from:"Darko Komnenić"

[Freesurfer] [error] no installation candidates for curl

2018-01-23 Thread Darko Komnenić

Dear FreeSurfer experts,
I am trying to perform hippocampal subfield segmentation with
FreeSurfer 6. I followed the instructions found on this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields which
said that I first need to download Matlab Runtime. Which brought me to
this page: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime

I reach the stage where I type in
curl
"https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bLinux.tar.gz";
-o "runtime.tar.gz"
after which I receive the following:
Die Anwendung »curl« ist momentan nicht installiert. Sie können sie
durch folgende Eingabe installieren:
sudo apt-get install curl

(my computer is in German, it basically says that curl is not
installed and that I can install it via apt-get command).
When I then type in that command and give my password, I receive:

Paketlisten werden gelesen... Fertig
Abhängigkeitsbaum wird aufgebaut
Status-Informationen einlesen... Fertig
Paket curl ist nicht verfügbar, wird aber von einem anderen Paket
referenziert. Das kann heißen, dass das Paket fehlt, dass es veraltet
ist oder nur aus einer anderen Quelle verfügbar ist.
E: Paket curl hat keinen Installationskandidaten

Which roughly translates to: reading package lists... done
building a dependency tree
reading status information... done
Package curl is not available, but is referred to by another package.
This could mean that the package is missing, outdated or available
only from a different source.
E: Package curl has no installation candidates.

I would be grateful for any solution suggestions!
Best,
Darko

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[Freesurfer] A question about FS6 hippocampal subfield segmentation output file

2018-01-30 Thread Darko Komnenić

Dear FreeSurfer experts,
in the txt files [lr]h.hippoSfVolumes-T1.v10.txt we can see the
volumes of individual hippocampal subfields - I was wondering what are
the units in which volume is given? Millimeters cubic, voxels, or
something else?
Thanks in advance!
Best,
Darko
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[Freesurfer] defining input images in a for-loop in recon-all

2018-03-29 Thread Darko Komnenić

Dear experts,
I would like to run a for-loop in FreeSurfer 5.1. so that I can have
multiple subjects analyzed over the holiday, without having to come to the
lab and start each of them myself. I searched the previous emails in this
list and know that I can make a file with a subject list, and then have the
loop go through that file.
I was wondering, however, how to handle the -i part of recon-all command?
Each subject in a loop needs to have one brain image assigned - I don't
think FreeSurfer will know where to look for images just by telling it what
the subject name is.
Thanks in advance for any help!
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Re: [Freesurfer] defining input images in a for-loop in recon-all

2018-03-29 Thread Darko Komnenić

Hi Bruce,
thanks for the reply. I only have one acquisition per subject. I guess
I can make a separate text file with a list of paths to dicoms and
then somehow try to pair the path and the subject name in the
recon-all command.

> From: Bruce Fischl 
> Subject: Re: [Freesurfer] defining input images in a for-loop in
>   recon-all
> To: Freesurfer support list 
> Message-ID:
>   
> Content-Type: text/plain; charset="utf-8"
>
> Hi Darko
>
> sorry, you need to sort this out yourself as there is no way for us to
> know where the dicoms are. An alternative is to create each subject dir,
> create the 00?.mgz files (if you have more than one acquistion) in the
> /mri/orig dir, then run recon-all without the -i flag. If you use
> -i you need to figure out a way to find one slice in the correct dicom
> series for each subject.
>
> cheers
> Bruce
>
>
> On
> Thu, 29 Mar 2018, Darko Komneni? wrote:
>
>> Dear experts,
>> I would like to run a for-loop in FreeSurfer 5.1. so that I can have
>> multiple subjects analyzed over
>> the holiday, without having to come to the lab and start each of them
>> myself. I searched the
>> previous emails in this list and know that I can make a file with a
>> subject list, and then have the
>> loop go through that file.
>> I was wondering, however, how to handle the -i part of recon-all command?
>> Each subject in a loop
>> needs to have one brain image assigned - I don't think FreeSurfer will
>> know where to look for images
>> just by telling it what the subject name is.
>> Thanks in advance for any help!
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[Freesurfer] mri_watershed Error: indices out of bounds

2018-03-30 Thread Darko Komnenić

Dear experts,
while running recon-all on FreeSurfer 5.1.0 I encountered the following error:
mri_watershed Error: indices out of bounds

I searched the email archive and found this thread:
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22\[Freesurfer\]+mri_watershed+Error\%3A+indices+out+of+bounds%22&o=newest&f=1
My problem seems identical to the one described by initial poster.
The suggestion was to try the following command:
set mdir=$SUBJECTS_DIR/$subject/mri
mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz
$mir/nu.mgz

When I tried it, the message I got was:
mri_add_xform_to_header: could not open source file /nu.mgz
No such file or directory
And indeed such file  does not exist in the mri subfolder of my
current subject's folder.

Any further suggestions on how to fix this?  Like the person asking
originally, this is the only participant where it happened, for
others, recon-all finished without error and all the images were
acquired in the same scanner.
Thanks in advance!
Best,
Darko
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Re: [Freesurfer] Freesurfer Digest, Vol 169, Issue 41

2018-04-03 Thread Darko Komnenić

Hi Bruce,
I attached the recon-all.log!
Thanks in advance for  taking a look!
Darko

Message: 3
Date: Sat, 31 Mar 2018 06:47:12 -0400
From: Bruce Fischl 
Subject: Re: [Freesurfer] mri_watershed Error: indices out of bounds
To: Freesurfer support list 
Message-ID: <23b23889-c042-4a04-9316-4c8ed5468...@nmr.mgh.harvard.edu>
Content-Type: text/plain;   charset=utf-8

Can you send us the recon-all.log?

> On Mar 30, 2018, at 11:32 AM, Darko Komneni?  wrote:
>
> Dear experts,
> while running recon-all on FreeSurfer 5.1.0 I encountered the following error:
> mri_watershed Error: indices out of bounds
>
> I searched the email archive and found this thread:
> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22\[Freesurfer\]+mri_watershed+Error\%3A+indices+out+of+bounds%22&o=newest&f=1
> My problem seems identical to the one described by initial poster.
> The suggestion was to try the following command:
> set mdir=$SUBJECTS_DIR/$subject/mri
> mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz
> $mir/nu.mgz
>
> When I tried it, the message I got was:
> mri_add_xform_to_header: could not open source file /nu.mgz
> No such file or directory
> And indeed such file  does not exist in the mri subfolder of my
> current subject's folder.
>
> Any further suggestions on how to fix this?  Like the person asking
> originally, this is the only participant where it happened, for
> others, recon-all finished without error and all the images were
> acquired in the same scanner.
> Thanks in advance!
> Best,
> Darko
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
Thu Mar 29 20:04:50 CEST 2018
/media/fmriDATA_4/Darko/Freesurfer_subjects/NMO_0008_3
/usr/local/freesurfer/bin/recon-all
-i /media/fmriDATA_4/Darko/newNMO_T1s/NMO_0008_3/NMO_0008.MR.PAUL_120_NMO.6.1.20151102.075821.yulj3m.dcm -subject NMO_0008_3 -all -hippo-subfields
subjid NMO_0008_3
setenv SUBJECTS_DIR /media/fmriDATA_4/Darko/Freesurfer_subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux carsten-ubuntu 2.6.32-55-generic #117-Ubuntu SMP Tue Dec 3 17:31:12 UTC 2013 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  unlimited

