External Email - Use Caution
Dear Free Surfer team,
Surely this is a basic question but I am having a trouble setting the subjects_dir in my terminal and, as a result, any of the commands work.
This is how I have my Free Surfer configurated in my computer:
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 --------------------------------------------------------------------------------------------------------
As it is, I cannot work in the SUBJECTS_DIR, as it is protected. I tried to set a new subjects_dir: export SUBJECTS_DIR=/home/rosalia/Desktop
Then I try to run the first step (autorecon1) with one subject, and it appears the following error: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ recon-all -s 001 -autorecon1 *ERROR: cannot find /usr/local/freesurfer/subjects/001* rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $
I have even changed my .bashrc file...but it seems I am doing something wrong as my terminal keeps pointing to the same subject_dir. I have tried to use sudo so in order to move my folder and subfolders to the subjects_dir set by default, and I am experiencing problems as well.
I would much appreciate any help with this basic question. Kind regards, Rosalia
Hi Rosalia
you either need to give recon-all an input file (or more than one) with the -i switch, or create the subject directory tree under SUBJECTS_DIR for that subject, and put a file named 001.mgz in the mri/orig subdir. Note you can also specify SUBJECTS_DIR explicitly on the recon-all command line with -sd <dir> if you don't want to put it in the environment.
That is, try this:
recon-all -s 001 -autorecon1 -sd ~/Desktop/subjects
cheers Bruce
On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Dear Free Surfer team,
Surely this is a basic question but I am having a trouble setting the subjects_dir in my terminal and, as a result, any of the commands work.
This is how I have my Free Surfer configurated in my computer:
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0
As it is, I cannot work in the SUBJECTS_DIR, as it is protected. I tried to set a new subjects_dir: export SUBJECTS_DIR=/home/rosalia/Desktop
Then I try to run the first step (autorecon1) with one subject, and it appears the following error: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ recon-all -s 001 -autorecon1 ERROR: cannot find /usr/local/freesurfer/subjects/001 rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $
I have even changed my .bashrc file...but it seems I am doing something wrong as my terminal keeps pointing to the same subject_dir. I have tried to use sudo so in order to move my folder and subfolders to the subjects_dir set by default, and I am experiencing problems as well.
I would much appreciate any help with this basic question. Kind regards, Rosalia
External Email - Use Caution
Hi Bruce,
Thank you very much for answering my questions. This is how I have organized my subject_dir for one subject so you can see better. It is still not working. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ ls FOLDERS S_011.nii.gz S_020.nii.gz S_028.nii.gz S_041.nii.gz MS001 S_012.nii.gz S_021.nii.gz S_029.nii.gz S_042.nii.gz S_004.nii.gz S_013.nii.gz S_022.nii.gz S_030.nii.gz S_043.nii.gz S_005.nii.gz S_014.nii.gz S_023.nii.gz S_031.nii.gz S_044.nii.gz S_006.nii.gz S_015.nii.gz S_024.nii.gz S_032.nii.gz S_045.nii.gz S_008.nii.gz S_016.nii.gz S_025.nii.gz S_033.nii.gz S_046.nii.gz S_009.nii.gz S_017.nii.gz S_026.nii.gz S_034.nii.gz S_047.nii.gz S_010.nii.gz S_018.nii.gz S_027.nii.gz S_040.nii.gz SCRIPTS rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ cd MS001/ rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ ls mri orig rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ cd mri/ rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/mri $ ls 001.nii.gz rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/mri $ cd ..rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ cd orig rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/orig $ ls 001.nii.gz rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/orig $
Regards, Rosalia
On Thu, Oct 18, 2018 at 6:55 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Rosalia
you either need to give recon-all an input file (or more than one) with the -i switch, or create the subject directory tree under SUBJECTS_DIR for that subject, and put a file named 001.mgz in the mri/orig subdir. Note you can also specify SUBJECTS_DIR explicitly on the recon-all command line with -sd <dir> if you don't want to put it in the environment.
That is, try this:
recon-all -s 001 -autorecon1 -sd ~/Desktop/subjects
cheers Bruce
On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use CautionDear Free Surfer team,
Surely this is a basic question but I am having a trouble setting the
subjects_dir in my terminal
and, as a result, any of the commands work.
This is how I have my Free Surfer configurated in my computer:
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0
As it is, I cannot work in the SUBJECTS_DIR, as it is protected. I tried to set a new subjects_dir: export SUBJECTS_DIR=/home/rosalia/Desktop
Then I try to run the first step (autorecon1) with one subject, and it
appears the following error:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ recon-all -s
001 -autorecon1
ERROR: cannot find /usr/local/freesurfer/subjects/001 rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $
I have even changed my .bashrc file...but it seems I am doing something
wrong as my terminal keeps
pointing to the same subject_dir. I have tried to use sudo so in order to move my folder and subfolders to
the subjects_dir set by
default, and I am experiencing problems as well.
