date:20140919


Hi Mahmoud

were you able to create a symlink to fsaverage in your SUBJECTS_DIR? If 
not, that is the reason for this error

Bruce

On Thu, 18 Sep 2014, Mahmoud wrote:


Dear all,

After running "recon-all -i $SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm
-subject case018_tp2 -all" I'm always getting the following error and really
don't know how to fix. 

Could anybody please help me. The recon-all.log file is attached.

Thank you,
Mahmoud

Reporting on  70 segmentations
mri_segstats done
/usr/local/freesurfer/subjects/case018_tp2/label
#
#@# BA Labels lh Thu Sep 18 20:23:27 EDT 2014
INFO: fsaverage subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to fsaverage subject...

 cd /usr/local/freesurfer/subjects; ln -s
/usr/local/freesurfer/subjects/fsaverage; cd - 


 mri_label2label --srcsubject fsaverage --srclabel
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject
case018_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface 

Too many levels of symbolic links
mri_label2label: could not open label file
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
srcsubject = fsaverage
trgsubject = case018_tp2
trglabel = ./lh.BA1.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Invalid argument
ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s case018_tp2 exited with ERRORS at Thu Sep 18 20:23:27 EDT 2014

For more details, see the log file
/usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log

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[Freesurfer] segmentation fault mri_convert Ubuntu 14.04

2014-09-19 Thread Alessandra Griffa


Dear all,

I am running FreeSurfer version [recon-all,v 1.313.2.6 2010/08/04] on an 
Ubuntu machine.
After updating my system from Ubuntu 12.04 to Ubuntu 14.04 I get a 
segmentation fault when I try to resample images using mri_convert:


/mri_convert -vs 1 1 1 /folder/original_image.nii.gz /folder/resampled 
image.nii.gz //

//$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $//
//reading from /folder/original_image.nii.gz...//
//Segmentation fault (core dumped)/

Any help on this?
(for consistency with an on-going study I would like not to install a 
newer FreeSurfer version)


Thank you very much!
Alessandra


--
--
Alessandra Griffa
Doctoral assistant

Signal Processing Laboratory 5
EPFL STI IEL LTS5
ELD 233 (Bâtiment ELD)
Station 11 CH-1015
Lausanne
Tel.: +41216934807

web: http://lts5www.epfl.ch/
personal page: http://people.epfl.ch/alessandra.griffa?lang=en
--

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Re: [Freesurfer] Freeview screenshot automation questions

2014-09-19 Thread Ruopeng Wang

There is no direct way. But you can try this workaround:

Write all the screenshot command in a text file, line by line like this:

-v brain.nii
-viewport sagittal -slice 80 127 127  -ss sag1 -noquit
-viewport sagittal -slice 127 127 127 -ss sag2 -noquit
…

Then run this command:

freeview -cmd cmd.txt

Ruopeng

On Sep 18, 2014, at 5:38 AM, Eric Xiuming ZHANG  
wrote:

> Dear FreeSurfer experts,
> 
> I understand that
>> freeview -v brain.nii.gz -ss screenshot
> takes the screenshots and quits the freeview.
> 
> Regarding this, I have the following two questions.
> 
> (1) Is it possible to suppress the redundant GUI flashing?
> 
> It is really a pain when many images are batch-processed, because the GUI 
> keeps flashing up and closing.
> 
> (2) Is it possible to take multiple screenshots with one session?
> 
> I wish to screenshot multiple slices of one image. I have tried 
>> freeview -v brain.nii.gz\
>> -viewport sagittal -slice 80 127 127  -ss sag1 \
>> -viewport sagittal -slice 127 127 127 -ss sag2 \
>> -viewport sagittal -slice 156 127 127 -ss sag3 \
> However, the session ends right after the first -ss, producing only one 
> screenshot (sag1.png). I can surely do freeview -v brain.nii.gz 3 times to 
> get these 3 screenshots, but that is very inefficient.
> 
> Thank you very much for your help in advance!
> 
> Best regards,
> Xiuming ZHANG (Eric)
> 
> Xiuming ZHANG (Mr.) :: Department of Electrical & Computer Engineering (ECE) 
> :: National University of Singapore (NUS)
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Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

Hi Bruce,

Actually I couldn't. It says: ls: cannot access
/usr/local/freesurfer/subjects/fsaverage: Too many levels of symbolic links
And even I couldn't cd to fsaverage !
In fact there is no directory  under SUBJETCS_DIR named fsaverage, it seems
the fsaverage under SUBJETCS_DIR is just a broken link, and I have no idea
why the the link is broken and how to fix it.
Any help would be highly appreciated !

Thank you,
Mahmoud


On Fri, Sep 19, 2014 at 8:21 AM, Bruce Fischl 
wrote:

> Hi Mahmoud
>
> were you able to create a symlink to fsaverage in your SUBJECTS_DIR? If
> not, that is the reason for this error
> Bruce
>
>
> On Thu, 18 Sep 2014, Mahmoud wrote:
>
>  Dear all,
>>
>> After running "recon-all -i $SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm
>> -subject case018_tp2 -all" I'm always getting the following error and
>> really
>> don't know how to fix.
>>
>> Could anybody please help me. The recon-all.log file is attached.
>>
>> Thank you,
>> Mahmoud
>>
>> Reporting on  70 segmentations
>> mri_segstats done
>> /usr/local/freesurfer/subjects/case018_tp2/label
>> #
>> #@# BA Labels lh Thu Sep 18 20:23:27 EDT 2014
>> INFO: fsaverage subject does not exist in SUBJECTS_DIR
>> INFO: Creating symlink to fsaverage subject...
>>
>>  cd /usr/local/freesurfer/subjects; ln -s
>> /usr/local/freesurfer/subjects/fsaverage; cd -
>>
>>
>>  mri_label2label --srcsubject fsaverage --srclabel
>> /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject
>> case018_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
>>
>> Too many levels of symbolic links
>> mri_label2label: could not open label file
>> /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
>>
>> srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
>> srcsubject = fsaverage
>> trgsubject = case018_tp2
>> trglabel = ./lh.BA1.label
>> regmethod = surface
>>
>> srchemi = lh
>> trghemi = lh
>> trgsurface = white
>> srcsurfreg = sphere.reg
>> trgsurfreg = sphere.reg
>> usehash = 1
>> Use ProjAbs  = 0, 0
>> Use ProjFrac = 0, 0
>> DoPaint 0
>>
>> SUBJECTS_DIR/usr/local/freesurfer/subjects
>> FREESURFER_HOME /usr/local/freesurfer
>> Loading source label.
>> Invalid argument
>> ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
>> Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014
>> x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s case018_tp2 exited with ERRORS at Thu Sep 18 20:23:27 EDT
>> 2014
>>
>> For more details, see the log file
>> /usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log
>>
>>
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

can you tell us what your FREESURFER_HOME is and what your SUBJECTS_DIR is? 
You will need to remove the broken link probably


On Fri, 19 Sep 2014, Mahmoud wrote:


Hi Bruce,

Actually I couldn't. It says: ls: cannot access
/usr/local/freesurfer/subjects/fsaverage: Too many levels of symbolic links
And even I couldn't cd to fsaverage !
In fact there is no directory  under SUBJETCS_DIR named fsaverage, it seems
the fsaverage under SUBJETCS_DIR is just a broken link, and I have no idea
why the the link is broken and how to fix it.
Any help would be highly appreciated !

Thank you,
Mahmoud


On Fri, Sep 19, 2014 at 8:21 AM, Bruce Fischl 
wrote:
  Hi Mahmoud

  were you able to create a symlink to fsaverage in your
  SUBJECTS_DIR? If not, that is the reason for this error
  Bruce

  On Thu, 18 Sep 2014, Mahmoud wrote:

Dear all,

After running "recon-all -i
$SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm
-subject case018_tp2 -all" I'm always getting the
following error and really
don't know how to fix. 

Could anybody please help me. The recon-all.log file
is attached.

