output should go. Make sure that the directory <SUBJECTS_DIR> exists and is writeable by you, as recon-all will create a subtree called <SUBJECT_ID> under it
cheers Bruce On Wed, 19 Oct 2016, Marja Caverle wrote: I changed it multiple times because I thought it would solvethe problem (applications, desktop, documents). Currently it is in Documents/MRI.
Marja Caverlé On 19 Oct 2016, at 15:29, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
what directory is the file L001.nii.gz in? cheers Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Hi Bruce, I tried a lot of different commands, trying tofigure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist. ---bash-3.2$ recon-all -i L001.nii -subjid L1 -all ERROR: cannot find L001.nii Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting --- bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Desktop/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Documents/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1 bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: cannot find L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting --- Where can I find the log? I have been looking for it, hoping to give me some insight in the problem, but I could not find it. It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out. Thank you! Best, Marja On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
can you send us the command you ran and thefull screen output and the recon-all.log file?
thanks Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear all, When I want to run a recon-all -all, Ikeep getting the error saying that the input file cannot be found. Any idea what is going wrong?
Best, Marja _______________________________________________ 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.
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The information in this e-mail is intended only for theperson 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
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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 Marja
you need to figure out where the input files are! How do you know they are there? Can you run:
ls -l /Desktop/MRI/*.nii*
cheers Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote:
Hi Bruce,
that command also says there is no file or directory:
bash-3.2$ ls -l /Documents/MRI/L001.nii.gz ls: /Documents/MRI/L001.nii.gz: No such file or directory bash-3.2$ ls -l /Desktop/MRI/L001.nii.gz ls: /Desktop/MRI/L001.nii.gz: No such file or directory
Even though, the niftis are really there.
Best,
Marja
On Wed, Oct 19, 2016 at 3:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: what does:
ls -l /Documents/MRI/L001.nii.gz show? On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear Bruce, Thanks for your reply. I tried that, but it does not change anything (at least if I did correctly what you suggested): bash-3.2$ recon-all -i /Documents/MRI/L001.nii.gz -sd MRI -subjid L1 -all ERROR: cannot find /Documents/MRI/L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 15:39:16 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On Wed, Oct 19, 2016 at 3:34 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: You need to provide the full path to it with the -i command. Then you can use -sd <SUBJECTS_DIR> and -s <SUBJECT ID> to specify where the output should go. Make sure that the directory <SUBJECTS_DIR> exists and is writeable by you, as recon-all will create a subtree called <SUBJECT_ID> under it cheers Bruce On Wed, 19 Oct 2016, Marja Caverle wrote: I changed it multiple times because I thought it would solve the problem (applications, desktop, documents). Currently it is in Documents/MRI. Marja Caverlé On 19 Oct 2016, at 15:29, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: what directory is the file L001.nii.gz in? cheers Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Hi Bruce, I tried a lot of different commands, trying to figure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist. ---bash-3.2$ recon-all -i L001.nii -subjid L1 -all ERROR: cannot find L001.nii Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --- bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Desktop/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Documents/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1 bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: cannot find L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --- Where can I find the log? I have been looking for it, hoping to give me some insight in the problem, but I could not find it. It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out. Thank you! Best, Marja On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja can you send us the command you ran and the full screen output and the recon-all.log file? thanks Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear all, When I want to run a recon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong? Best, Marja _______________________________________________ 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 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 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 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 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 Bruce,
After downloading, I have put the files in those folders, and I can see them. Furthermore, when I go to the folder and then do the ls command, they are listed as being there. however the command looking for all files with the .nii extension says there are no files there. I don't understand how this is possible, do you?
Thanks for helping out.