I would much appreciate any help with this basic question. Kind regards, Rosalia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Rosalia
can you send us the full command line, screen output and recon-all.log? In the arrangement you show below it would be:
recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i <path to dicom file> -all
cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Hi Bruce,
Thank you very much for answering my questions. This is how I have organized my subject_dir for one subject so you can see better. It is still not working. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ ls FOLDERS S_011.nii.gz S_020.nii.gz S_028.nii.gz S_041.nii.gz MS001 S_012.nii.gz S_021.nii.gz S_029.nii.gz S_042.nii.gz S_004.nii.gz S_013.nii.gz S_022.nii.gz S_030.nii.gz S_043.nii.gz S_005.nii.gz S_014.nii.gz S_023.nii.gz S_031.nii.gz S_044.nii.gz S_006.nii.gz S_015.nii.gz S_024.nii.gz S_032.nii.gz S_045.nii.gz S_008.nii.gz S_016.nii.gz S_025.nii.gz S_033.nii.gz S_046.nii.gz S_009.nii.gz S_017.nii.gz S_026.nii.gz S_034.nii.gz S_047.nii.gz S_010.nii.gz S_018.nii.gz S_027.nii.gz S_040.nii.gz SCRIPTS rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ cd MS001/ rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ ls mri orig rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ cd mri/ rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/mri $ ls 001.nii.gz rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/mri $ cd ..rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ cd orig rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/orig $ ls 001.nii.gz rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/orig $
Regards, Rosalia
On Thu, Oct 18, 2018 at 6:55 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Rosalia
you either need to give recon-all an input file (or more than one) with the -i switch, or create the subject directory tree under SUBJECTS_DIR for that subject, and put a file named 001.mgz in the mri/orig subdir. Note you can also specify SUBJECTS_DIR explicitly on the recon-all command line with -sd <dir> if you don't want to put it in the environment. That is, try this: recon-all -s 001 -autorecon1 -sd ~/Desktop/subjects cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > > Dear Free Surfer team, > > Surely this is a basic question but I am having a trouble setting the subjects_dir in my terminal > and, as a result, any of the commands work. > > This is how I have my Free Surfer configurated in my computer: > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer > FSFAST_HOME /usr/local/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer/subjects > MNI_DIR /usr/local/freesurfer/mni > FSL_DIR /usr/share/fsl/5.0 >--------------------------------------------------------------------------------------------------- > ----- > > As it is, I cannot work in the SUBJECTS_DIR, as it is protected. > I tried to set a new subjects_dir: > export SUBJECTS_DIR=/home/rosalia/Desktop > > Then I try to run the first step (autorecon1) with one subject, and it appears the following error: > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ recon-all -s 001 -autorecon1 > ERROR: cannot find /usr/local/freesurfer/subjects/001 > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ > > I have even changed my .bashrc file...but it seems I am doing something wrong as my terminal keeps > pointing to the same subject_dir. > I have tried to use sudo so in order to move my folder and subfolders to the subjects_dir set by > default, and I am experiencing problems as well. > > I would much appreciate any help with this basic question. > Kind regards, > Rosalia > > > > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Bruce,
There is not recon-all.log.
