[Freesurfer] How to export the image and label

2018-10-18 Thread Min Zhang 
External Email - Use Caution

Dear FreeSurfer Team :
I used the freeSurfer brainstem structure to segment the brainstem from the
MRI successfully. But I have several questions as followed:

1.  I want to export this data in dcm file with all the ROI information,
what should I do?
2. How to manually adjust the boundaries of existing brainstem segmentation
results?
3. How to generate surface of brainstem based on the segmentation.

Many Thanks!

Best
Jackie
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[Freesurfer] Mapping a custom measure to the pial surface of fsaverage

2018-10-18 Thread ts+ml 
External Email - Use Caution

Dear FreeSurfer experts,

I have created a custom measure on the pial surface of a number of subjects, 
and I would like to map the data to the fsaverage subject. (By custom measure I 
mean something like 'area' or 'curv', i.e., one scalar value per surface 
vertex.)

I have already done the same for the white surfaces, and it was pretty 
straight-forward:
1) Save the per-vertex data in a curv-format file in 
SUBJECTS_DIR//surf/?h.
2) Run 'recon-all -s  -qcache -measure '

This will map the data to fsaverage and create files named 
?h..fwhm.fsaverage.mgh in the surf/ directories as expected (where 
 is 0, 5, .., 25).

My question is: how can I do the same for my data from the pial surface? Are 
there any command line options for 'recon-all' (or maybe for mris_preproc) that 
can do this?

I already tried to put the pial per-vertex data into files named 
SUBJECTS_DIR//surf/?h.pial., but they are not handled by the 
recon-all command listed above: no fsaverage files show up for them.

Thanks in advance,

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Problems setting the directory

2018-10-18 Thread Bruce Fischl 

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  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 
 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 

  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 
  -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

Re: [Freesurfer] Problems setting the directory

2018-10-18 Thread Rosalia Dacosta Aguayo 
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 
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 
> 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 <
> fis...@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  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
> >   >

[Freesurfer] errors running mri_glmfit

2018-10-18 Thread Azeez, Azeezat 
External Email - Use Caution

Hello I keep getting the same error and am not sure how to address the
issue.
I have attached the design matrix and the FSGD file and contrast file of
interest

Thanks for the help



ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit --y STATS/lh.DEV_DIA_SEX.thickness.mgh --fsgd
STATS/DEV_DIA_SEX.fsgd dods --C STATS/mainDEV.mat --surf fsaverage lh
--cortex --glmdir STATS/lh.DEV_DIA_SEX.thickness.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above

-- 
Azeezat Azeez
Design matrix --
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000

Re: [Freesurfer] Problems setting the directory

2018-10-18 Thread Bruce Fischl 
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  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 
 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  -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 

  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

Re: [Freesurfer] Problems setting the directory

2018-10-18 Thread Rosalia Dacosta Aguayo 
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 
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 
> 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  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 <
> fis...@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
> >   
> >   >   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

Re: [Freesurfer] Problems setting the directory

2018-10-18 Thread Bruce Fischl 

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  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  
-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 
 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
  
  >       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
  >      
>-
  --
  >

Re: [Freesurfer] Problems setting the directory

2018-10-18 Thread Rosalia Dacosta Aguayo 
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 
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 
> -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 
> 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 
> >   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
> >   >

Re: [Freesurfer] Problems setting the directory

2018-10-18 Thread Bruce Fischl 

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  -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  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 

  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
  >
  >
  >
  >
  >
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Re: [Freesurfer] Problems setting the directory

2018-10-18 Thread Rosalia Dacosta Aguayo 
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 
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 
> 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
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Re: [Freesurfer] Problems setting the directory

2018-10-18 Thread Bruce Fischl 

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 

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





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[Freesurfer] Computing relative cortical measures maps instead of absolute cortical measures maps

2018-10-18 Thread Angela Martina Mueller 
External Email - Use Caution

Hi,





I am referring to a paper of Vuoksimaa et al. 2016. The authors used relative 
instead of absolute cortical measures (cortical thickness and surface area) to 
compute individual vertex-cognitive ability correlations throughout the cortex.



To compute individual relative cortical thickness and surface area maps of each 
individual subjects, the authors divided the surface area value at each vertex 
by the total surface area (sum across all vertices for each subject) and 
subtracted the mean cortical thickness value (for each subject) from the 
thickness at each vertex.



I would like to use the same approach (relative CT and SA maps instead of 
absolute maps) for one of the projects of our lab. In the Freesurfer mailing 
list, I found that the command "fscalc" can be used for simple mathematical 
transformations of mgh files.



Therefore my question: Would it be correct to use “fscalc” with the option 
“sub” resp “div” to compute these relative cortical measures maps for each of 
my subjects?