ls: /Desktop/MRI/L001.nii.gz: No such file or directory bash-3.2$ ls -l /Desktop/MRI/*.nii* ls: /Desktop/MRI/*.nii*: No such file or directory bash-3.2$ ls L001.nii.gz S1 S13 S4 S8 L1 S1.nii S13.nii S4.nii S8.nii bash-3.2$ cd .. bash-3.2$ cd .. bash-3.2$ ls 20151020volunteer Library Applications Movies Desktop Music oasys.log Desktop.feat OneDrive simdir Desktop.ica Pictures simdir- Documents Public simdir-- Downloads ibt_application.log simdir--- Dropbox ibtsa.log summary.txt Google Drive matlab bash-3.2$ cd Desktop bash-3.2$ ls ARCsleep TIMID printscreens MRI Uren.xlsx bash-3.2$ cd MRI bash-3.2$ ls L001.nii.gz S1 S13 S4 S8 L1 S1.nii S13.nii S4.nii S8.nii bash-3.2$
On Thu, Oct 20, 2016 at 3:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Marja
you need to figure out where the input files are! How do you know they are there? Can you run:
ls -l /Desktop/MRI/*.nii*
cheers Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote:
Hi Bruce,
that command also says there is no file or directory:
bash-3.2$ ls -l /Documents/MRI/L001.nii.gz ls: /Documents/MRI/L001.nii.gz: No such file or directory bash-3.2$ ls -l /Desktop/MRI/L001.nii.gz ls: /Desktop/MRI/L001.nii.gz: No such file or directory
Even though, the niftis are really there.
Best,
Marja
On Wed, Oct 19, 2016 at 3:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: what does:
ls -l /Documents/MRI/L001.nii.gz show? On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear Bruce, Thanks for your reply. I tried that, but it does not changeanything (at least if I did correctly what you suggested):
bash-3.2$ recon-all -i /Documents/MRI/L001.nii.gz -sd MRI-subjid L1 -all ERROR: cannot find /Documents/MRI/L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Wed Oct 19 15:39:16 CEST2016
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Wed, Oct 19, 2016 at 3:34 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
You need to provide the full path to it with the -icommand. Then you can use -sd <SUBJECTS_DIR> and -s <SUBJECT ID> to specify where the output should go. Make sure that the directory <SUBJECTS_DIR> exists and is writeable by you, as recon-all will create a subtree called <SUBJECT_ID> under it
cheers Bruce On Wed, 19 Oct 2016, Marja Caverle wrote: I changed it multiple times because I thought itwould solve the problem (applications, desktop, documents). Currently it is in Documents/MRI.
Marja Caverlé On 19 Oct 2016, at 15:29, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: what directory is the file L001.nii.gz in? cheers Bruce On Wed, 19 Oct 2016, Marja Caverléwrote:
Hi Bruce, I tried a lot of different commands,trying to figure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist. ---bash-3.2$ recon-all -i L001.nii -subjid L1 -all ERROR: cannot find L001.nii Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting --- bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Desktop/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Documents/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1 bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: cannot find L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting --- Where can I find the log? I have been looking for it, hoping to give me some insight in the problem, but I could not find it. It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out. Thank you! Best, Marja On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
can you send us the command youran and the full screen output and the recon-all.log file?
thanks Bruce On Wed, 19 Oct 2016, MarjaCaverlé wrote:
Dear all, When I want to run arecon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong?
Best, Marja ______________________________
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail isintended 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/compli anceline . 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.
______________________________
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The information in this e-mail is intendedonly 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 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 The information in this e-mail is intended only for theperson 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.
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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.
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you probably aren't in the MRI dir. What does the command:
pwd
return? And are there any mac-savvy users that can help you out nearby?
cheers Bruce
On Thu, 20 Oct 2016, Marja Caverlé wrote:
Hi Bruce,
After downloading, I have put the files in those folders, and I can see them. Furthermore, when I go to the folder and then do the ls command, they are listed as being there. however the command looking for all files with the .nii extension says there are no files there. I don't understand how this is possible, do you?
Thanks for helping out.