The full command line is: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ *recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri -autorecon1* *ERROR: You cannot give recon-all a folder as input. It must be an image file.* If you have multiple files, you need multiple -i flags. Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu SMP Thu Nov 9 15:37:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 001 exited with ERRORS at Thu 18 Oct 19:13:35 CEST 2018
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $
On Thu, Oct 18, 2018 at 7:11 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Rosalia
can you send us the full command line, screen output and recon-all.log? In the arrangement you show below it would be:
recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i <path to dicom file> -all
cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use CautionHi Bruce,
Thank you very much for answering my questions. This is how I have organized my subject_dir for one subject so you can
see better. It is still not
working. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ ls FOLDERS S_011.nii.gz S_020.nii.gz S_028.nii.gz S_041.nii.gz MS001 S_012.nii.gz S_021.nii.gz S_029.nii.gz S_042.nii.gz S_004.nii.gz S_013.nii.gz S_022.nii.gz S_030.nii.gz S_043.nii.gz S_005.nii.gz S_014.nii.gz S_023.nii.gz S_031.nii.gz S_044.nii.gz S_006.nii.gz S_015.nii.gz S_024.nii.gz S_032.nii.gz S_045.nii.gz S_008.nii.gz S_016.nii.gz S_025.nii.gz S_033.nii.gz S_046.nii.gz S_009.nii.gz S_017.nii.gz S_026.nii.gz S_034.nii.gz S_047.nii.gz S_010.nii.gz S_018.nii.gz S_027.nii.gz S_040.nii.gz SCRIPTS rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ cd
MS001/
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $
ls
mri orig rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $
cd mri/
rosalia@rosalia-Lenovo-Y520-15IKBN
~/Desktop/MS_STUDY/subjects/MS001/mri $ ls
001.nii.gz rosalia@rosalia-Lenovo-Y520-15IKBN
~/Desktop/MS_STUDY/subjects/MS001/mri $ cd
..rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001
$ cd orig
rosalia@rosalia-Lenovo-Y520-15IKBN
~/Desktop/MS_STUDY/subjects/MS001/orig $ ls
001.nii.gz rosalia@rosalia-Lenovo-Y520-15IKBN
~/Desktop/MS_STUDY/subjects/MS001/orig $
Regards, Rosalia
On Thu, Oct 18, 2018 at 6:55 PM Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Hi Rosalia you either need to give recon-all an input file (or more than one)with the
-i switch, or create the subject directory tree under SUBJECTS_DIRfor that
subject, and put a file named 001.mgz in the mri/orig subdir. Noteyou can
also specify SUBJECTS_DIR explicitly on the recon-all command linewith -sd <dir>
if you don't want to put it in the environment. That is, try this: recon-all -s 001 -autorecon1 -sd ~/Desktop/subjects cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > > Dear Free Surfer team, > > Surely this is a basic question but I am having a troublesetting the subjects_dir in
my terminal > and, as a result, any of the commands work. > > This is how I have my Free Surfer configurated in my computer: > > --------freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
> Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer > FSFAST_HOME /usr/local/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer/subjects > MNI_DIR /usr/local/freesurfer/mni > FSL_DIR /usr/share/fsl/5.0
> ----- > > As it is, I cannot work in the SUBJECTS_DIR, as it is protected. > I tried to set a new subjects_dir: > export SUBJECTS_DIR=/home/rosalia/Desktop > > Then I try to run the first step (autorecon1) with one subject,and it appears the
following error: > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $recon-all -s 001 -autorecon1
> ERROR: cannot find /usr/local/freesurfer/subjects/001 > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ > > I have even changed my .bashrc file...but it seems I am doingsomething wrong as my
terminal keeps > pointing to the same subject_dir. > I have tried to use sudo so in order to move my folder andsubfolders to the
subjects_dir set by > default, and I am experiencing problems as well. > > I would much appreciate any help with this basic question. > Kind regards, > Rosalia > > > > > >_______________________________________________ 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
Hi Rosalia
-i must point to a file that you want to import, usually a single dicom file in the correct (e.g. mprage) series. cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Hi Bruce,
There is not recon-all.log.
The full command line is: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri -autorecon1 ERROR: You cannot give recon-all a folder as input. It must be an image file. If you have multiple files, you need multiple -i flags. Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu SMP Thu Nov 9 15:37:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 001 exited with ERRORS at Thu 18 Oct 19:13:35 CEST 2018
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $
On Thu, Oct 18, 2018 at 7:11 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Rosalia
can you send us the full command line, screen output and recon-all.log? In the arrangement you show below it would be: recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i <path to dicom file> -all cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > > Hi Bruce, > > Thank you very much for answering my questions. > This is how I have organized my subject_dir for one subject so you can see better. It is still not > working. > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ ls > FOLDERS S_011.nii.gz S_020.nii.gz S_028.nii.gz S_041.nii.gz > MS001 S_012.nii.gz S_021.nii.gz S_029.nii.gz S_042.nii.gz > S_004.nii.gz S_013.nii.gz S_022.nii.gz S_030.nii.gz S_043.nii.gz > S_005.nii.gz S_014.nii.gz S_023.nii.gz S_031.nii.gz S_044.nii.gz > S_006.nii.gz S_015.nii.gz S_024.nii.gz S_032.nii.gz S_045.nii.gz > S_008.nii.gz S_016.nii.gz S_025.nii.gz S_033.nii.gz S_046.nii.gz > S_009.nii.gz S_017.nii.gz S_026.nii.gz S_034.nii.gz S_047.nii.gz > S_010.nii.gz S_018.nii.gz S_027.nii.gz S_040.nii.gz SCRIPTS > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ cd MS001/ > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ ls > mri orig > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ cd mri/ > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/mri $ ls > 001.nii.gz > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/mri $ cd > ..rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ cd orig > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/orig $ ls > 001.nii.gz > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/orig $ > > Regards, > Rosalia > > On Thu, Oct 18, 2018 at 6:55 