Thank you for helping me with this question



Angela

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Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

2018-10-18 Thread Azeez, Azeezat 
External Email - Use Caution

Thank you for the response.
Which smoothing option would you recommend, there is one in mris_preproc,
but there is also mris_smooth.
Thanks You

On Wed, Oct 17, 2018 at 1:56 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> You cannot use QDEC for this. You must use the "command line" stream,
> ie, create your FSGD file, run mris_preproc, smooth, run mri_glmfit,
> then mri_glmfit-sim. See the tutorial on the wiki.
>
> On 10/17/2018 01:30 PM, Azeez, Azeezat wrote:
> >
> > External Email - Use Caution
> >
> > Hello,
> >
> > I would like to know how I can run statistical analysis in QDEC on a
> > data set where there are 3 fixed factors each with 2 contrast levels.
> > (DEVELOPMENT : old vs young, SEX: male vs female, DIAGNOSE: Control Vs
> > disease )
> >
> > Any help would be much appreciated.
> > Thank You,
> >
> >
> > --
> > Azeezat Azeez
> > PhD Student
> > Department of Biomedical Engineering || New Jersey Institute of
> > Technology
> > Graduate School of Biomedical Sciences || Rutgers University
> > E: ak...@njit.edu 
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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-- 
Azeezat Azeez
PhD Student
Department of Biomedical Engineering || New Jersey Institute of Technology
Graduate School of Biomedical Sciences || Rutgers University
E: ak...@njit.edu
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[Freesurfer] Problems setting the directory

2018-10-18 Thread Rosalia Dacosta Aguayo 
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
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[Freesurfer] Physiological Noise Regression from rsMRI

2018-10-18 Thread Meisler, Steven Lee 
Hi all,


I am currently developing a pipeline to remove physiological noise (respiratory 
and cardiac) from rsMRI images. I am at the point where I have created the 
regressors using fast_retroicor.m from the physiological data logs. When I add 
the columns of the regressors up and plot the result, it appears to create 
pulses at the times when the physiological data peaked. I was wondering if 
anyone knows how to incorporate the regressor files into FreeSurfer. Please let 
me know at your earliest convenience.


Thank you,

Steven


--

Steven L. Meisler, M.S.E.

Clinical Research Coordinator II

Laboratory for NeuroImaging of Coma and 
Consciousness

175 Cambridge Street, Suite 300

Boston, MA 02114

smeis...@mgh.harvard.edu | (617)-726-1884

https://www.linkedin.com/in/steven-meisler

[cid:5962d6ba-7da0-445d-a7a9-91952132a976]
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[Freesurfer] Running DICOMS versus FreeSurfer5.3 Output

2018-10-18 Thread Scheffler, F, Mev [fre...@sun.ac.za] 
External Email - Use Caution

Dear FreeSurfer Developers

If we want to rerun FreeSurfer dev 6.1 on an old dataset, is it better to rerun 
with the original DICOMS or to rerun over the 5.3 output? Would that even work?

Thanks very much.

Kind regards,

FREDA SCHEFFLER

Research Assistant / PhD Candidate


[email.jpg]


MA Research Psychology
Faculty of Medicine and Health Sciences
Fakulteit Geneeskunde en Gesondheidswetenskappe
Universiteit Stellenbosch University
PO Box | Posbus 241, Cape Town | Kaapstad, 8000
Francie van Zijl Drive | -rylaan, Tygerberg, 7505
South Africa | Suid-Afrika

Tel:  +27 21 938 9771
Email | E-pos:  fre...@sun.ac.za



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Re: [Freesurfer] autorecon1 with skull stripped image

2018-10-18 Thread Falk Lüsebrink 
External Email - Use Caution

Dear Rosalina,

yes, it is. FreeSurfer can handle all formats given in the help of mri_convert.

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Rosalia Dacosta 
Aguayo
Gesendet: Donnerstag, 18. Oktober 2018 08:48
An: Freesurfer support list 
Betreff: Re: [Freesurfer] autorecon1 with skull stripped image


External Email - Use Caution
Dear Falk,

Thank you very much for your explanation. One more thing: nii.gz format is also 
good for FreeSurfer, right?

Best regards,
Rosalia


El jue., 18 oct. 2018 8:26, Falk Lüsebrink 
mailto:falk.luesebr...@ovgu.de>> escribió:

External Email - Use Caution
Dear Rosalia,

I’d suggest you run recon-all –autorecon1 with you native data. Then you use 
mri_mask to mask the T1.mgz with your skull stripped volume to get your desired 
skull stripping. Name the result brainmask.mgz and continue with recon-all 
–autorecon2 –autorecon3.

Remember that FreeSurfer requires to have the cerebellum attached to the brain. 
Also inputting the already skull stripped volume in autorecon1 may fail during 
talairach registration and potentially cause errors during skull stripping (if 
not skipped anyways).

Best,
Falk

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu]
 Im Auftrag von Rosalia Dacosta Aguayo
Gesendet: Donnerstag, 18. Oktober 2018 06:30
An: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: [Freesurfer] autorecon1 with skull stripped image


External Email - Use Caution
Dear Free Surfer's team,

I have a doubt. I have a sample of patients in which I already have done the 
skull stripping using specific options with bet, so the skull stripping has 
been successful. I wonder if I could feed autorecon1 with the skull stripped 
image instead of the T1 image with skull.
Thank you very much for your time,
Rosalia
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Re: [Freesurfer] autorecon1 with skull stripped image

2018-10-18 Thread Rosalia Dacosta Aguayo 
External Email - Use Caution

Dear Falk,

Thank you very much for your explanation. One more thing: nii.gz format is
also good for FreeSurfer, right?