ls: /Desktop/MRI/L001.nii.gz: No such file or directory bash-3.2$ ls -l /Desktop/MRI/*.nii* ls: /Desktop/MRI/*.nii*: No such file or directory bash-3.2$ ls L001.nii.gz S1 S13 S4 S8 L1 S1.nii S13.nii S4.nii S8.nii bash-3.2$ cd .. bash-3.2$ cd .. bash-3.2$ ls 20151020volunteer Library Applications Movies Desktop Music oasys.log Desktop.feat OneDrive simdir Desktop.ica Pictures simdir- Documents Public simdir-- Downloads ibt_application.log simdir--- Dropbox ibtsa.log summary.txt Google Drive matlab bash-3.2$ cd Desktop bash-3.2$ ls ARCsleep TIMID printscreens MRI Uren.xlsx bash-3.2$ cd MRI bash-3.2$ ls L001.nii.gz S1 S13 S4 S8 L1 S1.nii S13.nii S4.nii S8.nii bash-3.2$
On Thu, Oct 20, 2016 at 3:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
you need to figure out where the input files are! How do you know they are there? Can you run: ls -l /Desktop/MRI/*.nii* cheers Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Hi Bruce, that command also says there is no file or directory: bash-3.2$ ls -l /Documents/MRI/L001.nii.gz ls: /Documents/MRI/L001.nii.gz: No such file or directory bash-3.2$ ls -l /Desktop/MRI/L001.nii.gz ls: /Desktop/MRI/L001.nii.gz: No such file or directory Even though, the niftis are really there. Best, Marja On Wed, Oct 19, 2016 at 3:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: what does: ls -l /Documents/MRI/L001.nii.gz show? On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear Bruce, Thanks for your reply. I tried that, but it does not change anything (at least if I did correctly what you suggested): bash-3.2$ recon-all -i /Documents/MRI/L001.nii.gz -sd MRI -subjid L1 -all ERROR: cannot find /Documents/MRI/L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 15:39:16 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On Wed, Oct 19, 2016 at 3:34 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: You need to provide the full path to it with the -i command. Then you can use -sd <SUBJECTS_DIR> and -s <SUBJECT ID> to specify where the output should go. Make sure that the directory <SUBJECTS_DIR> exists and is writeable by you, as recon-all will create a subtree called <SUBJECT_ID> under it cheers Bruce On Wed, 19 Oct 2016, Marja Caverle wrote: I changed it multiple times because I thought it would solve the problem (applications, desktop, documents). Currently it is in Documents/MRI. Marja Caverlé On 19 Oct 2016, at 15:29, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: what directory is the file L001.nii.gz in? cheers Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Hi Bruce, I tried a lot of different commands, trying to figure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist. ---bash-3.2$ recon-all -i L001.nii -subjid L1 -all ERROR: cannot find L001.nii Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --- bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Desktop/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Documents/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1 bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: cannot find L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --- Where can I find the log? I have been looking for it, hoping to give me some insight in the problem, but I could not find it. It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out. Thank you! Best, Marja On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja can you send us the command you ran and the full screen output and the recon-all.log file? thanks Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear all, When I want to run a recon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong? Best, Marja _______________________________________________ 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 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 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 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 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.
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bash-3.2$ pwd /Users/MarjaCaverle/Desktop/MRI
(this means that I am in the right one right?)
Not really someone near, furthermore, almost no one uses mac. I did some analysis a few months back, and it worked just fine, but now I get these errors. I intentionally did not update to Sierra yet, because I was afraid that it might give problems with Freesurfer. Do you think I should update?
On Thu, Oct 20, 2016 at 11:59 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
you probably aren't in the MRI dir. What does the command:
pwd
return? And are there any mac-savvy users that can help you out nearby?
cheers Bruce
On Thu, 20 Oct 2016, Marja Caverlé wrote:
Hi Bruce,
After downloading, I have put the files in those folders, and I can see them. Furthermore, when I go to the folder and then do the ls command, they are listed as being there. however the command looking for all files with the .nii extension says there are no files there. I don't understand how this is possible, do you?
Thanks for helping out.