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Hi Rosalia > > you either need to give recon-all an input file (or more than one) with the > -i switch, or create the subject directory tree under SUBJECTS_DIR for that > subject, and put a file named 001.mgz in the mri/orig subdir. Note you can > also specify SUBJECTS_DIR explicitly on the recon-all command line with -sd <dir> > if you don't want to put it in the environment. > > That is, try this: > > recon-all -s 001 -autorecon1 -sd ~/Desktop/subjects > > cheers > Bruce > > On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: > > > > > External Email - Use Caution > > > > Dear Free Surfer team, > > > > Surely this is a basic question but I am having a trouble setting the subjects_dir in > my terminal > > and, as a result, any of the commands work. > > > > This is how I have my Free Surfer configurated in my computer: > > > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /usr/local/freesurfer > > FSFAST_HOME /usr/local/freesurfer/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /usr/local/freesurfer/subjects > > MNI_DIR /usr/local/freesurfer/mni > > FSL_DIR /usr/share/fsl/5.0 > >------------------------------------------------------------------------------------------------- -- > > > ----- > > > > As it is, I cannot work in the SUBJECTS_DIR, as it is protected. > > I tried to set a new subjects_dir: > > export SUBJECTS_DIR=/home/rosalia/Desktop > > > > Then I try to run the first step (autorecon1) with one subject, and it appears the > following error: > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ recon-all -s 001 -autorecon1 > > ERROR: cannot find /usr/local/freesurfer/subjects/001 > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ > > > > I have even changed my .bashrc file...but it seems I am doing something wrong as my > terminal keeps > > pointing to the same subject_dir. > > I have tried to use sudo so in order to move my folder and subfolders to the > subjects_dir set by > > default, and I am experiencing problems as well. > > > > I would much appreciate any help with this basic question. > > Kind regards, > > Rosalia > > > > > > > > > > > >_______________________________________________ > 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
External Email - Use Caution
Yes, you are right. I saw the error. I have been running one of the participants and here it is the report.log. Also, because these kind of participants are special, I used some bet parameters to run the skull-stripping. This is the main reason why I did not run recon all -all. I would like to replace the skull stripped image by my betted one. Is this right? Thanks, Rosalia
On Thu, Oct 18, 2018 at 7:47 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Rosalia
-i must point to a file that you want to import, usually a single dicom file in the correct (e.g. mprage) series. cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use CautionHi Bruce,
There is not recon-all.log.
The full command line is: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $
recon-all -sd
~/Desktop/MS_STUDY/subjects -s 001 -i
/home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri -autorecon1
ERROR: You cannot give recon-all a folder as input. It must be an image
file.
If you have multiple files, you need multiple -i flags. Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu
SMP Thu Nov 9 15:37:44 UTC
2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 001 exited with ERRORS at Thu 18 Oct 19:13:35 CEST 2018
For more details, see the log file To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $
On Thu, Oct 18, 2018 at 7:11 PM Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Hi Rosalia can you send us the full command line, screen output andrecon-all.log?
In the arrangement you show below it would be: recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i <path to dicomfile> -all
cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > > Hi Bruce, > > Thank you very much for answering my questions. > This is how I have organized my subject_dir for one subject soyou can see better. It
is still not > working. > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects$ ls
> FOLDERS S_011.nii.gz S_020.nii.gz S_028.nii.gzS_041.nii.gz
> MS001 S_012.nii.gz S_021.nii.gz S_029.nii.gzS_042.nii.gz
> S_004.nii.gz S_013.nii.gz S_022.nii.gz S_030.nii.gzS_043.nii.gz
> S_005.nii.gz S_014.nii.gz S_023.nii.gz S_031.nii.gzS_044.nii.gz
> S_006.nii.gz S_015.nii.gz S_024.nii.gz S_032.nii.gzS_045.nii.gz
> S_008.nii.gz S_016.nii.gz S_025.nii.gz S_033.nii.gzS_046.nii.gz
> S_009.nii.gz S_017.nii.gz S_026.nii.gz S_034.nii.gzS_047.nii.gz
> S_010.nii.gz S_018.nii.gz S_027.nii.gz S_040.nii.gz SCRIPTS > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects$ cd MS001/
> rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001 $ ls
> mri orig > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001 $ cd mri/
> rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001/mri $ ls
> 001.nii.gz > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001/mri $ cd
> ..rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001 $ cd orig
> rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001/orig $ ls
> 001.nii.gz > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001/orig $
> > Regards, > Rosalia > > On Thu, Oct 18, 2018 at 6:55 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> Hi Rosalia > > you either need to give recon-all an input file (or morethan one) with the
> -i switch, or create the subject directory tree underSUBJECTS_DIR for that
> subject, and put a file named 001.mgz in the mri/origsubdir. Note you can
> also specify SUBJECTS_DIR explicitly on the recon-allcommand line with -sd
<dir> > if you don't want to put it in the environment. > > That is, try this: > > recon-all -s 001 -autorecon1 -sd ~/Desktop/subjects > > cheers > Bruce > > On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: > > > > > External Email - Use Caution > > > > Dear Free Surfer team, > > > > Surely this is a basic question but I am having atrouble setting the
subjects_dir in > my terminal > > and, as a result, any of the commands work. > > > > This is how I have my Free Surfer configurated in mycomputer:
> > > > --------freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
> > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /usr/local/freesurfer > > FSFAST_HOME /usr/local/freesurfer/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /usr/local/freesurfer/subjects > > MNI_DIR /usr/local/freesurfer/mni > > FSL_DIR /usr/share/fsl/5.0 >
-- > > > ----- > > > > As it is, I cannot work in the SUBJECTS_DIR, as it isprotected.