 total   used   free sharedbuffers cached
Mem:  329561808139844   24816336  0 6131561753872
-/+ buffers/cache:5772816   27183364
Swap: 19530744  0   19530744


program versions used
$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/03/29-18:04:50-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $  User: darko  Machine: carsten-ubuntu  Platform: Linux  PlatformVersion: 2.6.32-55-generic  CompilerName: GCC  CompilerVersion: 30400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/03/29-18:04:50-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: darko  Machine: carsten-ubuntu  Platform: Linux  PlatformVersion: 2.6.32-55-generic  CompilerName: GCC  CompilerVersion: 30400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/03/29-18:04:50-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: darko  Machine: carsten-ubuntu  Platform: Linux  PlatformVersion: 2.6.32-55-generic  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/03/29-18:04:50-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $  User: darko  Machine: carsten-ubuntu  Platform: Linux  PlatformVersion: 2.6.32-55-generic  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/03/29-18:04:50-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $  User: darko  Machine: carsten-ubuntu

[Freesurfer] unable to open freeview

2018-04-17 Thread Darko Komnenić

Dear experts,
I encountered a problem when trying to open freeview. I am using FreeSurfer
v.5.3.0-HCP, and after sourcing it, I tried typing simply freeview in the
terminal, as described in this link:
http://freesurfer.net/fswiki/FreeviewGuide/FreeviewGeneralUsage/FreeviewQuickStart
but the feedback I get is: freeview.bin: Command not found.

Am I missing  something? When searching for freeview on my computer,
"freesurfer" and "freesurfer.bin" appear in my bin subfolder, but for some
reason they seem not to be recognized.
Any help is appreciated!
Best,
Darko
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Re: [Freesurfer] unable to open freeview

2018-04-17 Thread Darko Komnenić

Hi Andrew,
FreeSurfer is being sourced automatically each time I open the terminal,
and I see the usual lines:

Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/lisak/Desktop/freesurfer
FSFAST_HOME   /home/lisak/Desktop/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/lisak/Desktop/freesurfer/subjects
MNI_DIR   /home/lisak/Desktop/freesurfer/mni
FSL_DIR   /home/lisak/Desktop/fsl

The outputs of which freeview and which freeview.bin are, respectively: #
1. /home/lisak/Desktop/freesurfer/bin/freeview
2. /home/lisak/Desktop/freesurfer/bin/freeview.bin

These are actual locations of the file, so all seems good until that point.
I typed "freeview" again, after doing the "which freeview" commands, and I
got the "freeview.bin: Command not found." again.

Any further suggestions are appreciated!
Thanks in advance,
Darko

On Tue, Apr 17, 2018 at 5:28 PM, Hoopes, Andrew 
wrote:

> Hi Darko, how are you sourcing freesurfer? And what is the output of
> running “which freeview” and “which freeview.bin”?
>
>
>
> best,
>
> Andrew
>
>
>
> *From: * on behalf of Darko
> Komnenić 
> *Reply-To: *FS Help 
> *Date: *Tuesday, April 17, 2018 at 11:17 AM
> *To: *FS Help 
> *Subject: *[Freesurfer] unable to open freeview
>
>
>
> Dear experts,
>
> I encountered a problem when trying to open freeview. I am using
> FreeSurfer v.5.3.0-HCP, and after sourcing it, I tried typing simply
> freeview in the terminal, as described in this link:
> http://freesurfer.net/fswiki/FreeviewGuide/FreeviewGeneralUsage/
> FreeviewQuickStart
>
> but the feedback I get is: freeview.bin: Command not found.
>
> Am I missing  something? When searching for freeview on my computer,
> "freesurfer" and "freesurfer.bin" appear in my bin subfolder, but for some
> reason they seem not to be recognized.
>
> Any help is appreciated!
>
> Best,
>
> Darko
>
> 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] unable to open freeview

2018-04-17 Thread Darko Komnenić

Hi Andrew,
thanks for getting back so quickly.
Here are the outputs:
“tcsh --version” gives a "tcsh 6.18.01 (Astron) 2012-02-14
(x86_64-unknown-linux) options wide,nls,dl,al,kan,rh,nd,color,filec"

I added echo $PATH right before the “freeview.bin $argv” line in the
freeview script, and the output to
"freeview" is now:
"/home/lisak/Desktop/freesurfer/lib/qt/bin:/home/lisak/Desktop/freesurfer/lib/vtk/bin:$FS_TCL_HOME/bin:$PATH
freeview.bin: Command not found."

So it seems it has something to do with libraries.
If I type freeview.bin instead of just freeview, I get:
"freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6:
cannot open shared object file: No such file or directory"

There seems to be a similar entry in the mailing list already, but from
what I see, it hasn't been solved. This is the link to the old question:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-September/053992.html
Unlike the original poster, i don't get the "Abort" feedback, though.

Thanks a lot!
Best,
Darko

On Tue, Apr 17, 2018 at 6:26 PM, Hoopes, Andrew 
wrote:

> Do you have tcsh properly installed? You can check by running the command
> “tcsh --version”.
>
>
>
> If it is installed, I’m not quite sure why you’re experiencing this
> problem, but I would suggest modifying the freeview script at
> /home/lisak/Desktop/freesurfer/bin/freeview to debug. Try adding the
> following line right before the call to “freeview.bin $argv”:
>
>
>
> echo $PATH
>
>
>
> and send the output over.
>
>
>
> best
>
> Andrew
>
>
>
>
>
> *From: *Darko Komnenić 
> *Date: *Tuesday, April 17, 2018 at 11:35 AM
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> FreeSurfer is being sourced automatically each time I open the terminal,
> and I see the usual lines:
>
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /home/lisak/Desktop/freesurfer
> FSFAST_HOME   /home/lisak/Desktop/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /home/lisak/Desktop/freesurfer/subjects
> MNI_DIR   /home/lisak/Desktop/freesurfer/mni
> FSL_DIR   /home/lisak/Desktop/fsl
>
> The outputs of which freeview and which freeview.bin are, respectively: #
> 1. /home/lisak/Desktop/freesurfer/bin/freeview
> 2. /home/lisak/Desktop/freesurfer/bin/freeview.bin
>
> These are actual locations of the file, so all seems good until that
> point. I typed "freeview" again, after doing the "which freeview" commands,
> and I got the "freeview.bin: Command not found." again.
>
> Any further suggestions are appreciated!
>
> Thanks in advance,
>
> Darko
>
>
>
>
>
>
>
> On Tue, Apr 17, 2018 at 5:28 PM, Hoopes, Andrew 
> wrote:
>
> Hi Darko, how are you sourcing freesurfer? And what is the output of
> running “which freeview” and “which freeview.bin”?
>
>
>
> best,
>
> Andrew
>
>
>
> *From: * on behalf of Darko
> Komnenić 
> *Reply-To: *FS Help 
> *Date: *Tuesday, April 17, 2018 at 11:17 AM
> *To: *FS Help 
> *Subject: *[Freesurfer] unable to open freeview
>
>
>
> Dear experts,
>
> I encountered a problem when trying to open freeview. I am using
> FreeSurfer v.5.3.0-HCP, and after sourcing it, I tried typing simply
> freeview in the terminal, as described in this link:
> http://freesurfer.net/fswiki/FreeviewGuide/FreeviewGeneralUsage/
> FreeviewQuickStart
>
> but the feedback I get is: freeview.bin: Command not found.
>
> Am I missing  something? When searching for freeview on my computer,
> "freesurfer" and "freesurfer.bin" appear in my bin subfolder, but for some
> reason they seem not to be recognized.
>
> Any help is appreciated!
>
> Best,
>
> Darko
>
> 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] unable to open freeview

2018-04-17 Thread Darko Komnenić

also, not sure if this info will be useful, but
libvtkverdict.so.5.6
exists on my computer in /home/lisak/Desktop/freesurfer/lib/vtk/lib/vtk-5.6
subfolder,
but from the error message above it seems as if Freesurfer expects the file
to be located in lib/vtk/*bin *subfolder.

On Tue, Apr 17, 2018 at 6:36 PM, Darko Komnenić  wrote:

> Hi Andrew,
> thanks for getting back so quickly.
> Here are the outputs:
> “tcsh --version” gives a "tcsh 6.18.01 (Astron) 2012-02-14
> (x86_64-unknown-linux) options wide,nls,dl,al,kan,rh,nd,color,filec"
>
> I added echo $PATH right before the “freeview.bin $argv” line in the
> freeview script, and the output to
> "freeview" is now:
> "/home/lisak/Desktop/freesurfer/lib/qt/bin:/home/
> lisak/Desktop/freesurfer/lib/vtk/bin:$FS_TCL_HOME/bin:$PATH
> freeview.bin: Command not found."
>
> So it seems it has something to do with libraries.
> If I type freeview.bin instead of just freeview, I get:
> "freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6:
> cannot open shared object file: No such file or directory"
>
> There seems to be a similar entry in the mailing list already, but from
> what I see, it hasn't been solved. This is the link to the old question:
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/
> 2017-September/053992.html
> Unlike the original poster, i don't get the "Abort" feedback, though.
>
> Thanks a lot!
> Best,
> Darko
>
> On Tue, Apr 17, 2018 at 6:26 PM, Hoopes, Andrew 
> wrote:
>
>> Do you have tcsh properly installed? You can check by running the command
>> “tcsh --version”.
>>
>>
>>
>> If it is installed, I’m not quite sure why you’re experiencing this
>> problem, but I would suggest modifying the freeview script at
>> /home/lisak/Desktop/freesurfer/bin/freeview to debug. Try adding the
>> following line right before the call to “freeview.bin $argv”:
>>
>>
>>
>> echo $PATH
>>
>>
>>
>> and send the output over.
>>
>>
>>
>> best
>>
>> Andrew
>>
>>
>>
>>
>>
>> *From: *Darko Komnenić 
>> *Date: *Tuesday, April 17, 2018 at 11:35 AM
>> *To: *"Hoopes, Andrew" 
>> *Cc: *FS Help 
>> *Subject: *Re: [Freesurfer] unable to open freeview
>>
>>
>>
>> Hi Andrew,
>>
>> FreeSurfer is being sourced automatically each time I open the terminal,
>> and I see the usual lines:
>>
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /home/lisak/Desktop/freesurfer
>> FSFAST_HOME   /home/lisak/Desktop/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR  /home/lisak/Desktop/freesurfer/subjects
>> MNI_DIR   /home/lisak/Desktop/freesurfer/mni
>> FSL_DIR   /home/lisak/Desktop/fsl
>>
>> The outputs of which freeview and which freeview.bin are, respectively: #
>> 1. /home/lisak/Desktop/freesurfer/bin/freeview
>> 2. /home/lisak/Desktop/freesurfer/bin/freeview.bin
>>
>> These are actual locations of the file, so all seems good until that
>> point. I typed "freeview" again, after doing the "which freeview" commands,
>> and I got the "freeview.bin: Command not found." again.
>>
>> Any further suggestions are appreciated!
>>
>> Thanks in advance,
>>
>> Darko
>>
>>
>>
>>
>>
>>
>>
>> On Tue, Apr 17, 2018 at 5:28 PM, Hoopes, Andrew 
>> wrote:
>>
>> Hi Darko, how are you sourcing freesurfer? And what is the output of
>> running “which freeview” and “which freeview.bin”?
>>
>>
>>
>> best,
>>
>> Andrew
>>
>>
>>
>> *From: * on behalf of Darko
>> Komnenić 
>> *Reply-To: *FS Help 
>> *Date: *Tuesday, April 17, 2018 at 11:17 AM
>> *To: *FS Help 
>> *Subject: *[Freesurfer] unable to open freeview
>>
>>
>>
>> Dear experts,
>>
>> I encountered a problem when trying to open freeview. I am using
>> FreeSurfer v.5.3.0-HCP, and after sourcing it, I tried typing simply
>> freeview in the terminal, as described in this link:
>> http://freesurfer.net/fswiki/FreeviewGuide/FreeviewGeneralUs
>> age/FreeviewQuickStart
>>
>> but the feedback I get is: freeview.bin: Command not found.
>>
>> Am I missing  something? When searching for freeview on my computer,
>> "freesurfer" and "freesurfer.bin" appear in my bin subfolder, but for some
>> reason they seem not to be recognized.
>>
>>

Re: [Freesurfer] unable to open freeview

2018-04-17 Thread Darko Komnenić

Hi Andrew,
OK, so here is what happened:

After adding the echo $PATH under the first line, my output is now this:
"/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/b
in:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/
Desktop/freesurfer/tktools:/home/lisak/Desktop/fsl/bin:/
home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
Linuxbrew directory detected, but it seems to be broken.  Try to remove
'/home/lisak/.linuxbrew' and try again./bin:/home/lisak/Desktop
/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/usr/
local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/
usr/games:/usr/local/games:/snap/bin
/home/lisak/Desktop/freesurfer/lib/qt/bin:/home/lisak/
Desktop/freesurfer/lib/vtk/bin:$FS_TCL_HOME/bin:$PATH
freeview.bin: Command not found."