Thank you,
Mahmoud

Reporting on  70 segmentations
mri_segstats done
/usr/local/freesurfer/subjects/case018_tp2/label
#
#@# BA Labels lh Thu Sep 18 20:23:27 EDT 2014
INFO: fsaverage subject does not exist in
SUBJECTS_DIR
INFO: Creating symlink to fsaverage subject...

 cd /usr/local/freesurfer/subjects; ln -s
/usr/local/freesurfer/subjects/fsaverage; cd - 


 mri_label2label --srcsubject fsaverage --srclabel
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
--trgsubject
case018_tp2 --trglabel ./lh.BA1.label --hemi lh
--regmethod surface 

Too many levels of symbolic links
mri_label2label: could not open label file
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

srclabel =
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
srcsubject = fsaverage
trgsubject = case018_tp2
trglabel = ./lh.BA1.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR    /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Invalid argument
ERROR reading
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri
Aug 15 01:58:42 UTC 2014
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s case018_tp2 exited with ERRORS at Thu
Sep 18 20:23:27 EDT 2014

For more details, see the log file
/usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log


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e-mail
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HelpLine at
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Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

Bruce,

Here is the info when I open a new terminal:

 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
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
ubuntu:~>

On Fri, Sep 19, 2014 at 8:56 AM, Bruce Fischl 
wrote:

> can you tell us what your FREESURFER_HOME is and what your SUBJECTS_DIR
> is? You will need to remove the broken link probably
>
>
> On Fri, 19 Sep 2014, Mahmoud wrote:
>
>  Hi Bruce,
>>
>> Actually I couldn't. It says: ls: cannot access
>> /usr/local/freesurfer/subjects/fsaverage: Too many levels of symbolic
>> links
>> And even I couldn't cd to fsaverage !
>> In fact there is no directory  under SUBJETCS_DIR named fsaverage, it
>> seems
>> the fsaverage under SUBJETCS_DIR is just a broken link, and I have no idea
>> why the the link is broken and how to fix it.
>> Any help would be highly appreciated !
>>
>> Thank you,
>> Mahmoud
>>
>>
>> On Fri, Sep 19, 2014 at 8:21 AM, Bruce Fischl > >
>> wrote:
>>   Hi Mahmoud
>>
>>   were you able to create a symlink to fsaverage in your
>>   SUBJECTS_DIR? If not, that is the reason for this error
>>   Bruce
>>
>>   On Thu, 18 Sep 2014, Mahmoud wrote:
>>
>> Dear all,
>>
>> After running "recon-all -i
>> $SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm
>> -subject case018_tp2 -all" I'm always getting the
>> following error and really
>> don't know how to fix.
>>
>> Could anybody please help me. The recon-all.log file
>> is attached.
>>
>> Thank you,
>> Mahmoud
>>
>> Reporting on  70 segmentations
>> mri_segstats done
>> /usr/local/freesurfer/subjects/case018_tp2/label
>> #
>> #@# BA Labels lh Thu Sep 18 20:23:27 EDT 2014
>> INFO: fsaverage subject does not exist in
>> SUBJECTS_DIR
>> INFO: Creating symlink to fsaverage subject...
>>
>>  cd /usr/local/freesurfer/subjects; ln -s
>> /usr/local/freesurfer/subjects/fsaverage; cd -
>>
>>
>>  mri_label2label --srcsubject fsaverage --srclabel
>> /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
>> --trgsubject
>> case018_tp2 --trglabel ./lh.BA1.label --hemi lh
>> --regmethod surface
>>
>> Too many levels of symbolic links
>> mri_label2label: could not open label file
>> /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
>>
>> srclabel =
>> /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
>> srcsubject = fsaverage
>> trgsubject = case018_tp2
>> trglabel = ./lh.BA1.label
>> regmethod = surface
>>
>> srchemi = lh
>> trghemi = lh
>> trgsurface = white
>> srcsurfreg = sphere.reg
>> trgsurfreg = sphere.reg
>> usehash = 1
>> Use ProjAbs  = 0, 0
>> Use ProjFrac = 0, 0
>> DoPaint 0
>>
>> SUBJECTS_DIR/usr/local/freesurfer/subjects
>> FREESURFER_HOME /usr/local/freesurfer
>> Loading source label.
>> Invalid argument
>> ERROR reading
>> /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
>> Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri
>> Aug 15 01:58:42 UTC 2014
>> x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s case018_tp2 exited with ERRORS at Thu
>> Sep 18 20:23:27 EDT 2014
>>
>> For more details, see the log file
>> /usr/local/freesurfer/subjects/case018_tp2/scripts/
>> recon-all.log
>>
>>
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>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
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Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

the  directory /usr/local/freesurfer/subjects is for subjects that we 
distribute and NOT where you should be putting your subject data. Is that 
what you are doing? You may have overwritten the fsaverage dir there. Can 
you run:


ls -l /usr/local/freesurfer/subjects/fsaverage

and send us the results?

you should create a directory elsewhere with your subject data and point 
SUBJECTS_DIR at it


cheers
Bruce

On Fri, 19 Sep 2014, Mahmoud wrote:


Bruce,

Here is the info when I open a new terminal:

 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
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
ubuntu:~>

On Fri, Sep 19, 2014 at 8:56 AM, Bruce Fischl 
wrote:
  can you tell us what your FREESURFER_HOME is and what your
  SUBJECTS_DIR is? You will need to remove the broken link
  probably

  On Fri, 19 Sep 2014, Mahmoud wrote:

Hi Bruce,

Actually I couldn't. It says: ls: cannot access
/usr/local/freesurfer/subjects/fsaverage: Too many
levels of symbolic links
And even I couldn't cd to fsaverage !
In fact there is no directory  under SUBJETCS_DIR
named fsaverage, it seems
the fsaverage under SUBJETCS_DIR is just a broken
link, and I have no idea
why the the link is broken and how to fix it.
Any help would be highly appreciated !

Thank you,
Mahmoud


On Fri, Sep 19, 2014 at 8:21 AM, Bruce Fischl

wrote:
      Hi Mahmoud

      were you able to create a symlink to fsaverage
in your
      SUBJECTS_DIR? If not, that is the reason for
this error
      Bruce

      On Thu, 18 Sep 2014, Mahmoud wrote:

            Dear all,

            After running "recon-all -i
           
$SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm
            -subject case018_tp2 -all" I'm always
getting the
            following error and really
            don't know how to fix. 

            Could anybody please help me. The
recon-all.log file
            is attached.

            Thank you,
            Mahmoud

            Reporting on  70 segmentations
            mri_segstats done
           
/usr/local/freesurfer/subjects/case018_tp2/label
           
#
            #@# BA Labels lh Thu Sep 18 20:23:27 EDT
2014
            INFO: fsaverage subject does not exist
in
            SUBJECTS_DIR
            INFO: Creating symlink to fsaverage
subject...

             cd /usr/local/freesurfer/subjects; ln
-s
           
/usr/local/freesurfer/subjects/fsaverage; cd - 


             mri_label2label --srcsubject fsaverage
--srclabel
           
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
            --trgsubject
            case018_tp2 --trglabel ./lh.BA1.label
--hemi lh
            --regmethod surface 

            Too many levels of symbolic links
            mri_label2label: could not open label
file
           
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

            srclabel =
           
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
            srcsubject = fsaverage
            trgsubject = case018_tp2
            trglabel = ./lh.BA1.label
            regmethod = surface

            srchemi = lh
            trghemi = lh
            trgsurface = white
            srcsurfreg = sphere.reg
            trgsurfreg = sphere.reg
            usehash = 1
            Use ProjAbs  = 0, 0
            Use ProjFrac = 0, 0
            DoPaint 0

            SUBJECTS_DIR  
 /usr/local/freesurfer/subjects
            FREESURFER_HOME /usr/local/freesurfer
            Loading source label.
            Invalid argument
            ERROR reading
           
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
            Linux ubuntu 3.13.0-35-generi

Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

Bruce,

I already had my data in a shared folder (/mnt/hgfs/mydata) but I got the
permission error the same point that I got the symlink error lastly. So, I
tought that might be due to something related to shared directory.
Then I copied my subjects under the $SUBJECTS_DIR but got the symlink error.

running ls -l /usr/local/freesurfer/subjects /fsaverage  shows me this:

lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 18 20:23
/usr/local/freesurfer/subjects/fsaverage ->
/usr/local/freesurfer/subjects/fsaverage

Thank you,
Mahmoud


On Fri, Sep 19, 2014 at 9:23 AM, Bruce Fischl 
wrote:

> the  directory /usr/local/freesurfer/subjects is for subjects that we
> distribute and NOT where you should be putting your subject data. Is that
> what you are doing? You may have overwritten the fsaverage dir there. Can
> you run:
>
> ls -l /usr/local/freesurfer/subjects/fsaverage
>
> and send us the results?
>
> you should create a directory elsewhere with your subject data and point
> SUBJECTS_DIR at it
>
> cheers
> Bruce
>
>
> On Fri, 19 Sep 2014, Mahmoud wrote:
>
>  Bruce,
>>
>> Here is the info when I open a new terminal:
>>
>>  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
>> 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
>> ubuntu:~>
>>
>> On Fri, Sep 19, 2014 at 8:56 AM, Bruce Fischl > >
>> wrote:
>>   can you tell us what your FREESURFER_HOME is and what your
>>   SUBJECTS_DIR is? You will need to remove the broken link
>>   probably
>>
>>   On Fri, 19 Sep 2014, Mahmoud wrote:
>>
>> Hi Bruce,
>>
>> Actually I couldn't. It says: ls: cannot access
>> /usr/local/freesurfer/subjects/fsaverage: Too many
>> levels of symbolic links
>> And even I couldn't cd to fsaverage !
>> In fact there is no directory  under SUBJETCS_DIR
>> named fsaverage, it seems
>> the fsaverage under SUBJETCS_DIR is just a broken
>> link, and I have no idea
>> why the the link is broken and how to fix it.
>> Any help would be highly appreciated !
>>
>> Thank you,
>> Mahmoud
>>
>>
>> On Fri, Sep 19, 2014 at 8:21 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Mahmoud
>>
>>   were you able to create a symlink to fsaverage
>> in your
>>   SUBJECTS_DIR? If not, that is the reason for
>> this error
>>   Bruce
>>
>>   On Thu, 18 Sep 2014, Mahmoud wrote:
>>
>> Dear all,
>>
>> After running "recon-all -i
>>
>> $SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm
>> -subject case018_tp2 -all" I'm always
>> getting the
>> following error and really
>> don't know how to fix.
>>
>> Could anybody please help me. The
>> recon-all.log file
>> is attached.
>>
>> Thank you,
>> Mahmoud
>>
>> Reporting on  70 segmentations
>> mri_segstats done
>>
>> /usr/local/freesurfer/subjects/case018_tp2/label
>>
>> #
>> #@# BA Labels lh Thu Sep 18 20:23:27 EDT
>> 2014
>> INFO: fsaverage subject does not exist
>> in
>> SUBJECTS_DIR
>> INFO: Creating symlink to fsaverage
>> subject...
>>
>>  cd /usr/local/freesurfer/subjects; ln
>> -s
>>
>> /usr/local/freesurfer/subjects/fsaverage; cd -
>>
>>
>>  mri_label2label --srcsubject fsaverage
>> --srclabel
>>
>> /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
>> --trgsubject
>> case018_tp2 --trglabel ./lh.BA1.label
>> --hemi lh
>> --regmethod surface
>>
>> Too many levels of symbolic links
>> mri_label2label: could not open label
>> file
>>
>> /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
>>
>> srclabel =
>>
>> /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
>> srcsubject = fsaverage
>> trgsubject = case018_tp2
>> trglabel = ./lh.BA1.label
>> regmethod = surface
>>
>> srchemi = lh
>>

[Freesurfer] talairach coordinates

2014-09-19 Thread ri

Hi  all
I was wondering whether it’s possible to get the talairach coordinates 
associated with each label in the segmentation. I would like to use 
Freesurfer’s segmentation for analysis in Matlab.How to  create a text file 
with the talairach coordinates of each label (or of a specific label, by label 
number), 
Thanks

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Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

yes, you symlinked it to itself which is why you are getting the infinite 
recursion error. You need to delete 
/usr/local/freesurfer/subjects/fsaverage


and download the fsaverage dir again, put it in that directory, then 
symlink from your /mnt/hgfs/mydata/fsaverage to 
/usr/local/freesurfer/subjects/fsaverage


cheers
Bruce
On Fri, 19 Sep 2014, Mahmoud wrote:


Bruce,

I already had my data in a shared folder (/mnt/hgfs/mydata) but I got the
permission error the same point that I got the symlink error lastly. So, I
tought that might be due to something related to shared directory.
Then I copied my subjects under the $SUBJECTS_DIR but got the symlink error.

running ls -l /usr/local/freesurfer/subjects /fsaverage  shows me this:

lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 18 20:23
/usr/local/freesurfer/subjects/fsaverage ->
/usr/local/freesurfer/subjects/fsaverage

Thank you,
Mahmoud


On Fri, Sep 19, 2014 at 9:23 AM, Bruce Fischl 
wrote:
  the  directory /usr/local/freesurfer/subjects is for subjects
  that we distribute and NOT where you should be putting your
  subject data. Is that what you are doing? You may have
  overwritten the fsaverage dir there. Can you run:

  ls -l /usr/local/freesurfer/subjects/fsaverage

  and send us the results?

  you should create a directory elsewhere with your subject data
  and point SUBJECTS_DIR at it

  cheers
  Bruce

  On Fri, 19 Sep 2014, Mahmoud wrote:

Bruce,

Here is the info when I open a new terminal:


freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

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
ubuntu:~>

On Fri, Sep 19, 2014 at 8:56 AM, Bruce Fischl

wrote:
      can you tell us what your FREESURFER_HOME is
and what your
      SUBJECTS_DIR is? You will need to remove the
broken link
      probably

      On Fri, 19 Sep 2014, Mahmoud wrote:

            Hi Bruce,

            Actually I couldn't. It says: ls: cannot
access
           
/usr/local/freesurfer/subjects/fsaverage: Too many
            levels of symbolic links
            And even I couldn't cd to fsaverage !
            In fact there is no directory  under
SUBJETCS_DIR
            named fsaverage, it seems
            the fsaverage under SUBJETCS_DIR is just
a broken
            link, and I have no idea
            why the the link is broken and how to
fix it.
            Any help would be highly appreciated !

            Thank you,
            Mahmoud


            On Fri, Sep 19, 2014 at 8:21 AM, Bruce
Fischl
            
            wrote:
                  Hi Mahmoud

                  were you able to create a symlink
to fsaverage
            in your
                  SUBJECTS_DIR? If not, that is the
reason for
            this error
                  Bruce

                  On Thu, 18 Sep 2014, Mahmoud
wrote:

                        Dear all,

                        After running "recon-all -i
                       
           
$SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm
                        -subject case018_tp2 -all"
I'm always
            getting the
                        following error and really
                        don't know how to fix. 

                        Could anybody please help
me. The
            recon-all.log file
                        is attached.

                        Thank you,
                        Mahmoud

                        Reporting on  70
segmentations
                        mri_segstats done
                       
           
/usr/local/freesurfer/subjects/case018_tp2/label
                       
           
#
                        #@# BA Labels lh Thu Sep 18
20:23:27 EDT
            2014
                        INFO: fsaverage subject does

Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

Bruce,

Thank you for your follow up and advice. Please let me know:
1- How to download the fsaverage again?
2- should I do the symlink manually or it will be done by recon-all later ?
3- What steps should I take before running the recon-all -all ? should I
create any specific directory? set any permission ?

Best,
Mahmoud

On Fri, Sep 19, 2014 at 9:41 AM, Bruce Fischl 
wrote:

> yes, you symlinked it to itself which is why you are getting the infinite
> recursion error. You need to delete /usr/local/freesurfer/
> subjects/fsaverage
>
> and download the fsaverage dir again, put it in that directory, then
> symlink from your /mnt/hgfs/mydata/fsaverage to /usr/local/freesurfer/
> subjects/fsaverage
>
>
> cheers
> Bruce
> On Fri, 19 Sep 2014, Mahmoud wrote:
>
>  Bruce,
>>
>> I already had my data in a shared folder (/mnt/hgfs/mydata) but I got the
>> permission error the same point that I got the symlink error lastly. So, I
>> tought that might be due to something related to shared directory.
>> Then I copied my subjects under the $SUBJECTS_DIR but got the symlink
>> error.
>>
>> running ls -l /usr/local/freesurfer/subjects /fsaverage  shows me this:
>>
>> lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 18 20:23
>> /usr/local/freesurfer/subjects/fsaverage ->
>> /usr/local/freesurfer/subjects/fsaverage
>>
>> Thank you,
>> Mahmoud
>>
>>
>> On Fri, Sep 19, 2014 at 9:23 AM, Bruce Fischl > >
>> wrote:
>>   the  directory /usr/local/freesurfer/subjects is for subjects
>>   that we distribute and NOT where you should be putting your
>>   subject data. Is that what you are doing? You may have
>>   overwritten the fsaverage dir there. Can you run:
>>
>>   ls -l /usr/local/freesurfer/subjects/fsaverage
>>
>>   and send us the results?
>>
>>   you should create a directory elsewhere with your subject data
>>   and point SUBJECTS_DIR at it
>>
>>   cheers
>>   Bruce
>>
>>   On Fri, 19 Sep 2014, Mahmoud wrote:
>>
>> Bruce,
>>
>> Here is the info when I open a new terminal:
>>
>> 
>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> 
>> 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
>> ubuntu:~>
>>
>> On Fri, Sep 19, 2014 at 8:56 AM, Bruce Fischl
>> 
>> wrote:
>>   can you tell us what your FREESURFER_HOME is
>> and what your
>>   SUBJECTS_DIR is? You will need to remove the
>> broken link
>>   probably
>>
>>   On Fri, 19 Sep 2014, Mahmoud wrote:
>>
>> Hi Bruce,
>>
>> Actually I couldn't. It says: ls: cannot
>> access
>>
>> /usr/local/freesurfer/subjects/fsaverage: Too many
>> levels of symbolic links
>> And even I couldn't cd to fsaverage !
>> In fact there is no directory  under
>> SUBJETCS_DIR
>> named fsaverage, it seems
>> the fsaverage under SUBJETCS_DIR is just
>> a broken
>> link, and I have no idea
>> why the the link is broken and how to
>> fix it.
>> Any help would be highly appreciated !
>>
>> Thank you,
>> Mahmoud
>>
>>
>> On Fri, Sep 19, 2014 at 8:21 AM, Bruce
>> Fischl
>> 
>> wrote:
>>   Hi Mahmoud
>>
>>   were you able to create a symlink
>> to fsaverage
>> in your
>>   SUBJECTS_DIR? If not, that is the
>> reason for
>> this error
>>   Bruce
>>
>>   On Thu, 18 Sep 2014, Mahmoud
>> wrote:
>>
>> Dear all,
>>
>> After running "recon-all -i
>>
>>
>> $SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm
>> -subject case018_tp2 -all"
>> I'm always
>> getting the
>> following error and really
>> don't know how to fix.
>>
>> Could anybody please help
>> me. The
>> recon-all.log file
>> is attached.
>>

[Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion

2014-09-19 Thread Matthieu Vanhoutte

Dear Freesurfer's experts,

I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing
pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data.