> > I tried to set a new subjects_dir: > > export SUBJECTS_DIR=/home/rosalia/Desktop > > > > Then I try to run the first step (autorecon1) with onesubject, and it appears
the > following error: > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $recon-all -s 001
-autorecon1 > > ERROR: cannot find /usr/local/freesurfer/subjects/001 > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ > > > > I have even changed my .bashrc file...but it seems I amdoing something wrong
as my > terminal keeps > > pointing to the same subject_dir. > > I have tried to use sudo so in order to move my folderand subfolders to the
> subjects_dir set by > > default, and I am experiencing problems as well. > > > > I would much appreciate any help with this basicquestion.
> > Kind regards, > > Rosalia > > > > > > > > > > > >_______________________________________________ > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, you can do that. If you run recon-all through the skill stripping, then replace the brainmask.mgz with yours generated by bet, we should detect that and retain it for further processing
cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Yes, you are right. I saw the error. I have been running one of the participants and here it is the report.log. Also, because these kind of participants are special, I used some bet parameters to run the skull-stripping. This is the main reason why I did not run recon all -all. I would like to replace the skull stripped image by my betted one. Is this right? Thanks, Rosalia
On Thu, Oct 18, 2018 at 7:47 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Rosalia
-i must point to a file that you want to import, usually a single dicom file in the correct (e.g. mprage) series. cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > > Hi Bruce, > > There is not recon-all.log. > > The full command line is: > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ recon-all -sd > ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri -autorecon1 > ERROR: You cannot give recon-all a folder as input. It must be an image file. > If you have multiple files, you need multiple -i flags. > Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu SMP Thu Nov 9 15:37:44 UTC > 2017 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s 001 exited with ERRORS at Thu 18 Oct 19:13:35 CEST 2018 > > For more details, see the log file > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ > > > > On Thu, Oct 18, 2018 at 7:11 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Hi Rosalia > > can you send us the full command line, screen output and recon-all.log? > In the arrangement you show below it would be: > > recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i <path to dicom file> -all > > cheers > Bruce > On Thu, 18 Oct 2018, Rosalia > Dacosta Aguayo wrote: > > > > > External Email - Use Caution > > > > Hi Bruce, > > > > Thank you very much for answering my questions. > > This is how I have organized my subject_dir for one subject so you can see better. It > is still not > > working. > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ ls > > FOLDERS S_011.nii.gz S_020.nii.gz S_028.nii.gz S_041.nii.gz > > MS001 S_012.nii.gz S_021.nii.gz S_029.nii.gz S_042.nii.gz > > S_004.nii.gz S_013.nii.gz S_022.nii.gz S_030.nii.gz S_043.nii.gz > > S_005.nii.gz S_014.nii.gz S_023.nii.gz S_031.nii.gz S_044.nii.gz > > S_006.nii.gz S_015.nii.gz S_024.nii.gz S_032.nii.gz S_045.nii.gz > > S_008.nii.gz S_016.nii.gz S_025.nii.gz S_033.nii.gz S_046.nii.gz > > S_009.nii.gz S_017.nii.gz S_026.nii.gz S_034.nii.gz S_047.nii.gz > > S_010.nii.gz S_018.nii.gz S_027.nii.gz S_040.nii.gz SCRIPTS > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ cd MS001/ > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ ls > > mri orig > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ cd mri/ > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/mri $ ls > > 001.nii.gz > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/mri $ cd > > ..rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ cd orig > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/orig $ ls > > 001.nii.gz > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/orig $ > > > > Regards, > > Rosalia > > > > On Thu, Oct 18, 2018 at 6:55 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > > Hi