Also sending attached the tcf_setup files.
I guess now I know a  bit more about what happened. I was running the Human
Connectome Project pipelines, and had an error that included an unmatched
quote. It turned out that, for some reason, my computer had an issue with
single quotes in some setup files, including a tcf_setup file. For that
reason, we changed the single to double quotes and that error went away.
(If you're interested in more details, one of the commands performed in the
FreeSurferPipeline was the tkregister2 command. After trying to run this
command in isolation (having previously defined $mridir variable in the
terminal), we finally got the same *Unmatched ".* error that we got
initially, by running the entire pipeline.
Playing with double and single quotes in that line did not do anything, and
it seemed that the error arises instantaneously, without FreeSurfer having
the time to even try anything. so we opened the tkregister2 file in
desktop/freesurfer/bin folder. This file seemed to refer to a tcl_setup
file within the same subfolder. So, we opened that one, and replaced all
double quotes with single quotes, in accordance with this forum post:
https://stackoverflow.com/questions/10761838/getting-unmatched
-on-a-simple-csh-ssh-script
Even though csh is not my default shell, I think it is still being used by
some processes. (Not sure if that makes any sense, I am a beginner when it
comes to using Linux.)

Running the tkregister2 command then in the terminal did not return
Unmatched ". error, and the Pipeline was able to be completed.)

The tcf_setup file in the attachment is the file we edited, whereas the
tcl_setup_backup is the original file.
Would you then recommend renaming the old file to tcl_setup? That would
mean then renaming them back and forth, depending on the step we are doing
in the analysis, but I guess it's doable.

Best,
Darko

On Tue, Apr 17, 2018 at 6:57 PM, Hoopes, Andrew 
wrote:

> Hi Darko, the freeview wrapper script sets up libraries used by
> freeview.bin, so the error you get when only calling freeview.bin is
> expected. There is something odd going on with your PATH after sourcing the
> TCL package. Can you send me your tcl_setup file in $FREESURFER_HOME/bin?
>
>
>
> It would also be helpful if you add another “echo $PATH” line right below
> the “#!/bin/tcsh -ef” in the freeview script
>
>
>
> best
>
> Andrew
>
>
>
> *From: *Darko Komnenić 
> *Date: *Tuesday, April 17, 2018 at 12:36 PM
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> thanks for getting back so quickly.
>
> Here are the outputs:
>
> “tcsh --version” gives a "tcsh 6.18.01 (Astron) 2012-02-14
> (x86_64-unknown-linux) options wide,nls,dl,al,kan,rh,nd,color,filec"
>
>
>
> I added echo $PATH right before the “freeview.bin $argv” line in the
> freeview script, and the output to
>
> "freeview" is now:
>
> "/home/lisak/Desktop/freesurfer/lib/qt/bin:/home/
> lisak/Desktop/freesurfer/lib/vtk/bin:$FS_TCL_HOME/bin:$PATH
> freeview.bin: Command not found."
>
>
>
> So it seems it has something to do with libraries.
>
> If I type freeview.bin instead of just freeview, I get:
>
> "freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6:
> cannot open shared object file: No such file or directory"
>
>
>
> There seems to be a similar entry in the mailing list already, but from
> what I see, it hasn't been solved. This is the link to the old question:
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/
> 2017-September/053992.html
> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-September/053992.html>
>
> Unlike the original poster, i don't get the "Abort" feedback, though.
>
> Thanks a lot!
>
> Best,
>
> Darko
>
>
>
> On Tue, Apr 17, 2018 at 6:26 PM, Hoopes, Andrew 
> wrote:
>
> Do you hav

Re: [Freesurfer] unable to open freeview

2018-04-17 Thread Darko Komnenić

Hi Andrew,
thanks a lot for your feedback!
I renamed the original fine, so it is now called just tcl_setup, and here
is the output I got after typing "freeview"

/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/bi
n:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/
Desktop/freesurfer/tktools:/home/lisak/Desktop/fsl/bin:/
home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
Linuxbrew directory detected, but it seems to be broken.  Try to remove
'/home/lisak/.linuxbrew' and try again./bin:/home/lisak/Desktop
/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/usr/
local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/
usr/games:/usr/local/games:/snap/bin
Unmatched ".

So this looks pretty much like the error I got when using Human Connectome
Project pipelines (to answer your earlier question, the only time I got
this error before was while running FreeSurferPipelineBatch.sh in HCP
pipelines, specifically after the start of FreeSurferHighResWhite script).
I don't use FreeSurfer for anything else on this computer, since this is
the special 5.3-HCP version, and I use FS6 on a different computer. Also,
the Unmatched quote error does not appear when running FSL or other
programs.
(Not sure if you're familiar with HCP pipelines, but they are used (among
other things) to estimate cortical myelin content, and have 3 main
preprocessing pipelines, PreeFS one, FS one, and PostFS one - I got the
Unmatched ". error in the FS one. When writing to their mailing list, I was
told that it seems like an error unique to my computer, and they have not
encountered it before.)

Anyway, the Linuxbrew error appears again now after trying to start
freeview.
I searched for bashrc on my computer and I got two locations, one in perl
subfolder, and one in miniconda3 subfolder. The latter just has 2 lines, so
it's probably not the one you meant. The former is quite a long file, but
does not mention linuxbrew at any point. I am sending the file attached.
I would be really very grateful if you would try helping out with this. I
have been googling this error, but was not able to find anything.
Thanks a bunch!
Darko

On Tue, Apr 17, 2018 at 7:52 PM, Hoopes, Andrew 
wrote:

> Hi Darko, there’s a big difference between using single vs double quotes
> in shell scripting – single quotes prevent variable expansion. Your
> modification to tcl_setup actually renders your PATH completely unusable.
> The quote syntax in the setup scripts shouldn’t cause any problems, and
> your unmatched errors indicate a more low-level issue that should probably
> get fixed directly. Are you only getting these unmatched errors with
> freesurfer tools? I can try to help you solve this, but I’m not quite sure
> I understand the initial problem.
>
>
>
> PS: At some point in your .bashrc is linuxbrew called? You don’t want that
> “Linuxbrew directory detected…” error in your PATH variable
>
>
>
> *From: *Darko Komnenić 
> *Date: *Tuesday, April 17, 2018 at 1:21 PM
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> OK, so here is what happened:
>
>
>
> After adding the echo $PATH under the first line, my output is now this:
> "/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/
> bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/
> lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/
> fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
> Linuxbrew directory detected, but it seems to be broken.  Try to remove
> '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/
> Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/
> usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:
> /usr/games:/usr/local/games:/snap/bin
> /home/lisak/Desktop/freesurfer/lib/qt/bin:/home/
> lisak/Desktop/freesurfer/lib/vtk/bin:$FS_TCL_HOME/bin:$PATH
> freeview.bin: Command not found."
>
> Also sending attached the tcf_setup files.
>
> I guess now I know a  bit more about what happened. I was running the
> Human Connectome Project pipelines, and had an error that included an
> unmatched quote. It turned out that, for some reason, my computer had an
> issue with single quotes in some setup files, including a tcf_setup file.
> For that reason, we changed the single to double quotes and that error went
> away.
>
> (If you're interested in more details, one of the commands performed in
> the FreeSurferPipeline was the tkregister2 command. After trying to run
> this command in isolation (having previously defined $mridir variable in
> the terminal), we finally got the same *Unmatched** ".* error that we got
> initially, by running the entire pipeline.
>
> Playing with double and single quot

Re: [Freesurfer] unable to open freeview

2018-04-19 Thread Darko Komnenić

Hi Andrew,
sorry for the delay. Attached is the hidden bashrc file from my Home
folder. It doesn't seem to specify anything about linuxbrew, so I don't
know why this error is showing up. Thanks a lot for any suggestions!
Best,
Darko

On Tue, Apr 17, 2018 at 11:07 PM, Hoopes, Andrew 
wrote:

> Are you using a bash shell? If you are, there should be a file located at
> ~/.bashrc (it’s a hidden file in your home folder)
>
> Andrew
>
>
>
>
>
> *From: *Darko Komnenić 
> *Date: *Tuesday, April 17, 2018 at 2:24 PM
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> thanks a lot for your feedback!
>
> I renamed the original fine, so it is now called just tcl_setup, and here
> is the output I got after typing "freeview"
>
> /home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/
> bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/
> lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/
> fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
> Linuxbrew directory detected, but it seems to be broken.  Try to remove
> '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/
> Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/
> usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:
> /usr/games:/usr/local/games:/snap/bin
> Unmatched ".
>
> So this looks pretty much like the error I got when using Human Connectome
> Project pipelines (to answer your earlier question, the only time I got
> this error before was while running FreeSurferPipelineBatch.sh in HCP
> pipelines, specifically after the start of FreeSurferHighResWhite script).
> I don't use FreeSurfer for anything else on this computer, since this is
> the special 5.3-HCP version, and I use FS6 on a different computer. Also,
> the Unmatched quote error does not appear when running FSL or other
> programs.
>
> (Not sure if you're familiar with HCP pipelines, but they are used (among
> other things) to estimate cortical myelin content, and have 3 main
> preprocessing pipelines, PreeFS one, FS one, and PostFS one - I got the
> Unmatched ". error in the FS one. When writing to their mailing list, I was
> told that it seems like an error unique to my computer, and they have not
> encountered it before.)
>
>
>
> Anyway, the Linuxbrew error appears again now after trying to start
> freeview.
>
> I searched for bashrc on my computer and I got two locations, one in perl
> subfolder, and one in miniconda3 subfolder. The latter just has 2 lines, so
> it's probably not the one you meant. The former is quite a long file, but
> does not mention linuxbrew at any point. I am sending the file attached.
>
> I would be really very grateful if you would try helping out with this. I
> have been googling this error, but was not able to find anything.
>
> Thanks a bunch!
>
> Darko
>
>
>
>
>
> On Tue, Apr 17, 2018 at 7:52 PM, Hoopes, Andrew 
> wrote:
>
> Hi Darko, there’s a big difference between using single vs double quotes
> in shell scripting – single quotes prevent variable expansion. Your
> modification to tcl_setup actually renders your PATH completely unusable.
> The quote syntax in the setup scripts shouldn’t cause any problems, and
> your unmatched errors indicate a more low-level issue that should probably
> get fixed directly. Are you only getting these unmatched errors with
> freesurfer tools? I can try to help you solve this, but I’m not quite sure
> I understand the initial problem.
>
>
>
> PS: At some point in your .bashrc is linuxbrew called? You don’t want that
> “Linuxbrew directory detected…” error in your PATH variable
>
>
>
> *From: *Darko Komnenić 
> *Date: *Tuesday, April 17, 2018 at 1:21 PM
>
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> OK, so here is what happened:
>
>
>
> After adding the echo $PATH under the first line, my output is now this:
> "/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/
> bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/
> lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/
> fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
> Linuxbrew directory detected, but it seems to be broken.  Try to remove
> '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/
> Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/
> usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:
> /usr/games:/usr/local/games:/snap/bin
> /home/lisak/Desktop/freesurfer/lib/qt/bin:/home/
>

Re: [Freesurfer] unable to open freeview

2018-04-19 Thread Darko Komnenić

An update,
in the .bash_profile file, there is a line about linuxbrew. Do you
recommend that I remove it? Sending the file attached.
Best,
Darko

On Thu, Apr 19, 2018 at 11:59 AM, Darko Komnenić 
wrote:

> Hi Andrew,
> sorry for the delay. Attached is the hidden bashrc file from my Home
> folder. It doesn't seem to specify anything about linuxbrew, so I don't
> know why this error is showing up. Thanks a lot for any suggestions!
> Best,
> Darko
>
> On Tue, Apr 17, 2018 at 11:07 PM, Hoopes, Andrew 
> wrote:
>
>> Are you using a bash shell? If you are, there should be a file located at
>> ~/.bashrc (it’s a hidden file in your home folder)
>>
>> Andrew
>>
>>
>>
>>
>>
>> *From: *Darko Komnenić 
>> *Date: *Tuesday, April 17, 2018 at 2:24 PM
>>
>> *To: *"Hoopes, Andrew" 
>> *Cc: *FS Help 
>> *Subject: *Re: [Freesurfer] unable to open freeview
>>
>>
>>
>> Hi Andrew,
>>
>> thanks a lot for your feedback!
>>
>> I renamed the original fine, so it is now called just tcl_setup, and here
>> is the output I got after typing "freeview"
>>
>> /home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/bi
>> n:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/
>> Desktop/freesurfer/tktools:/home/lisak/Desktop/fsl/bin:/
>> home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
>> Linuxbrew directory detected, but it seems to be broken.  Try to remove
>> '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/Desktop
>> /fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/usr/
>> local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/
>> usr/games:/usr/local/games:/snap/bin
>> Unmatched ".
>>
>> So this looks pretty much like the error I got when using Human
>> Connectome Project pipelines (to answer your earlier question, the only
>> time I got this error before was while running FreeSurferPipelineBatch.sh
>> in HCP pipelines, specifically after the start of FreeSurferHighResWhite
>> script). I don't use FreeSurfer for anything else on this computer, since
>> this is the special 5.3-HCP version, and I use FS6 on a different computer.
>> Also, the Unmatched quote error does not appear when running FSL or other
>> programs.
>>
>> (Not sure if you're familiar with HCP pipelines, but they are used (among
>> other things) to estimate cortical myelin content, and have 3 main
>> preprocessing pipelines, PreeFS one, FS one, and PostFS one - I got the
>> Unmatched ". error in the FS one. When writing to their mailing list, I was
>> told that it seems like an error unique to my computer, and they have not
>> encountered it before.)
>>
>>
>>
>> Anyway, the Linuxbrew error appears again now after trying to start
>> freeview.
>>
>> I searched for bashrc on my computer and I got two locations, one in perl
>> subfolder, and one in miniconda3 subfolder. The latter just has 2 lines, so
>> it's probably not the one you meant. The former is quite a long file, but
>> does not mention linuxbrew at any point. I am sending the file attached.
>>
>> I would be really very grateful if you would try helping out with this. I
>> have been googling this error, but was not able to find anything.
>>
>> Thanks a bunch!
>>
>> Darko
>>
>>
>>
>>
>>
>> On Tue, Apr 17, 2018 at 7:52 PM, Hoopes, Andrew 
>> wrote:
>>
>> Hi Darko, there’s a big difference between using single vs double quotes
>> in shell scripting – single quotes prevent variable expansion. Your
>> modification to tcl_setup actually renders your PATH completely unusable.
>> The quote syntax in the setup scripts shouldn’t cause any problems, and
>> your unmatched errors indicate a more low-level issue that should probably
>> get fixed directly. Are you only getting these unmatched errors with
>> freesurfer tools? I can try to help you solve this, but I’m not quite sure
>> I understand the initial problem.
>>
>>
>>
>> PS: At some point in your .bashrc is linuxbrew called? You don’t want
>> that “Linuxbrew directory detected…” error in your PATH variable
>>
>>
>>
>> *From: *Darko Komnenić 
>> *Date: *Tuesday, April 17, 2018 at 1:21 PM
>>
>>
>> *To: *"Hoopes, Andrew" 
>> *Cc: *FS Help 
>> *Subject: *Re: [Freesurfer] unable to open freeview
>>
>>
>>
>> Hi Andrew,
>>
>> OK, so here is what happened:
>>
>>
>>
>> After adding the echo $PATH under

Re: [Freesurfer] unable to open freeview

2018-04-19 Thread Darko Komnenić

External Email - Use Caution

Hi Andrew,
I commented out the last two lines, and the same error message still
appears. Please let me know if you have any other suggestions. Thanks!
Best,
Darko

On Thu, Apr 19, 2018 at 6:08 PM, Hoopes, Andrew 
wrote:

> Hi Darko, try commenting out the last two lines and rerunning freeview
> (it’s possible that the error message getting inserted into your PATH is
> the source of these issues):
>
> # export PATH="$HOME/.linuxbrew/bin:$PATH"
>
> # export PATH="$(brew --prefix)/bin:$PATH"
>
>
>
>
>
> *From: *Darko Komnenić 
> *Date: *Thursday, April 19, 2018 at 6:54 AM
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> An update,
>
> in the .bash_profile file, there is a line about linuxbrew. Do you
> recommend that I remove it? Sending the file attached.
>
> Best,
>
> Darko
>
>
>
> On Thu, Apr 19, 2018 at 11:59 AM, Darko Komnenić 
> wrote:
>
> Hi Andrew,
>
> sorry for the delay. Attached is the hidden bashrc file from my Home
> folder. It doesn't seem to specify anything about linuxbrew, so I don't
> know why this error is showing up. Thanks a lot for any suggestions!
>
> Best,
>
> Darko
>
>
>
> On Tue, Apr 17, 2018 at 11:07 PM, Hoopes, Andrew 
> wrote:
>
> Are you using a bash shell? If you are, there should be a file located at
> ~/.bashrc (it’s a hidden file in your home folder)
>
> Andrew
>
>
>
>
>
> *From: *Darko Komnenić 
> *Date: *Tuesday, April 17, 2018 at 2:24 PM
>
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> thanks a lot for your feedback!
>
> I renamed the original fine, so it is now called just tcl_setup, and here
> is the output I got after typing "freeview"
>
> /home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/
> bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/
> lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/
> fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
> Linuxbrew directory detected, but it seems to be broken.  Try to remove
> '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/
> Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/
> usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:
> /usr/games:/usr/local/games:/snap/bin
> Unmatched ".
>
> So this looks pretty much like the error I got when using Human Connectome
> Project pipelines (to answer your earlier question, the only time I got
> this error before was while running FreeSurferPipelineBatch.sh in HCP
> pipelines, specifically after the start of FreeSurferHighResWhite script).
> I don't use FreeSurfer for anything else on this computer, since this is
> the special 5.3-HCP version, and I use FS6 on a different computer. Also,
> the Unmatched quote error does not appear when running FSL or other
> programs.
>
> (Not sure if you're familiar with HCP pipelines, but they are used (among
> other things) to estimate cortical myelin content, and have 3 main
> preprocessing pipelines, PreeFS one, FS one, and PostFS one - I got the
> Unmatched ". error in the FS one. When writing to their mailing list, I was
> told that it seems like an error unique to my computer, and they have not
> encountered it before.)
>
>
>
> Anyway, the Linuxbrew error appears again now after trying to start
> freeview.
>
> I searched for bashrc on my computer and I got two locations, one in perl
> subfolder, and one in miniconda3 subfolder. The latter just has 2 lines, so
> it's probably not the one you meant. The former is quite a long file, but
> does not mention linuxbrew at any point. I am sending the file attached.
>
> I would be really very grateful if you would try helping out with this. I
> have been googling this error, but was not able to find anything.
>
> Thanks a bunch!
>
> Darko
>
>
>
>
>
> On Tue, Apr 17, 2018 at 7:52 PM, Hoopes, Andrew 
> wrote:
>
> Hi Darko, there’s a big difference between using single vs double quotes
> in shell scripting – single quotes prevent variable expansion. Your
> modification to tcl_setup actually renders your PATH completely unusable.
> The quote syntax in the setup scripts shouldn’t cause any problems, and
> your unmatched errors indicate a more low-level issue that should probably
> get fixed directly. Are you only getting these unmatched errors with
> freesurfer tools? I can try to help you solve this, but I’m not quite sure
> I understand the initial problem.
>
>
>
&g

Re: [Freesurfer] unable to open freeview

2018-04-19 Thread Darko Komnenić

External Email - Use Caution

Hi Andrew,
I did close it and reopen it.
There seem to be two different errors in this output.
If I just run echo $PATH, I get:
"/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
Linuxbrew directory detected, but it seems to be broken. Try to remove
'/home/lisak/.linuxbrew' and try
again./bin:/home/lisak/Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"

meaning the same error from before, but without the Unmatched ".
whereas, if I cd into Desktop/freesurfer/bin
and then run tcl_setup
I just get the Unmatched ".
I hope this helps.
Best,
Darko