The first step has to be the correction of gradient-nonlinearity-induced
distortion. The correction is then done with a customized version of the
gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al.,
2006).

I couldn't manage to find this package on internet, the only things I've
found is the freesurfer grad_unwarp command and a webpage (
https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping) with no
download link...

Where can I find this package and how to use it ?

Many thanks !

Best,

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
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[Freesurfer] A question about spherical registration

2014-09-19 Thread Reza Rajimehr

Hi,

I have a question about spherical registration, and I couldn't find a
relevant answer in the mailing list.

I have two subjects S1 and S2 with corresponding functionals. I want to
show the functionals of each subject on the surfaces of the third subject
S3. I have .sphere files for S1, S2, and S3, but I don't have .sphere.reg
files yet because these are monkey subjects and I did not want to register
them to the buckner40.tif template. Since my goal is not group averaging,
and it is just to map functionals to the same-subject anatomicals and then
to the target-subject anatomicals, I was thinking of one of the following
solutions:

1) Convert sphere of S3 to a template .tif file, then use mris_register to
register spheres of S1, S2, and S3 to that template and generate
sphere.reg for all the subjects. Not sure if mris_make_template works for
one subject though.

2) Make a template from "S1 and S2" through the procedure described at
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates#Creatingaregistrationtemplatefromscratch.28GW.29.
Then register S1, S2, and S3 to that template and generate sphere.reg for
all the subjects.

Which approach is recommended?

BTW, I do not know of a monkey template that is based on the surfaces from
a large group of monkeys.

Thanks for any advice,
Reza
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Re: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion

2014-09-19 Thread Harms, Michael







Hi,
I suggest you start with the documentation that accompanies the recently released HCP pipelines.
see
http://www.humanconnectome.org/documentation/HCP-pipelines/
and the link therein to the pipelines on GitHub.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Matthieu Vanhoutte 
Reply-To: Freesurfer support list 
Date: Friday, September 19, 2014 9:23 AM
To: Freesurfer support list 
Subject: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion









Dear Freesurfer's experts,


I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data.


The first step has to be the correction of gradient-nonlinearity-induced distortion. The correction is then done with a customized version of the gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al., 2006).


I couldn't manage to find this package on internet, the only things I've found is the freesurfer grad_unwarp command and a webpage (https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping)
 with no download link...


Where can I find this package and how to use it ?


Many thanks !


Best,










-
Matthieu Vanhoutte, MSc

Research Engineer - Department of Neuroradiology

Regional University Hospital, Lille, France















 



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Re: [Freesurfer] segmentation fault mri_convert Ubuntu 14.04

Hello Alessandra,

This is a known issue with pre-freesurfer v5.3 releases and the most
recent version of Ubuntu. To fix the issue, if you have access to a
machine that still runs Ubuntu 12.04, please do the following:

  1) On the Ubuntu 12.04 system, find the find the file "libcrypt-2.*.so"
usually located in the /lib64 folder. (/lib/i386-linux-gnu on 32bit
machines).

  2) Copy that file into the $FREESURFER_HOME/lib on your new Ubuntu 14.04
machine and give it the name "libcrypt.so.1".

  3) Lastly, after loading freesurfer, update your LD_LIBRARY_PATH
environment variable to include the $FREESURFER_HOME/lib directory. This
can either be done manually in the terminal or in your .cshrc file (or
.bashrc file).

  $> setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib:$LD_LIBRARY_PATH

Hope this helps. Contact me directly if you have a any specific issues. Also,
if you are unable to find a version of libcrypt on an older version of
Ubuntu let me know and I will search for one.

-Zeke






> Dear all,
>
> I am running FreeSurfer version [recon-all,v 1.313.2.6 2010/08/04] on an
> Ubuntu machine.
> After updating my system from Ubuntu 12.04 to Ubuntu 14.04 I get a
> segmentation fault when I try to resample images using mri_convert:
>
> /mri_convert -vs 1 1 1 /folder/original_image.nii.gz /folder/resampled
> image.nii.gz //
> //$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $//
> //reading from /folder/original_image.nii.gz...//
> //Segmentation fault (core dumped)/
>
> Any help on this?
> (for consistency with an on-going study I would like not to install a
> newer FreeSurfer version)
>
> Thank you very much!
> Alessandra
>
>
> --
> --
> Alessandra Griffa
> Doctoral assistant
>
> Signal Processing Laboratory 5
> EPFL STI IEL LTS5
> ELD 233 (BÃ¢timent ELD)
> Station 11 CH-1015
> Lausanne
> Tel.: +41216934807
>
> web: http://lts5www.epfl.ch/
> personal page: http://people.epfl.ch/alessandra.griffa?lang=en
> --
>
> ___
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion

2014-09-19 Thread Matthieu Vanhoutte

Thank you Michael for this link !

However, it seems that we have to install very precise versions of FSL and
Freesurfer.

Once we get *fsl-5.0.6* package (
http://fsl.fmrib.ox.ac.uk/fsldownloads/oldversions/), how to install this
one and which wiki to follow ?

Cheers,

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2014-09-19 16:35 GMT+02:00 Harms, Michael :

>
>  Hi,
> I suggest you start with the documentation that accompanies the recently
> released HCP pipelines.
> see
> http://www.humanconnectome.org/documentation/HCP-pipelines/
> and the link therein to the pipelines on GitHub.
>
>  cheers,
> -MH
>
>   --
> Michael Harms, Ph.D.
>  ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
>   From: Matthieu Vanhoutte 
> Reply-To: Freesurfer support list 
> Date: Friday, September 19, 2014 9:23 AM
> To: Freesurfer support list 
> Subject: [Freesurfer] HCP pipelines: fMRIVolume --> correction of
> gradient-nonlinearity-induced distortion
>
> Dear Freesurfer's experts,
>
>  I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing
> pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data.
>
> The first step has to be the correction of gradient-nonlinearity-induced
> distortion. The correction is then done with a customized version of the
> gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al.,
> 2006).
>
>  I couldn't manage to find this package on internet, the only things I've
> found is the freesurfer grad_unwarp command and a webpage (
> https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping) with no
> download link...
>
>  Where can I find this package and how to use it ?
>
>  Many thanks !
>
>  Best,
>
>  -
> Matthieu Vanhoutte, MSc
>  Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
>
>  --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion

2014-09-19 Thread Matthieu Vanhoutte

More precisely how to install *fsl-5.0.6* on ubuntu 12.10 or 14.04 ?

Thanks !

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2014-09-19 17:18 GMT+02:00 Matthieu Vanhoutte :

> Thank you Michael for this link !
>
> However, it seems that we have to install very precise versions of FSL and
> Freesurfer.
>
> Once we get *fsl-5.0.6* package (
> http://fsl.fmrib.ox.ac.uk/fsldownloads/oldversions/), how to install this
> one and which wiki to follow ?
>
> Cheers,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2014-09-19 16:35 GMT+02:00 Harms, Michael :
>
>>
>>  Hi,
>> I suggest you start with the documentation that accompanies the recently
>> released HCP pipelines.
>> see
>> http://www.humanconnectome.org/documentation/HCP-pipelines/
>> and the link therein to the pipelines on GitHub.
>>
>>  cheers,
>> -MH
>>
>>   --
>> Michael Harms, Ph.D.
>>  ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>>   From: Matthieu Vanhoutte 
>> Reply-To: Freesurfer support list 
>> Date: Friday, September 19, 2014 9:23 AM
>> To: Freesurfer support list 
>> Subject: [Freesurfer] HCP pipelines: fMRIVolume --> correction of
>> gradient-nonlinearity-induced distortion
>>
>> Dear Freesurfer's experts,
>>
>>  I'm trying to follow fMRI Volume pipeline from "The minimal
>> preprocessing pipelines for the Human Connectome Project" (NeuroImage,
>> 2013) on HCP data.
>>
>> The first step has to be the correction of gradient-nonlinearity-induced
>> distortion. The correction is then done with a customized version of the
>> gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al.,
>> 2006).
>>
>>  I couldn't manage to find this package on internet, the only things I've
>> found is the freesurfer grad_unwarp command and a webpage (
>> https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping) with no
>> download link...
>>
>>  Where can I find this package and how to use it ?
>>
>>  Many thanks !
>>
>>  Best,
>>
>>  -
>> Matthieu Vanhoutte, MSc
>>  Research Engineer - Department of Neuroradiology
>> Regional University Hospital, Lille, France
>>
>>
>>  --
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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Re: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion

2014-09-19 Thread Harms, Michael







The pipelines documentation should include fairly extensive documentation to get you going.
If you have further questions, you should switch over to using the HCP-Users list.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: Matthieu Vanhoutte 
Reply-To: Freesurfer support list 
Date: Friday, September 19, 2014 10:18 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion








Thank you Michael for this link !