ls: /Desktop/MRI/L001.nii.gz: No such file or directory bash-3.2$ ls -l /Desktop/MRI/*.nii* ls: /Desktop/MRI/*.nii*: No such file or directory bash-3.2$ ls L001.nii.gz S1 S13 S4 S8 L1 S1.nii S13.nii S4.nii S8.nii bash-3.2$ cd .. bash-3.2$ cd .. bash-3.2$ ls 20151020volunteer Library Applications Movies Desktop Music oasys.log Desktop.feat OneDrive simdir Desktop.ica Pictures simdir- Documents Public simdir-- Downloads ibt_application.log simdir--- Dropbox ibtsa.log summary.txt Google Drive matlab bash-3.2$ cd Desktop bash-3.2$ ls ARCsleep TIMID printscreens MRI Uren.xlsx bash-3.2$ cd MRI bash-3.2$ ls L001.nii.gz S1 S13 S4 S8 L1 S1.nii S13.nii S4.nii S8.nii bash-3.2$
On Thu, Oct 20, 2016 at 3:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
you need to figure out where the input files are! How do you knowthey are there? Can you run:
ls -l /Desktop/MRI/*.nii* cheers Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Hi Bruce, that command also says there is no file or directory: bash-3.2$ ls -l /Documents/MRI/L001.nii.gz ls: /Documents/MRI/L001.nii.gz: No such file or directory bash-3.2$ ls -l /Desktop/MRI/L001.nii.gz ls: /Desktop/MRI/L001.nii.gz: No such file or directory Even though, the niftis are really there. Best, Marja On Wed, Oct 19, 2016 at 3:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: what does:
ls -l /Documents/MRI/L001.nii.gz show? On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear Bruce, Thanks for your reply. I tried that, but it doesnot change anything (at least if I did correctly what you suggested):
bash-3.2$ recon-all -i /Documents/MRI/L001.nii.gz-sd MRI -subjid L1 -all ERROR: cannot find /Documents/MRI/L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Wed Oct 1915:39:16 CEST 2016
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On Wed, Oct 19, 2016 at 3:34 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: You need to provide the full path to itwith the -i command. Then you can use -sd <SUBJECTS_DIR> and -s <SUBJECT ID> to specify where the output should go. Make sure that the directory <SUBJECTS_DIR> exists and is writeable by you, as recon-all will create a subtree called <SUBJECT_ID> under it
cheers Bruce On Wed, 19 Oct 2016, Marja Caverle wrote: I changed it multiple times because Ithought it would solve the problem (applications, desktop, documents). Currently it is in Documents/MRI.
Marja Caverlé On 19 Oct 2016, at 15:29, BruceFischl fischl@nmr.mgh.harvard.edu wrote:
what directory is the fileL001.nii.gz in?
cheers Bruce On Wed, 19 Oct 2016,Marja Caverlé wrote:
Hi Bruce, I tried a lot ofdifferent commands, trying to figure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist. ---bash-3.2$ recon-all -i L001.nii -subjid L1 -all ERROR: cannot find L001.nii Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016;
root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016 For more details, see the log file To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --- bash-3.2$ recon-all -iL001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Desktop/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Documents/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1 bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: cannot find L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016;
root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016 For more details, see the log file To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --- Where can I find the log?I have been looking for it, hoping to give me some insight in the problem, but I could not find it. It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out. Thank you! Best, Marja On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Marja
can you send us thecommand you ran and the full screen output and the recon-all.log file?
thanks Bruce On Wed, 19 Oct 2016,Marja Caverlé wrote:
Dear all, When I want torun a recon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong?
Best, Marja _______________________________________________ Freesurfer mailing listFreesurfer@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.
______________________________
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______________________________
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
The information in this e-mail is intended onlyfor 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 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 theperson 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.
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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.
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Try using /Users/MarjaCaverle/Desktop/MRI as the path in your -i
On Oct 20, 2016, at 6:03 PM, Marja Caverlé marja.caverle@gmail.com wrote:
/Users/MarjaCaverle/Desktop/MRI
Hi Bruce,
Today I restarted my computer, and tried everything again. This time I indeed used the full path in the -i and the sub_dir, and now it seems to work!
Thanks for helping out.
Best,
Marja
On Fri, Oct 21, 2016 at 4:35 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Try using /Users/MarjaCaverle/Desktop/MRI as the path in your -i
On Oct 20, 2016, at 6:03 PM, Marja Caverlé marja.caverle@gmail.com
wrote:
/Users/MarjaCaverle/Desktop/MRI
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.
glad it worked out
cheers Bruce On Fri, 21 Oct 2016, Marja Caverlé wrote:
Hi Bruce,
Today I restarted my computer, and tried everything again. This time I indeed used the full path in the -i and the sub_dir, and now it seems to work!
Thanks for helping out.
Best,
Marja
On Fri, Oct 21, 2016 at 4:35 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Try using /Users/MarjaCaverle/Desktop/MRI as the path in your -i
> On Oct 20, 2016, at 6:03 PM, Marja Caverlé <marja.caverle@gmail.com> wrote: > > /Users/MarjaCaverle/Desktop/MRI _______________________________________________ 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
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Bruce Fischl -
Marja Caverle -
Marja Caverlé