On Thu, Apr 19, 2018 at 7:17 PM, Hoopes, Andrew 
wrote:

> Did you close and open a new terminal window first? Sorry, I forgot to
> mention that the bash_profile needs to be re-sourced if you make changes.
> After this, run “echo $PATH” to make sure that the brew error is no longer
> present
>
> Andrew
>
>
>
> *From: *Darko Komnenić 
> *Date: *Thursday, April 19, 2018 at 1:08 PM
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> I commented out the last two lines, and the same error message still
> appears. Please let me know if you have any other suggestions. Thanks!
>
> Best,
>
> Darko
>
>
>
> On Thu, Apr 19, 2018 at 6:08 PM, Hoopes, Andrew 
> wrote:
>
> Hi Darko, try commenting out the last two lines and rerunning freeview
> (it’s possible that the error message getting inserted into your PATH is
> the source of these issues):
>
> # export PATH="$HOME/.linuxbrew/bin:$PATH"
>
> # export PATH="$(brew --prefix)/bin:$PATH"
>
>
>
>
>
> *From: *Darko Komnenić 
> *Date: *Thursday, April 19, 2018 at 6:54 AM
>
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> An update,
>
> in the .bash_profile file, there is a line about linuxbrew. Do you
> recommend that I remove it? Sending the file attached.
>
> Best,
>
> Darko
>
>
>
> On Thu, Apr 19, 2018 at 11:59 AM, Darko Komnenić 
> wrote:
>
> Hi Andrew,
>
> sorry for the delay. Attached is the hidden bashrc file from my Home
> folder. It doesn't seem to specify anything about linuxbrew, so I don't
> know why this error is showing up. Thanks a lot for any suggestions!
>
> Best,
>
> Darko
>
>
>
> On Tue, Apr 17, 2018 at 11:07 PM, Hoopes, Andrew 
> wrote:
>
> Are you using a bash shell? If you are, there should be a file located at
> ~/.bashrc (it’s a hidden file in your home folder)
>
> Andrew
>
>
>
>
>
> *From: *Darko Komnenić 
> *Date: *Tuesday, April 17, 2018 at 2:24 PM
>
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> thanks a lot for your feedback!
>
> I renamed the original fine, so it is now called just tcl_setup, and here
> is the output I got after typing "freeview"
>
> /home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/
> bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/
> lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/
> fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
> Linuxbrew directory detected, but it seems to be broken.  Try to remove
> '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/
> Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/
> usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:
> /usr/games:/usr/local/games:/snap/bin
> Unmatched ".
>
> So this looks pretty much like the error I got when using Human Connectome
> Project pipelines (to answer your earlier question, the only time I got
> this error before was while running FreeSurferPipelineBatch.sh in HCP
> pipelines, specifically after the start of FreeSurferHighResWhite script).
> I don't use FreeSurfer for anything else on this computer, since this is
> the special 5.3-HCP version, and I use FS6 on a different computer. Also,
> the Unmatched quote error does not appear when running FSL or other
> programs.
>
> (Not sure if you're familiar with HCP pipelines, but they are used (among
> other things) to estimate cortical myelin content, and have 3 main
> preprocessing pipelines, PreeFS one, FS one, and PostFS one - I got the
> Unmatched

[Freesurfer] Question about the input for longitudinal processing pipeline

2019-11-15 Thread Darko Komnenić

External Email - Use Caution

Dear Freesurfer experts,
I wanted to run the Freesurfer's longitudinal processing pipeline
(described here
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) on a
series of MRI scans from a single patient. However, after looking at the
scans, i realized that for most time points, the patient doesn't have a
"simple/normal" T1 MPRAGE sequence available. Instead, they have a T1
sequence with a contrast agent, as well as T1 mp2rage sequences.

Is it possible/advisable to run recon-all in general or this pipeline in
particular on T1 MPRAGE scans that have a contrast agent, or that are
mp2rage instead of MPRAGE?

Thanks in advance!
Best,
Darko
___
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Re: [Freesurfer] Question about the input for longitudinal processing pipeline

2019-11-19 Thread Darko Komnenić

External Email - Use Caution

Hi Douglas,
thanks for your reply. Indeed, in this particular data set they don't all
have contrast, which is unfortunate. But my question was also general, if
we assume that they all have contrast, would it be OK to use those images
as inputs in the longitudinal pipeline? And the same question for mp2rage
images, are they OK to use as well, or are they not suitable for this
pipeline?
Best,
Darko


--
>
> Message: 11
> Date: Mon, 18 Nov 2019 18:41:37 +
> From: "Greve, Douglas N.,Ph.D." 
> Subject: Re: [Freesurfer] Question about the input for longitudinal
> processing pipeline
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Message-ID: 
> Content-Type: text/plain; charset="utf-8"
>
> Do all images and time points have contrast? If some do and some don't,
> then I don't think you can properly do the analysis?
>
> On 11/15/19 10:06 AM, Darko Komneni? wrote:
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> > I wanted to run the Freesurfer's longitudinal processing pipeline
> > (described here
> > https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) on a
> > series of MRI scans from a single patient. However, after looking at
> > the scans, i realized that for most time points, the patient doesn't
> > have a "simple/normal" T1 MPRAGE sequence available. Instead, they
> > have a T1 sequence with a contrast agent, as well as T1 mp2rage
> > sequences.
> >
> > Is it possible/advisable to run recon-all in general or this pipeline
> > in particular on T1 MPRAGE scans that have a contrast agent, or that
> > are mp2rage instead of MPRAGE?
> >
> > Thanks in advance!
> > Best,
> > Darko
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
___
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Re: [Freesurfer] Question about the input for longitudinal processing pipeline

2019-11-21 Thread Darko Komnenić

External Email - Use Caution

Thanks a lot for the reply and the suggestions, Douglas! These scans are at
3T.
Best,
Darko