Rosalia > > > > you either need to give recon-all an input file (or more than one) with the > > -i switch, or create the subject directory tree under SUBJECTS_DIR for that > > subject, and put a file named 001.mgz in the mri/orig subdir. Note you can > > also specify SUBJECTS_DIR explicitly on the recon-all command line with -sd > <dir> > > if you don't want to put it in the environment. > > > > That is, try this: > > > > recon-all -s 001 -autorecon1 -sd ~/Desktop/subjects > > > > cheers > > Bruce > > > > On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear Free Surfer team, > > > > > > Surely this is a basic question but I am having a trouble setting the > subjects_dir in > > my terminal > > > and, as a result, any of the commands work. > > > > > > This is how I have my Free Surfer configurated in my computer: > > > > > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > FREESURFER_HOME /usr/local/freesurfer > > > FSFAST_HOME /usr/local/freesurfer/fsfast > > > FSF_OUTPUT_FORMAT nii.gz > > > SUBJECTS_DIR /usr/local/freesurfer/subjects > > > MNI_DIR /usr/local/freesurfer/mni > > > FSL_DIR /usr/share/fsl/5.0 > > >------------------------------------------------------------------------------------------------ - > -- > > > > > ----- > > > > > > As it is, I cannot work in the SUBJECTS_DIR, as it is protected. > > > I tried to set a new subjects_dir: > > > export SUBJECTS_DIR=/home/rosalia/Desktop > > > > > > Then I try to run the first step (autorecon1) with one subject, and it appears > the > > following error: > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ recon-all -s 001 > -autorecon1 > > > ERROR: cannot find /usr/local/freesurfer/subjects/001 > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ > > > > > > I have even changed my .bashrc file...but it seems I am doing something wrong > as my > > terminal keeps > > > pointing to the same subject_dir. > > > I have tried to use sudo so in order to move my folder and subfolders to the > > subjects_dir set by > > > default, and I am experiencing problems as well. > > > > > > I would much appreciate any help with this basic question. > > > Kind regards, > > > Rosalia > > > > > > > > > > > > > > > > > >_______________________________________________ > > 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 > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you a lot Bruce. Just one more question. If I would like to run all the participants. where should I include the subject.list? Regards, Rosalia
On Thu, Oct 18, 2018 at 7:56 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
yes, you can do that. If you run recon-all through the skill stripping, then replace the brainmask.mgz with yours generated by bet, we should detect that and retain it for further processing
cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use CautionYes, you are right. I saw the error. I have been running one of the participants and here it is the
report.log.
Also, because these kind of participants are special, I used some bet
parameters to run the
skull-stripping. This is the main reason why I did not run recon all
-all. I would like to replace
the skull stripped image by my betted one. Is this right? Thanks, Rosalia
On Thu, Oct 18, 2018 at 7:47 PM Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Hi Rosalia -i must point to a file that you want to import, usually a singledicom
file in the correct (e.g. mprage) series. cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > > Hi Bruce, > > There is not recon-all.log. > > The full command line is: > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects$ recon-all -sd
> ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri -autorecon1 > ERROR: You cannot give recon-all a folder as input. It must bean image file.
> If you have multiple files, you need multiple -i flags. > Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic#44~16.04.1-Ubuntu SMP Thu Nov 9
15:37:44 UTC > 2017 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s 001 exited with ERRORS at Thu 18 Oct 19:13:35 CEST2018
> > For more details, see the log file > To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ > > > > On Thu, Oct 18, 2018 at 7:11 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> Hi Rosalia > > can you send us the full command line, screen output andrecon-all.log?