Best regards,
Rosalia



El jue., 18 oct. 2018 8:26, Falk Lüsebrink 
escribió:

> External Email - Use Caution
>
> Dear Rosalia,
>
>
>
> I’d suggest you run recon-all –autorecon1 with you native data. Then you
> use mri_mask to mask the T1.mgz with your skull stripped volume to get your
> desired skull stripping. Name the result brainmask.mgz and continue with
> recon-all –autorecon2 –autorecon3.
>
>
>
> Remember that FreeSurfer requires to have the cerebellum attached to the
> brain. Also inputting the already skull stripped volume in autorecon1 may
> fail during talairach registration and potentially cause errors during
> skull stripping (if not skipped anyways).
>
>
>
> Best,
>
> Falk
>
>
>
> *Von:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] *Im Auftrag von *Rosalia Dacosta
> Aguayo
> *Gesendet:* Donnerstag, 18. Oktober 2018 06:30
> *An:* Freesurfer support list 
> *Betreff:* [Freesurfer] autorecon1 with skull stripped image
>
>
>
> *External Email - Use Caution*
>
> Dear Free Surfer's team,
>
>
>
> I have a doubt. I have a sample of patients in which I already have done
> the skull stripping using specific options with bet, so the skull stripping
> has been successful. I wonder if I could feed autorecon1 with the skull
> stripped image instead of the T1 image with skull.
>
> Thank you very much for your time,
>
> Rosalia
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Re: [Freesurfer] Ask for your help about freesurfer submillimeter reconstruction!

2018-10-18 Thread Falk Lüsebrink 
External Email - Use Caution

Dear Rui,

there is no hard limit to resolution. Your data should have a decent quality 
(no motion artifacts, high SNR, high contrast, isotropic resolution) and the 
suggestions of the submillimeter reconstruction should give good results. I 
have run FreeSurfer on 250 µm human data with reasonable, but improvable 
results. Still working on it.

>From my experience skull stripping seems to fail using data with higher 
>resolution than 0.7 mm. Therefore, I suggest you to follow the first steps of 
>the guideline: https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon to create 
>a low resolution brainmask, upsampling, and applying it on your high 
>resolution data. Apart from that everything should run smoothly.

Expect it to run for a few weeks, especially the topological fixation and 
autorecon3 will take time.

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Nian Rui
Gesendet: Donnerstag, 18. Oktober 2018 00:50
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Ask for your help about freesurfer submillimeter 
reconstruction!
Priorität: Hoch


External Email - Use Caution
Dear FreeSurfer Developers,


I am now working on the analysis of MRI images with the voxel resolution less 
than 0.2mm3.
I read your webpage about submillimeter reconstruction, 
https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_SubmillimeterRecon=DwIFaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=NtVAAoNRuurWjiGc9gF6zmjCj-yhJX2FiqIQWantaTc=HTIr5eeTbJbG9K4SRzOVI_oGR2mBLs0SJ7kNktw_Jls=G5pESXnip5oTcvgA30e0qjSVsAcnKGo1DekVAyP1VaY=,
 which said Freesurfer 6.0 works well for voxel sizes 0.75 mm3, and inputs with 
0.5 mm3 voxels or below will have a brainmask failure (we are working on it!).
So I am writing to ask for your help about the reconstruction with freesurfer.
I would like to know, have you solved the higher resolution problem in the new 
version v6.0?
Could I use it to analyze the cortical thickness of these MRI images now?
If not, is there any other way to help processing these MRI images and we could 
run freesurfer step by step for evaluation?
Look forward to your timely help!
Thanks a lot in advance!
yours sincerely,
Rui
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Re: [Freesurfer] autorecon1 with skull stripped image

2018-10-18 Thread Falk Lüsebrink 
External Email - Use Caution

Dear Rosalia,

I’d suggest you run recon-all –autorecon1 with you native data. Then you use 
mri_mask to mask the T1.mgz with your skull stripped volume to get your desired 
skull stripping. Name the result brainmask.mgz and continue with recon-all 
–autorecon2 –autorecon3.

Remember that FreeSurfer requires to have the cerebellum attached to the brain. 
Also inputting the already skull stripped volume in autorecon1 may fail during 
talairach registration and potentially cause errors during skull stripping (if 
not skipped anyways).

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Rosalia Dacosta 
Aguayo
Gesendet: Donnerstag, 18. Oktober 2018 06:30
An: Freesurfer support list 
Betreff: [Freesurfer] autorecon1 with skull stripped image


External Email - Use Caution
Dear Free Surfer's team,

I have a doubt. I have a sample of patients in which I already have done the 
skull stripping using specific options with bet, so the skull stripping has 
been successful. I wonder if I could feed autorecon1 with the skull stripped 
image instead of the T1 image with skull.
Thank you very much for your time,
Rosalia
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