However, it seems that we have to install very precise versions of FSL and Freesurfer.


Once we get fsl-5.0.6 package (http://fsl.fmrib.ox.ac.uk/fsldownloads/oldversions/), how to install this one and which wiki to follow ?


Cheers,








-
Matthieu Vanhoutte, MSc

Research Engineer - Department of Neuroradiology

Regional University Hospital, Lille, France




2014-09-19 16:35 GMT+02:00 Harms, Michael 
:





Hi,
I suggest you start with the documentation that accompanies the recently released HCP pipelines.
see
http://www.humanconnectome.org/documentation/HCP-pipelines/
and the link therein to the pipelines on GitHub.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 
314-747-6173
St. Louis, MO  63110 Email: 
mha...@wustl.edu






From: Matthieu Vanhoutte 
Reply-To: Freesurfer support list 
Date: Friday, September 19, 2014 9:23 AM
To: Freesurfer support list 
Subject: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion











Dear Freesurfer's experts,


I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data.


The first step has to be the correction of gradient-nonlinearity-induced distortion. The correction is then done with a customized version of the gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al., 2006).


I couldn't manage to find this package on internet, the only things I've found is the freesurfer grad_unwarp command and a webpage (https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping)
 with no download link...


Where can I find this package and how to use it ?


Many thanks !


Best,










-
Matthieu Vanhoutte, MSc

Research Engineer - Department of Neuroradiology

Regional University Hospital, Lille, France

















 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
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Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

Bruce,

By "symlink from your /mnt/hgfs/mydata/fsaverage to
/usr/local/freesurfer/subjects/fsaverage" you mean "ln -s
/mnt/hgfs/mydata/fsaverage  /usr/local/freesurfer/subjects/fsaverage" ?
which fsaverage is the target ?

Thanks,
Mahmoud

On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud  wrote:

> Bruce,
>
> Thank you for your follow up and advice. Please let me know:
> 1- How to download the fsaverage again?
> 2- should I do the symlink manually or it will be done by recon-all later ?
> 3- What steps should I take before running the recon-all -all ? should I
> create any specific directory? set any permission ?
>
> Best,
> Mahmoud
>
> On Fri, Sep 19, 2014 at 9:41 AM, Bruce Fischl 
> wrote:
>
>> yes, you symlinked it to itself which is why you are getting the infinite
>> recursion error. You need to delete /usr/local/freesurfer/
>> subjects/fsaverage
>>
>> and download the fsaverage dir again, put it in that directory, then
>> symlink from your /mnt/hgfs/mydata/fsaverage to /usr/local/freesurfer/
>> subjects/fsaverage
>>
>>
>> cheers
>> Bruce
>> On Fri, 19 Sep 2014, Mahmoud wrote:
>>
>>  Bruce,
>>>
>>> I already had my data in a shared folder (/mnt/hgfs/mydata) but I got the
>>> permission error the same point that I got the symlink error lastly. So,
>>> I
>>> tought that might be due to something related to shared directory.
>>> Then I copied my subjects under the $SUBJECTS_DIR but got the symlink
>>> error.
>>>
>>> running ls -l /usr/local/freesurfer/subjects /fsaverage  shows me this:
>>>
>>> lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 18 20:23
>>> /usr/local/freesurfer/subjects/fsaverage ->
>>> /usr/local/freesurfer/subjects/fsaverage
>>>
>>> Thank you,
>>> Mahmoud
>>>
>>>
>>> On Fri, Sep 19, 2014 at 9:23 AM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   the  directory /usr/local/freesurfer/subjects is for subjects
>>>   that we distribute and NOT where you should be putting your
>>>   subject data. Is that what you are doing? You may have
>>>   overwritten the fsaverage dir there. Can you run:
>>>
>>>   ls -l /usr/local/freesurfer/subjects/fsaverage
>>>
>>>   and send us the results?
>>>
>>>   you should create a directory elsewhere with your subject data
>>>   and point SUBJECTS_DIR at it
>>>
>>>   cheers
>>>   Bruce
>>>
>>>   On Fri, 19 Sep 2014, Mahmoud wrote:
>>>
>>> Bruce,
>>>
>>> Here is the info when I open a new terminal:
>>>
>>> 
>>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>> 
>>> 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
>>> ubuntu:~>
>>>
>>> On Fri, Sep 19, 2014 at 8:56 AM, Bruce Fischl
>>> 
>>> wrote:
>>>   can you tell us what your FREESURFER_HOME is
>>> and what your
>>>   SUBJECTS_DIR is? You will need to remove the
>>> broken link
>>>   probably
>>>
>>>   On Fri, 19 Sep 2014, Mahmoud wrote:
>>>
>>> Hi Bruce,
>>>
>>> Actually I couldn't. It says: ls: cannot
>>> access
>>>
>>> /usr/local/freesurfer/subjects/fsaverage: Too many
>>> levels of symbolic links
>>> And even I couldn't cd to fsaverage !
>>> In fact there is no directory  under
>>> SUBJETCS_DIR
>>> named fsaverage, it seems
>>> the fsaverage under SUBJETCS_DIR is just
>>> a broken
>>> link, and I have no idea
>>> why the the link is broken and how to
>>> fix it.
>>> Any help would be highly appreciated !
>>>
>>> Thank you,
>>> Mahmoud
>>>
>>>
>>> On Fri, Sep 19, 2014 at 8:21 AM, Bruce
>>> Fischl
>>> 
>>> wrote:
>>>   Hi Mahmoud
>>>
>>>   were you able to create a symlink
>>> to fsaverage
>>> in your
>>>   SUBJECTS_DIR? If not, that is the
>>> reason for
>>> this error
>>>   Bruce
>>>
>>>   On Thu, 18 Sep 2014, Mahmoud
>>> wrote:
>>>
>>> Dear all,
>>>
>>> After running "recon-all -i
>>>
>>>
>>> $SUBJECTS_DIR/Case018/ca

Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label


the easiest thing to do is:

cd  /mnt/hgfs/mydata
ln -s /usr/local/freesurfer/subjects/fsaverage


then you don't have to worry about source and target. It will implicitly 
create the symlink in $PWD


cheers
Bruce
On Fri, 19 Sep 
2014, Mahmoud 
wrote:



Bruce,

By "symlink from your /mnt/hgfs/mydata/fsaverage to
/usr/local/freesurfer/subjects/fsaverage" you mean "ln -s
/mnt/hgfs/mydata/fsaverage  /usr/local/freesurfer/subjects/fsaverage" ?
which fsaverage is the target ?

Thanks,
Mahmoud

On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud  wrote:
  Bruce,
Thank you for your follow up and advice. Please let me know:
1- How to download the fsaverage again?
2- should I do the symlink manually or it will be done by recon-all
later ?
3- What steps should I take before running the recon-all -all ? should
I create any specific directory? set any permission ?

Best,
Mahmoud

On Fri, Sep 19, 2014 at 9:41 AM, Bruce Fischl
 wrote:
  yes, you symlinked it to itself which is why you are
  getting the infinite recursion error. You need to delete
  /usr/local/freesurfer/subjects/fsaverage

  and download the fsaverage dir again, put it in that
  directory, then symlink from your
  /mnt/hgfs/mydata/fsaverage to
  /usr/local/freesurfer/subjects/fsaverage

  cheers
  Bruce
  On Fri, 19 Sep 2014, Mahmoud wrote:

Bruce,

I already had my data in a shared folder
(/mnt/hgfs/mydata) but I got the
permission error the same point that I got the
symlink error lastly. So, I
tought that might be due to something related
to shared directory.
Then I copied my subjects under the
$SUBJECTS_DIR but got the symlink error.

running ls -l /usr/local/freesurfer/subjects
/fsaverage  shows me this:

lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 18 20:23
/usr/local/freesurfer/subjects/fsaverage ->
/usr/local/freesurfer/subjects/fsaverage

Thank you,
Mahmoud


On Fri, Sep 19, 2014 at 9:23 AM, Bruce Fischl

wrote:
      the  directory
/usr/local/freesurfer/subjects is for subjects
      that we distribute and NOT where you
should be putting your
      subject data. Is that what you are
doing? You may have
      overwritten the fsaverage dir there. Can
you run:

      ls -l
/usr/local/freesurfer/subjects/fsaverage

      and send us the results?

      you should create a directory elsewhere
with your subject data
      and point SUBJECTS_DIR at it

      cheers
      Bruce

      On Fri, 19 Sep 2014, Mahmoud wrote:

            Bruce,

            Here is the info when I open a new
terminal:

            
           
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
            
            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
            ubuntu:~>

            On Fri, Sep 19, 2014 at 8:56 AM,
Bruce Fischl
            
            wrote:
                  can you tell us what your
FREESURFER_HOME is
            and what your
                  SUBJECTS_DIR is? You will
need to remove the
            broken link
                  probably

                  On Fri, 19 Sep 2014, Mahmoud
wrote:

                        Hi Bruce,

                        Actually I couldn't.
It says: ls: cannot
            access
                       
           
/usr/local/freesurfer/subjects/fsaverage: Too
many
                        levels of symbolic
links
                        And even I couldn't cd
to fsaverage !
                        In fact there is no
directory  under
            SUBJETCS_DIR
                        named fsaverage, it
seems
                        the fsaverage under
SUBJETCS_DIR is just
            a broken
                        link, and I

Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

> Bruce,
>
> By "symlink from your /mnt/hgfs/mydata/fsaverage to
> /usr/local/freesurfer/subjects/fsaverage" you mean "ln -s
> /mnt/hgfs/mydata/fsaverage  /usr/local/freesurfer/subjects/fsaverage" ?
> which fsaverage is the target ?
>
> Thanks,
> Mahmoud
>

The "target" fsaverage is the one that came with the installation. Which
you no longer have so I have created a link for you to download it again
and put it back in your $SUBJECTS_DIR (see next answer).