> In the arrangement you show below it would be: > > recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i <pathto dicom file> -all
> > cheers > Bruce > On Thu, 18 Oct 2018, Rosalia > Dacosta Aguayo wrote: > > > > > External Email - Use Caution > > > > Hi Bruce, > > > > Thank you very much for answering my questions. > > This is how I have organized my subject_dir for onesubject so you can see
better. It > is still not > > working. > > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects $ ls
> > FOLDERS S_011.nii.gz S_020.nii.gz S_028.nii.gzS_041.nii.gz
> > MS001 S_012.nii.gz S_021.nii.gz S_029.nii.gzS_042.nii.gz
> > S_004.nii.gz S_013.nii.gz S_022.nii.gz S_030.nii.gzS_043.nii.gz
> > S_005.nii.gz S_014.nii.gz S_023.nii.gz S_031.nii.gzS_044.nii.gz
> > S_006.nii.gz S_015.nii.gz S_024.nii.gz S_032.nii.gzS_045.nii.gz
> > S_008.nii.gz S_016.nii.gz S_025.nii.gz S_033.nii.gzS_046.nii.gz
> > S_009.nii.gz S_017.nii.gz S_026.nii.gz S_034.nii.gzS_047.nii.gz
> > S_010.nii.gz S_018.nii.gz S_027.nii.gz S_040.nii.gzSCRIPTS
> > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects $ cd MS001/
> > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001 $ ls
> > mri orig > > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001 $ cd mri/
> > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001/mri $ ls
> > 001.nii.gz > > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001/mri $ cd
> > ..rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001 $ cd
orig > > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001/orig $ ls
> > 001.nii.gz > > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/MS_STUDY/subjects/MS001/orig $
> > > > Regards, > > Rosalia > > > > On Thu, Oct 18, 2018 at 6:55 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote: > > Hi Rosalia > > > > you either need to give recon-all an input file(or more than one) with
the > > -i switch, or create the subject directory treeunder SUBJECTS_DIR for
that > > subject, and put a file named 001.mgz in themri/orig subdir. Note you
can > > also specify SUBJECTS_DIR explicitly on therecon-all command line with
-sd > <dir> > > if you don't want to put it in the environment. > > > > That is, try this: > > > > recon-all -s 001 -autorecon1 -sd ~/Desktop/subjects > > > > cheers > > Bruce > > > > On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear Free Surfer team, > > > > > > Surely this is a basic question but I am havinga trouble setting the
> subjects_dir in > > my terminal > > > and, as a result, any of the commands work. > > > > > > This is how I have my Free Surfer configuratedin my computer:
> > > > > > --------freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
-------- > > > Setting up environment for FreeSurfer/FS-FAST(and FSL)
> > > FREESURFER_HOME /usr/local/freesurfer > > > FSFAST_HOME /usr/local/freesurfer/fsfast > > > FSF_OUTPUT_FORMAT nii.gz > > > SUBJECTS_DIR /usr/local/freesurfer/subjects > > > MNI_DIR /usr/local/freesurfer/mni > > > FSL_DIR /usr/share/fsl/5.0 > >
- > -- > > > > > ----- > > > > > > As it is, I cannot work in the SUBJECTS_DIR, asit is protected.
> > > I tried to set a new subjects_dir: > > > export SUBJECTS_DIR=/home/rosalia/Desktop > > > > > > Then I try to run the first step (autorecon1)with one subject, and it
appears > the > > following error: > > > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/subjects $ recon-all -s
001 > -autorecon1 > > > ERROR: cannot find/usr/local/freesurfer/subjects/001
> > > rosalia@rosalia-Lenovo-Y520-15IKBN~/Desktop/subjects $
> > > > > > I have even changed my .bashrc file...but itseems I am doing
something wrong > as my > > terminal keeps > > > pointing to the same subject_dir. > > > I have tried to use sudo so in order to move myfolder and subfolders
to the > > subjects_dir set by > > > default, and I am experiencing problems as well. > > > > > > I would much appreciate any help with this basicquestion.
> > > Kind regards, > > > Rosalia > > > > > > > > > > > > > > > > > >_______________________________________________ > > 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
> > >_______________________________________________ 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
Hi Rosalia
that you would do outside of FreeSurfer, probably with a shell script. I typically make a scripts dir under SUBJECTS_DIR and put a file names subjects.csh that creates an env variable listing the subjects and setting the SUBJECTS_DIR, then write scripts that source it and run things like recons, etc.... cheers Bruce
On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Thank you a lot Bruce. Just one more question. If I would like to run all the participants. where should I include the subject.list? Regards, Rosalia
On Thu, Oct 18, 2018 at 7:56 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: yes, you can do that. If you run recon-all through the skill stripping, then replace the brainmask.mgz with yours generated by bet, we should detect that and retain it for further processing
cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > > Yes, you are right. I saw the error. > I have been running one of the participants and here it is the report.log. > Also, because these kind of participants are special, I used some bet parameters to run the > skull-stripping. This is the main reason why I did not run recon all -all. I would like to replace > the skull stripped image by my betted one. Is this right? > Thanks, > Rosalia > > On Thu, Oct 18, 2018 at 7:47 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Hi Rosalia > > -i must point to a file that you want to import, usually a single dicom > file in the correct (e.g. mprage) series. > cheers > Bruce > On Thu, 18 Oct 2018, Rosalia > Dacosta Aguayo wrote: > > > > > External Email - Use Caution > > > > Hi Bruce, > > > > There is not recon-all.log. > > > > The full command line is: > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ recon-all -sd > > ~/Desktop/MS_STUDY/subjects -s 001 -i > /home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri -autorecon1 > > ERROR: You cannot give recon-all a folder as input. It must be an image file. > > If you have multiple files, you need multiple -i flags. > > Linux rosalia-Lenovo-Y520-15IKBN 4.10.0-40-generic #44~16.04.1-Ubuntu SMP Thu Nov 9 > 15:37:44 UTC > > 2017 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s 001 exited with ERRORS at Thu 18 Oct 19:13:35 CEST 2018 > > > > For more details, see the log file > > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ > > > > > > > > On Thu, Oct 18, 2018 at 7:11 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > > Hi Rosalia > > > > can you send us the full command line, screen output and recon-all.log? > > In the arrangement you show below it would be: > > > > recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i <path to dicom file> -all > > > > cheers > > Bruce > > On Thu, 18 Oct 2018, Rosalia > > Dacosta Aguayo wrote: > > > > > > > > External Email - Use Caution > > > > > > Hi Bruce, > > > > > > Thank you very much for answering my questions. > > > This is how I have organized my subject_dir for one subject so you can see > better. It > > is still not > > > working. > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ ls > > > FOLDERS S_011.nii.gz S_020.nii.gz S_028.nii.gz S_041.nii.gz > > > MS001 S_012.nii.gz S_021.nii.gz S_029.nii.gz S_042.nii.gz > > > S_004.nii.gz S_013.nii.gz S_022.nii.gz S_030.nii.gz S_043.nii.gz > > > S_005.nii.gz S_014.nii.gz S_023.nii.gz S_031.nii.gz S_044.nii.gz > > > S_006.nii.gz S_015.nii.gz S_024.nii.gz S_032.nii.gz S_045.nii.gz > > > S_008.nii.gz S_016.nii.gz S_025.nii.gz S_033.nii.gz S_046.nii.gz > > > S_009.nii.gz S_017.nii.gz S_026.nii.gz S_034.nii.gz S_047.nii.gz > > > S_010.nii.gz S_018.nii.gz S_027.nii.gz S_040.nii.gz SCRIPTS > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ cd MS001/ > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ ls > > > mri orig > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ cd mri/ > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/mri $ ls > > > 001.nii.gz > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/mri $ cd > > > ..rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001 $ cd > orig > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/orig $ ls > > > 001.nii.gz > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/MS001/orig $ > > > > > > Regards, > > > Rosalia > > > > > > On Thu, Oct 18, 2018 at 6:55 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> > wrote: > > > Hi Rosalia > > > > > > you either need to give recon-all an input file (or more than one) with > the > > > -i switch, or create the subject directory tree under SUBJECTS_DIR for > that > > > subject, and put a file named 001.mgz in the mri/orig subdir. Note you > can > > > also specify SUBJECTS_DIR explicitly on the recon-all command line with > -sd > > <dir> > > > if you don't want to put it in the environment. > > > > > > That is, try this: > > > > > > recon-all -s 001 -autorecon1 -sd ~/Desktop/subjects > > > > > > cheers > > > Bruce > > > > > > On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: > > > > > > > > > > > External Email - Use Caution > > > > > > > > Dear Free Surfer team, > > > > > > > > Surely this is a basic question but I am having a trouble setting the > > subjects_dir in > > > my terminal > > > > and, as a result, any of the commands work. > > > > > > > > This is how I have my Free Surfer configurated in my computer: > > > > > > > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > -------- > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > > FREESURFER_HOME /usr/local/freesurfer > > > > FSFAST_HOME /usr/local/freesurfer/fsfast > > > > FSF_OUTPUT_FORMAT nii.gz > > > > SUBJECTS_DIR /usr/local/freesurfer/subjects > > > > MNI_DIR /usr/local/freesurfer/mni > > > > FSL_DIR /usr/share/fsl/5.0 > > > >----------------------------------------------------------------------------------------------- - > - > > -- > > > > > > > ----- > > > > > > > > As it is, I cannot work in the SUBJECTS_DIR, as it is protected. > > > > I tried to set a new subjects_dir: > > > > export SUBJECTS_DIR=/home/rosalia/Desktop > > > > > > > > Then I try to run the first step (autorecon1) with one subject, and it > appears > > the > > > following error: > > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ recon-all -s > 001 > > -autorecon1 > > > > ERROR: cannot find /usr/local/freesurfer/subjects/001 > > > > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/subjects $ > > > > > > > > I have even changed my .bashrc file...but it seems I am doing > something wrong > > as my > > > terminal keeps > > > > pointing to the same subject_dir. > > > > I have tried to use sudo so in order to move my folder and subfolders > to the > > > subjects_dir set by > > > > default, and I am experiencing problems as well. > > > > > > > > I would much appreciate any help with this basic question. > > > > Kind regards, > > > > Rosalia > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > 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 > > > > > >_______________________________________________ > 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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Rosalia Dacosta Aguayo