> --
>
> Message: 4
> Date: Wed, 20 Nov 2019 22:45:18 +
> From: "Greve, Douglas N.,Ph.D." 
> Subject: Re: [Freesurfer] Question about the input for longitudinal
> processing pipeline
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Message-ID: <8be29ed9-8627-d005-fd9b-ca3ec56f8...@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> I have not run images with contrast, but I think it should? work. Some
> people have tried to use the mp2rage UNI scan, but it often fails
> because of very bright voxels outside of the brain. If you can remove
> those (eg, skull stripping), then it might work. Alternatively, if you
> have a quantitative T1 that comes out of the mp2rage if you have the
> license, then you can simulate an mp1rage that will then work in FS (but
> it will have bias fields). If you don't have a qT1, it is not too hard
> to convert the UNI to qT1. Is this at 3T or 7t?
>
> On 11/19/19 5:35 AM, Darko Komneni? wrote:
> >
> > External Email - Use Caution
> >
> > Hi Douglas,
> > thanks for your reply. Indeed, in this particular data set they don't
> > all have contrast, which is unfortunate. But my question was also
> > general, if we assume that they all have contrast, would it be OK to
> > use those images as inputs in the longitudinal pipeline? And the same
> > question for mp2rage images, are they OK to use as well, or are they
> > not suitable for this pipeline?
> > Best,
> > Darko
> >
> >
> > --
> >
> > Message: 11
> > Date: Mon, 18 Nov 2019 18:41:37 +
> > From: "Greve, Douglas N.,Ph.D."  > >
> > Subject: Re: [Freesurfer] Question about the input for longitudinal
> > ? ? ? ? processing pipeline
> > To: "freesurfer@nmr.mgh.harvard.edu
> > "
> >  > >
> > Message-ID:  > >
> > Content-Type: text/plain; charset="utf-8"
> >
> > Do all images and time points have contrast? If some do and some
> > don't,
> > then I don't think you can properly do the analysis?
> >
> > On 11/15/19 10:06 AM, Darko Komneni? wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Dear Freesurfer experts,
> > > I wanted to run the Freesurfer's longitudinal processing pipeline
> > > (described here
> > >
> > https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing)
> > on a
> > > series of MRI scans from a single patient. However, after
> > looking at
> > > the scans, i realized that for most time points, the patient
> > doesn't
> > > have a "simple/normal" T1 MPRAGE sequence available. Instead, they
> > > have a T1 sequence with a contrast agent, as well as T1 mp2rage
> > > sequences.
> > >
> > > Is it possible/advisable to run recon-all in general or this
> > pipeline
> > > in particular on T1 MPRAGE scans that have a contrast agent, or
> > that
> > > are mp2rage instead of MPRAGE?
> > >
> > > Thanks in advance!
> > > Best,
> > > Darko
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>
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[Freesurfer] arguments to use after pial edits {Disarmed}

2020-11-30 Thread Darko Komnenić

External Email - Use Caution

Dear Freesurfer experts,
I am using Human Connectone Project pipelines to calculate cortical myelin
levels. These pipelines use Freesurfer 6.
Since certain subjects' brain surfaces had some chunks and spikes sticking
out, I edited the brainmask.mgz file for those subjects as described in
this tutorial.
https://secure-web.cisco.com/134OA5xpyRuAJ4raLibeAZDGkJ8VFvtiCm69m7hXhYD4428DFSCfEHGfgqrFW8Iy9j3fJwoPH3RYxnGtC4RODybQrKIB7cYVEtiYb5Ht890ElcGU27h8UJTajTxw8bQM6DNX8uqRuTEsFMh720x4PCSoFbpcnXQ1qN-TcVNAFNAKkD81ND2J8smWHqWlI6qkxbWEjDiDRHI0m_qszNz9xnV1WceNN4uBMUUzCFu9IWx7lud9Ln0YGfV8xpSphDINNwS1qCvV2U95jfq_jYQLp_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FPialEdits_freeview

To get the myelin maps again, I got the instruction from the HCP mailing
list that I should call again the FreeSurferPipeline script, but add the
--existing-subject and --extra-reconall-arg flags.
If I understood correctly, after --extra-reconall-arg flag, there should be
an equal sign, and then keywords that specify which recon-all stages I want
to run.

Could you please tell me what those stages are, i.e. what keywords I should
use after the equal sign? I want to keep the brainmask.mgz file that I
edited, and then repeat all the steps that happen after braimask.mgz is
generated. I was referred to the FS tutorials/wiki at the HCP mailing list,
but I would like to double-check with someone here. Based on the tutorial
link above, it seems this should be "-autorecon-pial -subjid
pial_edits_before", but I'm not sure if this would be applicable in this
case.

Thanks in advance and I hope my question wasn't too confusing.
Best,
Darko
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Re: [Freesurfer] arguments to use after pial edits

2020-11-30 Thread Darko Komnenić

External Email - Use Caution

Thanks Matt!
Should I also add the -autorecon3 flag, or does that get performed
automatically if I put in "autorecon2"?
Best,
Darko


> Message: 4
> Date: Mon, 30 Nov 2020 19:16:06 +
> From: "Glasser, Matthew" 
> Subject: Re: [Freesurfer] arguments to use after pial edits {Disarmed}
> To: Freesurfer support list 
> Message-ID: <274fd511-f94f-4bc1-ae0c-804f1a6a3...@wustl.edu>
> Content-Type: text/plain; charset="utf-8"
>
> External Email - Use Caution
>
> I find the recon-all table to be helpful:
>
>
> http://secure-web.cisco.com/1rQT1vL5GWrATp5z0Ct2LBj8MsEx75qijDiNOIOc1xsGTqc0VC-s7rH5tRIiUV_kHXR7CsV_-uoWR6y_oPuNxiCAZCmbkgfSfUxHd4oB4gX7XvLCt40MlQR_Ejq0tpN0lnJJt1uO1jl_1XWYZQv92-3NGME0PKZPC51_qjOKHk9cLfcojjN-AssGWAZ7y0t-UJXooxg2G2tzrQqm9emqIASj8_asI8t84TuQRjHEjkEj7KDq8IvfbXNQIT5xDLxB5A7a-aT2IrgX3QZs0Stdt7Q/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllTableStableV6.0
>
> In this case, you probably need to run -autorecon2, as all subsequent
> steps are affected by the brainmask.mgz file.
>
> Matt.
>
>
>
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[Freesurfer] [error] no installation candidates for curl

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Re: [Freesurfer] defining input images in a for-loop in recon-all

[Freesurfer] mri_watershed Error: indices out of bounds

Re: [Freesurfer] Freesurfer Digest, Vol 169, Issue 41

[Freesurfer] unable to open freeview

Re: [Freesurfer] unable to open freeview

Re: [Freesurfer] unable to open freeview

Re: [Freesurfer] unable to open freeview

Re: [Freesurfer] unable to open freeview

Re: [Freesurfer] unable to open freeview

Re: [Freesurfer] unable to open freeview

Re: [Freesurfer] unable to open freeview

Re: [Freesurfer] unable to open freeview

Re: [Freesurfer] unable to open freeview

[Freesurfer] Question about the input for longitudinal processing pipeline

Re: [Freesurfer] Question about the input for longitudinal processing pipeline

Re: [Freesurfer] Question about the input for longitudinal processing pipeline

[Freesurfer] arguments to use after pial edits {Disarmed}

Re: [Freesurfer] arguments to use after pial edits

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