> On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud  wrote:
>
>> Bruce,
>>
>> Thank you for your follow up and advice. Please let me know:
>> 1- How to download the fsaverage again?

Ive created a link for you to download it:
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/Linux_centos4_x86_64/fsaverage.tar.gz

>> 2- should I do the symlink manually or it will be done by recon-all
>> later ?

Just extract the file above into your $SUBJECTS_DIR so that you have a
$SUBJECTS_DIR/fsaverage directory and recon-all will take care of the
rest.

>> 3- What steps should I take before running the recon-all -all ? should I
>> create any specific directory? set any permission ?

None. Hopefully this will just work.

-Zeke
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Re: [Freesurfer] CORRECTION ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label


Here is the proper link.

ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/fsaverage.tar.gz


>> Bruce,
>>
>> By "symlink from your /mnt/hgfs/mydata/fsaverage to
>> /usr/local/freesurfer/subjects/fsaverage" you mean "ln -s
>> /mnt/hgfs/mydata/fsaverage  /usr/local/freesurfer/subjects/fsaverage" ?
>> which fsaverage is the target ?
>>
>> Thanks,
>> Mahmoud
>>
>
> The "target" fsaverage is the one that came with the installation. Which
> you no longer have so I have created a link for you to download it again
> and put it back in your $SUBJECTS_DIR (see next answer).
>
>
>> On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud  wrote:
>>
>>> Bruce,
>>>
>>> Thank you for your follow up and advice. Please let me know:
>>> 1- How to download the fsaverage again?
>
> Ive created a link for you to download it:
> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/Linux_centos4_x86_64/fsaverage.tar.gz
>
>>> 2- should I do the symlink manually or it will be done by recon-all
>>> later ?
>
> Just extract the file above into your $SUBJECTS_DIR so that you have a
> $SUBJECTS_DIR/fsaverage directory and recon-all will take care of the
> rest.
>
>>> 3- What steps should I take before running the recon-all -all ? should
>>> I
>>> create any specific directory? set any permission ?
>
> None. Hopefully this will just work.
>
>
> -Zeke
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

Bruce and Zeke,

Thank you so much for your advice.
The last question before running the recon again. if I say:
cd  /mnt/hgfs/mydata
ln -s /usr/local/freesurfer/subjects/fsaverage

It means that I shouldn't already have the fsaverage under /mydata
directory, right ?

Mahmoud

On Fri, Sep 19, 2014 at 12:09 PM, Bruce Fischl 
wrote:

> the easiest thing to do is:
>
> cd  /mnt/hgfs/mydata
> ln -s /usr/local/freesurfer/subjects/fsaverage
>
>
> then you don't have to worry about source and target. It will implicitly
> create the symlink in $PWD
>
>
> cheers
> Bruce
> On Fri, 19 Sep 2014, Mahmoud wrote:
>
>  Bruce,
>>
>> By "symlink from your /mnt/hgfs/mydata/fsaverage to
>> /usr/local/freesurfer/subjects/fsaverage" you mean "ln -s
>> /mnt/hgfs/mydata/fsaverage  /usr/local/freesurfer/subjects/fsaverage" ?
>> which fsaverage is the target ?
>>
>> Thanks,
>> Mahmoud
>>
>> On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud  wrote:
>>   Bruce,
>> Thank you for your follow up and advice. Please let me know:
>> 1- How to download the fsaverage again?
>> 2- should I do the symlink manually or it will be done by recon-all
>> later ?
>> 3- What steps should I take before running the recon-all -all ? should
>> I create any specific directory? set any permission ?
>>
>> Best,
>> Mahmoud
>>
>> On Fri, Sep 19, 2014 at 9:41 AM, Bruce Fischl
>>  wrote:
>>   yes, you symlinked it to itself which is why you are
>>   getting the infinite recursion error. You need to delete
>>   /usr/local/freesurfer/subjects/fsaverage
>>
>>   and download the fsaverage dir again, put it in that
>>   directory, then symlink from your
>>   /mnt/hgfs/mydata/fsaverage to
>>   /usr/local/freesurfer/subjects/fsaverage
>>
>>   cheers
>>   Bruce
>>   On Fri, 19 Sep 2014, Mahmoud wrote:
>>
>> Bruce,
>>
>> I already had my data in a shared folder
>> (/mnt/hgfs/mydata) but I got the
>> permission error the same point that I got the
>> symlink error lastly. So, I
>> tought that might be due to something related
>> to shared directory.
>> Then I copied my subjects under the
>> $SUBJECTS_DIR but got the symlink error.
>>
>> running ls -l /usr/local/freesurfer/subjects
>> /fsaverage  shows me this:
>>
>> lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 18 20:23
>> /usr/local/freesurfer/subjects/fsaverage ->
>> /usr/local/freesurfer/subjects/fsaverage
>>
>> Thank you,
>> Mahmoud
>>
>>
>> On Fri, Sep 19, 2014 at 9:23 AM, Bruce Fischl
>> 
>> wrote:
>>   the  directory
>> /usr/local/freesurfer/subjects is for subjects
>>   that we distribute and NOT where you
>> should be putting your
>>   subject data. Is that what you are
>> doing? You may have
>>   overwritten the fsaverage dir there. Can
>> you run:
>>
>>   ls -l
>> /usr/local/freesurfer/subjects/fsaverage
>>
>>   and send us the results?
>>
>>   you should create a directory elsewhere
>> with your subject data
>>   and point SUBJECTS_DIR at it
>>
>>   cheers
>>   Bruce
>>
>>   On Fri, 19 Sep 2014, Mahmoud wrote:
>>
>> Bruce,
>>
>> Here is the info when I open a new
>> terminal:
>>
>> 
>>
>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> 
>> 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
>> ubuntu:~>
>>
>> On Fri, Sep 19, 2014 at 8:56 AM,
>> Bruce Fischl
>> 
>> wrote:
>>   can you tell us what your
>> FREESURFER_HOME is
>> and what your
>>   SUBJECTS_DIR is? You will
>> need to remove the
>> broken link
>>   probably
>>
>>   On Fri, 19 Sep 2014, Mahmoud
>> wrote:
>>
>> Hi Bruce,
>>
>> Actually I couldn't.
>> It says: ls: cannot
>> access

Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

yes, that is true. If it's already there the symlink will fail. You 
should be able to rm it if it is there an incorrect (or leave it if it is 
there and correct)

On Fri, 19 Sep 2014, Mahmoud wrote:


Bruce and Zeke,
Thank you so much for your advice.
The last question before running the recon again. if I say:
cd  /mnt/hgfs/mydata
ln -s /usr/local/freesurfer/subjects/fsaverage

It means that I shouldn't already have the fsaverage under /mydata
directory, right ?

Mahmoud

On Fri, Sep 19, 2014 at 12:09 PM, Bruce Fischl 
wrote:
  the easiest thing to do is:

  cd  /mnt/hgfs/mydata
  ln -s /usr/local/freesurfer/subjects/fsaverage


  then you don't have to worry about source and target. It will
  implicitly create the symlink in $PWD

  cheers
  Bruce
  On Fri, 19 Sep 2014, Mahmoud wrote:

Bruce,

By "symlink from your /mnt/hgfs/mydata/fsaverage to
/usr/local/freesurfer/subjects/fsaverage" you mean
"ln -s
/mnt/hgfs/mydata/fsaverage 
/usr/local/freesurfer/subjects/fsaverage" ?
which fsaverage is the target ?

Thanks,
Mahmoud

On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud
 wrote:
      Bruce,
Thank you for your follow up and advice. Please let
me know:
1- How to download the fsaverage again?
2- should I do the symlink manually or it will be
done by recon-all
later ?
3- What steps should I take before running the
recon-all -all ? should
I create any specific directory? set any permission
?

Best,
Mahmoud

On Fri, Sep 19, 2014 at 9:41 AM, Bruce Fischl
 wrote:
      yes, you symlinked it to itself which is why
you are
      getting the infinite recursion error. You need
to delete
      /usr/local/freesurfer/subjects/fsaverage

      and download the fsaverage dir again, put it
in that
      directory, then symlink from your
      /mnt/hgfs/mydata/fsaverage to
      /usr/local/freesurfer/subjects/fsaverage

      cheers
      Bruce
      On Fri, 19 Sep 2014, Mahmoud wrote:

            Bruce,

            I already had my data in a shared folder
            (/mnt/hgfs/mydata) but I got the
            permission error the same point that I
got the
            symlink error lastly. So, I
            tought that might be due to something
related
            to shared directory.
            Then I copied my subjects under the
            $SUBJECTS_DIR but got the symlink error.

            running ls -l
/usr/local/freesurfer/subjects
            /fsaverage  shows me this:

            lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 18
20:23
            /usr/local/freesurfer/subjects/fsaverage
->
            /usr/local/freesurfer/subjects/fsaverage

            Thank you,
            Mahmoud


            On Fri, Sep 19, 2014 at 9:23 AM, Bruce
Fischl
            
            wrote:
                  the  directory
            /usr/local/freesurfer/subjects is for
subjects
                  that we distribute and NOT where
you
            should be putting your
                  subject data. Is that what you are
            doing? You may have
                  overwritten the fsaverage dir
there. Can
            you run:

                  ls -l
            /usr/local/freesurfer/subjects/fsaverage

                  and send us the results?

                  you should create a directory
elsewhere
            with your subject data
                  and point SUBJECTS_DIR at it

                  cheers
                  Bruce

                  On Fri, 19 Sep 2014, Mahmoud
wrote:

                        Bruce,

                        Here is the info when I open
a new
            terminal:

                        
                       
           
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
                        
                        Setting up environment for
            FreeSurfer/FS-FAST (and

Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

Mahmoud,

If I recall correctly, your on a virtual machine with the /mnt/hgfs/mydata
directory being a shared directory, and you werent able to write to it
when running recon-all.

So, what you want to do is create another directory within your virtual
machine that holds your subjects data. You will still need the
$FREESURFER_HOME/subjects directory because that directory contains files
required by recon-all, so you will have a separate directory which
contains your subjects.

You should not be creating symlinks or anything like that.

Just restore the fsaverage directory from the link I sent you back into
$FREESURFER_HOME/subjects, put your subject data somewhere else in the VM,
and run recon-all with the correct arguments.

-Zeke


> yes, that is true. If it's already there the symlink will fail. You
> should be able to rm it if it is there an incorrect (or leave it if it is
> there and correct)
> On Fri, 19 Sep 2014, Mahmoud wrote:
>
>> Bruce and Zeke,
>> Thank you so much for your advice.
>> The last question before running the recon again. if I say:
>> cdÂ  /mnt/hgfs/mydata
>> ln -s /usr/local/freesurfer/subjects/fsaverage
>>
>> It means that I shouldn't already have the fsaverage under /mydata
>> directory, right ?
>>
>> Mahmoud
>>
>> On Fri, Sep 19, 2014 at 12:09 PM, Bruce Fischl
>> 
>> wrote:
>>   the easiest thing to do is:
>>
>>   cdÂ  /mnt/hgfs/mydata
>>   ln -s /usr/local/freesurfer/subjects/fsaverage
>>
>>
>>   then you don't have to worry about source and target. It will
>>   implicitly create the symlink in $PWD
>>
>>   cheers
>>   Bruce
>>   On Fri, 19 Sep 2014, Mahmoud wrote:
>>
>> Bruce,
>>
>> By "symlink from your /mnt/hgfs/mydata/fsaverage to
>> /usr/local/freesurfer/subjects/fsaverage" you mean
>> "ln -s
>> /mnt/hgfs/mydata/fsaverageÂ 
>> /usr/local/freesurfer/subjects/fsaverage" ?
>> which fsaverage is the target ?
>>
>> Thanks,
>> Mahmoud
>>
>> On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud
>>  wrote:
>> Â  Â  Â  Bruce,
>> Thank you for your follow up and advice. Please let
>> me know:
>> 1- How to download the fsaverage again?
>> 2- should I do the symlink manually or it will be
>> done by recon-all
>> later ?
>> 3- What steps should I take before running the
>> recon-all -all ? should
>> I create any specific directory? set any permission
>> ?
>>
>> Best,
>> Mahmoud
>>
>> On Fri, Sep 19, 2014 at 9:41 AM, Bruce Fischl
>>  wrote:
>> Â  Â  Â  yes, you symlinked it to itself which is why
>> you are
>> Â  Â  Â  getting the infinite recursion error. You need
>> to delete
>> Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage
>>
>> Â  Â  Â  and download the fsaverage dir again, put it
>> in that
>> Â  Â  Â  directory, then symlink from your
>> Â  Â  Â  /mnt/hgfs/mydata/fsaverage to
>> Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage
>>
>> Â  Â  Â  cheers
>> Â  Â  Â  Bruce
>> Â  Â  Â  On Fri, 19 Sep 2014, Mahmoud wrote:
>>
>> Â  Â  Â  Â  Â  Â  Bruce,
>>
>> Â  Â  Â  Â  Â  Â  I already had my data in a shared folder
>> Â  Â  Â  Â  Â  Â  (/mnt/hgfs/mydata) but I got the
>> Â  Â  Â  Â  Â  Â  permission error the same point that I
>> got the
>> Â  Â  Â  Â  Â  Â  symlink error lastly. So, I
>> Â  Â  Â  Â  Â  Â  tought that might be due to something
>> related
>> Â  Â  Â  Â  Â  Â  to shared directory.
>> Â  Â  Â  Â  Â  Â  Then I copied my subjects under the
>> Â  Â  Â  Â  Â  Â  $SUBJECTS_DIR but got the symlink error.
>>
>> Â  Â  Â  Â  Â  Â  running ls -l
>> /usr/local/freesurfer/subjects
>> Â  Â  Â  Â  Â  Â  /fsaverageÂ  shows me this:
>>
>> Â  Â  Â  Â  Â  Â  lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 18
>> 20:23
>> Â  Â  Â  Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage
>> ->
>> Â  Â  Â  Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage
>>
>> Â  Â  Â  Â  Â  Â  Thank you,
>> Â  Â  Â  Â  Â  Â  Mahmoud
>>
>>
>> Â  Â  Â  Â  Â  Â  On Fri, Sep 19, 2014 at 9:23 AM, Bruce
>> Fischl
>> Â  Â  Â  Â  Â  Â  
>> Â  Â  Â  Â  Â  Â  wrote:
>> Â  Â  Â  Â  Â  Â  Â  Â  Â  theÂ  directory
>> Â  Â  Â  Â  Â  Â  /usr/local/freesurfer/subjects is for
>> subjects
>> Â  Â  Â  Â  Â  Â  Â  Â  Â  that we distribute and NOT where
>> you
>> Â  Â  Â  Â  Â  Â  should be putting your

Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

Zeke,

I created another directory named "volumetric" and put my data under it.
To final check before running the recon-all, here is the info from terminal:
 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
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
ubuntu:~> cd /volumetric
ubuntu:/volumetric> ls
Case018  Case022


and I'm going to run this:

#!/bin/tcsh

clear
cd  /volumetric
ln -s /usr/local/freesurfer/subjects/fsaverage

recon-all -i /volumetric/Case018/case018_tp2/22-1.dcm -subject case018_tp2
-all

On Fri, Sep 19, 2014 at 1:24 PM,  wrote:

> Mahmoud,
>
> If I recall correctly, your on a virtual machine with the /mnt/hgfs/mydata
> directory being a shared directory, and you werent able to write to it
> when running recon-all.
>
> So, what you want to do is create another directory within your virtual
> machine that holds your subjects data. You will still need the
> $FREESURFER_HOME/subjects directory because that directory contains files
> required by recon-all, so you will have a separate directory which
> contains your subjects.
>
> You should not be creating symlinks or anything like that.
>
> Just restore the fsaverage directory from the link I sent you back into
> $FREESURFER_HOME/subjects, put your subject data somewhere else in the VM,
> and run recon-all with the correct arguments.
>
> -Zeke
>
>
> > yes, that is true. If it's already there the symlink will fail. You
> > should be able to rm it if it is there an incorrect (or leave it if it is
> > there and correct)
> > On Fri, 19 Sep 2014, Mahmoud wrote:
> >
> >> Bruce and Zeke,
> >> Thank you so much for your advice.
> >> The last question before running the recon again. if I say:
> >> cdÂ  /mnt/hgfs/mydata
> >> ln -s /usr/local/freesurfer/subjects/fsaverage
> >>
> >> It means that I shouldn't already have the fsaverage under /mydata
> >> directory, right ?
> >>
> >> Mahmoud
> >>
> >> On Fri, Sep 19, 2014 at 12:09 PM, Bruce Fischl
> >> 
> >> wrote:
> >>   the easiest thing to do is:
> >>
> >>   cdÂ  /mnt/hgfs/mydata
> >>   ln -s /usr/local/freesurfer/subjects/fsaverage
> >>
> >>
> >>   then you don't have to worry about source and target. It will
> >>   implicitly create the symlink in $PWD
> >>
> >>   cheers
> >>   Bruce
> >>   On Fri, 19 Sep 2014, Mahmoud wrote:
> >>
> >> Bruce,
> >>
> >> By "symlink from your /mnt/hgfs/mydata/fsaverage to
> >> /usr/local/freesurfer/subjects/fsaverage" you mean
> >> "ln -s
> >> /mnt/hgfs/mydata/fsaverageÂ
> >> /usr/local/freesurfer/subjects/fsaverage" ?
> >> which fsaverage is the target ?
> >>
> >> Thanks,
> >> Mahmoud
> >>
> >> On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud
> >>  wrote:
> >> Â  Â  Â  Bruce,
> >> Thank you for your follow up and advice. Please let
> >> me know:
> >> 1- How to download the fsaverage again?
> >> 2- should I do the symlink manually or it will be
> >> done by recon-all
> >> later ?
> >> 3- What steps should I take before running the
> >> recon-all -all ? should
> >> I create any specific directory? set any permission
> >> ?
> >>
> >> Best,
> >> Mahmoud
> >>
> >> On Fri, Sep 19, 2014 at 9:41 AM, Bruce Fischl
> >>  wrote:
> >> Â  Â  Â  yes, you symlinked it to itself which is why
> >> you are
> >> Â  Â  Â  getting the infinite recursion error. You need
> >> to delete
> >> Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage
> >>
> >> Â  Â  Â  and download the fsaverage dir again, put it
> >> in that
> >> Â  Â  Â  directory, then symlink from your
> >> Â  Â  Â  /mnt/hgfs/mydata/fsaverage to
> >> Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage
> >>
> >> Â  Â  Â  cheers
> >> Â  Â  Â  Bruce
> >> Â  Â  Â  On Fri, 19 Sep 2014, Mahmoud wrote:
> >>
> >> Â  Â  Â  Â  Â  Â  Bruce,
> >>
> >> Â  Â  Â  Â  Â  Â  I already had my data in a shared folder
> >> Â  Â  Â  Â  Â  Â  (/mnt/hgfs/mydata) but I got the
> >> Â  Â  Â  Â  Â  Â  permission error the same point that I
> >> got the
> >> Â  Â  Â  Â  Â  Â  symlink error lastly. So, I
> >> Â  Â  Â  Â  Â  Â  tought that might be due to something
> >> related
> >> Â  Â  Â  Â  Â  Â  to shared directory.
> >> Â  Â  Â  Â  Â  Â  Then I copied my subjects under the
> >> Â  Â  Â  Â  Â  Â  $SUBJECTS_DIR but got

Re: [Freesurfer] ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

I believe if you simply run:

$> recon-all -i /volumetric/Case018/case018_tp2/22-1.dcm -subject
case018_tp2 -all

You should be all set. You do not need to type any of the following commands:

> clear
> cd  /volumetric
> ln -s /usr/local/freesurfer/subjects/fsaverage


-Zeke



> Zeke,
>
> I created another directory named "volumetric" and put my data under it.
> To final check before running the recon-all, here is the info from
> terminal:
>  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
> 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
> ubuntu:~> cd /volumetric
> ubuntu:/volumetric> ls
> Case018  Case022
>
>
> and I'm going to run this:
>
> #!/bin/tcsh
>
> clear
> cd  /volumetric
> ln -s /usr/local/freesurfer/subjects/fsaverage
>
> recon-all -i /volumetric/Case018/case018_tp2/22-1.dcm -subject
> case018_tp2
> -all
>
> On Fri, Sep 19, 2014 at 1:24 PM,  wrote:
>
>> Mahmoud,
>>
>> If I recall correctly, your on a virtual machine with the
>> /mnt/hgfs/mydata
>> directory being a shared directory, and you werent able to write to it
>> when running recon-all.
>>
>> So, what you want to do is create another directory within your virtual
>> machine that holds your subjects data. You will still need the
>> $FREESURFER_HOME/subjects directory because that directory contains
>> files
>> required by recon-all, so you will have a separate directory which
>> contains your subjects.
>>
>> You should not be creating symlinks or anything like that.
>>
>> Just restore the fsaverage directory from the link I sent you back into
>> $FREESURFER_HOME/subjects, put your subject data somewhere else in the
>> VM,
>> and run recon-all with the correct arguments.
>>
>> -Zeke
>>
>>
>> > yes, that is true. If it's already there the symlink will fail. You
>> > should be able to rm it if it is there an incorrect (or leave it if it
>> is
>> > there and correct)
>> > On Fri, 19 Sep 2014, Mahmoud wrote:
>> >
>> >> Bruce and Zeke,
>> >> Thank you so much for your advice.
>> >> The last question before running the recon again. if I say:
>> >> cdÃ  /mnt/hgfs/mydata
>> >> ln -s /usr/local/freesurfer/subjects/fsaverage
>> >>
>> >> It means that I shouldn't already have the fsaverage under /mydata
>> >> directory, right ?
>> >>
>> >> Mahmoud
>> >>
>> >> On Fri, Sep 19, 2014 at 12:09 PM, Bruce Fischl
>> >> 
>> >> wrote:
>> >>   the easiest thing to do is:
>> >>
>> >>   cdÃ  /mnt/hgfs/mydata
>> >>   ln -s /usr/local/freesurfer/subjects/fsaverage
>> >>
>> >>
>> >>   then you don't have to worry about source and target. It will
>> >>   implicitly create the symlink in $PWD
>> >>
>> >>   cheers
>> >>   Bruce
>> >>   On Fri, 19 Sep 2014, Mahmoud wrote:
>> >>
>> >> Bruce,
>> >>
>> >> By "symlink from your /mnt/hgfs/mydata/fsaverage to
>> >> /usr/local/freesurfer/subjects/fsaverage" you mean
>> >> "ln -s
>> >> /mnt/hgfs/mydata/fsaverageÃ
>> >> /usr/local/freesurfer/subjects/fsaverage" ?
>> >> which fsaverage is the target ?
>> >>
>> >> Thanks,
>> >> Mahmoud
>> >>
>> >> On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud
>> >>  wrote:
>> >> Ã  Ã  Ã  Bruce,
>> >> Thank you for your follow up and advice. Please let
>> >> me know:
>> >> 1- How to download the fsaverage again?
>> >> 2- should I do the symlink manually or it will be
>> >> done by recon-all
>> >> later ?
>> >> 3- What steps should I take before running the
>> >> recon-all -all ? should
>> >> I create any specific directory? set any permission
>> >> ?
>> >>
>> >> Best,
>> >> Mahmoud
>> >>
>> >> On Fri, Sep 19, 2014 at 9:41 AM, Bruce Fischl
>> >>  wrote:
>> >> Ã  Ã  Ã  yes, you symlinked it to itself which is why
>> >> you are
>> >> Ã  Ã  Ã  getting the infinite recursion error. You
>> need
>> >> to delete
>> >> Ã  Ã  Ã  /usr/local/freesurfer/subjects/fsaverage
>> >>
>> >> Ã  Ã  Ã  and download the fsaverage dir again, put it
>> >> in that
>> >> Ã  Ã  Ã  directory, then symlink from your
>> >> Ã  Ã  Ã  /mnt/hgfs/mydata/fsaverage to
>> >> Ã  Ã  Ã  /usr/local/freesurfer/subjects/fsaverage
>> >>
>> >> Ã  Ã  Ã  cheers
>> >> Ã  Ã  Ã  Bruce
>> >> Ã  Ã  Ã  On Fri, 19 Sep 2014, Mahmoud wrote:
>> >>
>> >> Ã  Ã  Ã  Ã  Ã  Ã  Bruce,
>> >>
>> >> Ã  Ã  Ã  Ã  Ã  Ã  I already had my data in a shared
>> folder
>> >>

[Freesurfer] Converting GIFTI files to Freesurfer files

2014-09-19 Thread Reza Rajimehr

Hi,

To convert GIFTI files to the Freesurfer files, I just need to do
something like this?

mris_convert F99.R.inflated.74k_f99.surf.gii rh.inflated

Thanks,
Reza
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[Freesurfer] Question about Voxel Quantification with Thresholds

2014-09-19 Thread Karishma Smart

Dear all,

Is there a way to get a count of the voxels in a manually drawn ROI while
retaining each voxel's intensity value?  *In particular, I would like to
get a count of how many voxels in this manually drawn ROI fall above and
below an assigned intensity threshold.*

I have used mri_segstats to quantify the number of voxels in a particular
ROI that I have drawn manually (i.e. not using aseg).  However, in doing so
(I created a label for the ROI and used mri_segstats to count the number of
voxels in the label), I assigned each voxel the intensity of the label,
thus losing the intensity information.

Any guidance or assistance would be greatly appreciated.  Preferably, it
would be helpful if anybody knows a way to do this that is not
modality-dependent.

Thank you in advance for your help,
Karishma

--
Karishma Smart
B.A. Biological Sciences Cornell University Class of 2013
Boston University School of Graduate Medical Sciences Class of 2015
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Re: [Freesurfer] Question about Voxel Quantification with Thresholds