subject:"\[Freesurfer\] Tracula Inquiry"

Re: [Freesurfer] Tracula Inquiry

2020-03-11 Thread Yendiki, Anastasia

Hi Jason - Please save the config file as a simple text file, not a rich text 
file (rtf). When you view it with the more command on the command line, it 
should just show you the text that you typed, and not all the other stuff.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ledesma, Jason 

Sent: Monday, March 9, 2020 2:15 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula Inquiry


External Email - Use Caution

Hi,


I am seeing the following error:


Admins-iMac:XXXneurology$ trac-all -prep -c XXX.24.14Configfile.rtf
Missing }.
Missing }.
}: Command not found.
Missing }.
red255green255blue255: Command not found.
}: Command not found.
Missing }.
}: Command not found.
margl1440margr1440vieww9460viewh8400viewkind0: Command not found.
pardtx720tx1440tx2160tx2880tx3600tx4320tx5040tx5760tx6480tx7200tx7920tx8640pardirnaturalpartightenfactor0:
 Command not found.
Badly placed (.
ERROR: run list is longer than subject list


Attached is my config file. Can you tell me what might be wrong? Thanks.


Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@labiomed.org<mailto:jason.lede...@labiomed.org>



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[Freesurfer] Tracula Inquiry

2020-03-09 Thread Ledesma, Jason

External Email - Use Caution

Hi,


I am seeing the following error:


Admins-iMac:XXXneurology$ trac-all -prep -c XXX.24.14Configfile.rtf
Missing }.
Missing }.
}: Command not found.
Missing }.
red255green255blue255: Command not found.
}: Command not found.
Missing }.
}: Command not found.
margl1440margr1440vieww9460viewh8400viewkind0: Command not found.
pardtx720tx1440tx2160tx2880tx3600tx4320tx5040tx5760tx6480tx7200tx7920tx8640pardirnaturalpartightenfactor0:
 Command not found.
Badly placed (.
ERROR: run list is longer than subject list


Attached is my config file. Can you tell me what might be wrong? Thanks.


Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@labiomed.org



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XXX7.24.14Configfile.rtf
Description: XXX7.24.14Configfile.rtf
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Re: [Freesurfer] Tracula Inquiry

2020-03-06 Thread Ledesma, Jason

External Email - Use Caution

Hi,


Thanks for your help.


I am now seeing this error:

Admins-iMac:XXXneurology$ trac-all -prep -c XXX.24.14Configfile.rtf
Missing }.
Missing }.
}: Command not found.
Missing }.
red255green255blue255: Command not found.
}: Command not found.
Missing }.
}: Command not found.
margl1440margr1440vieww9460viewh8400viewkind0: Command not found.
pardtx720tx1440tx2160tx2880tx3600tx4320tx5040tx5760tx6480tx7200tx7920tx8640pardirnaturalpartightenfactor0:
 Command not found.
Badly placed (.
ERROR: run list is longer than subject list



Attached is my config file. Can you tell me what might be wrong?  Thanks.


Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@labiomed.org<mailto:jason.lede...@labiomed.org>



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Paul Wighton 

Sent: Thursday, March 5, 2020 11:29:23 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Inquiry

[External Email]

External Email - Use Caution

Hi Jason,

Tracula depends on FSL.  If you have FSL installed, all that should be needed 
is to define FSL_DIR before sourcing  `$FREESURFER_HOME/SetUpFreeSurfer.sh`

So using your example above, you could go

```
export FREESURFER_HOME=/Applications/freesurfer
export FSL_DIR=/location/of/fsl/binaries
source $FREESURFER_HOME/SetUpFreeSurfer.sh
```

-Paul


On Thu, Mar 5, 2020 at 12:45 PM Ledesma, Jason 
mailto:jason.lede...@lundquist.org>> wrote:

External Email - Use Caution

Hello,


I am having trouble carrying out Tracula on Freesurfer. See the following 
script (for confidentiality, patient's name has been replaced by XXX):


Admins-iMac:~ neurology$ export FREESURFER_HOME=/Applications/freesurfer

Admins-iMac:~ neurology$

Admins-iMac:~ neurology$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME   /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  /Applications/freesurfer/subjects

MNI_DIR   /Applications/freesurfer/mni

Admins-iMac:~ neurology$ export 
SUBJECTS_DIR=/Applications/freesurfer/subjects/XXX

Admins-iMac:~ neurology$ cd /Applications/freesurfer/subjects/XXX

Admins-iMac:XXX neurology$ trac-all -prep -c XXX7.24.14Configfile

FSLDIR: Undefined variable.

Admins-iMac:XXX neurology$


My Config text file has the following info:


setenv SUBJECTS_DIR Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri

set dtroot = Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri

set subjlist = (XXX7.24.14)

set dcmroot = Applications/freesurfer/subjects/XXX/XXX7.24.14AXDWI

set dcmlist = ( MR0001.dcm )

set bvecfile = 
(Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bvec.txt)

set bvalfile = 
(Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bval.txt)

set doeddy = 1

set dorotbvecs = 1

set usemaskanat = 1

set threat = 0.3

set doregflt = 0

set doregbbr = 1

set doregmni = 1

set doregcvs = 0

set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

set pathlist = ( lh.cst_AS rh.cst_AS \

   lh.ilf_AS rh.ilf_AS \

   lh.unc_AS rh.unc_AS \

   fmajor_PP fminor_PP \

   lh.atr_PP rh.atr_PP \

   lh.cab_PP rh.cab_PP \

   lh.ccg_PP rh.ccg_PP \

   lh.slfp_PP rh.slfp_PP \

   lh.slft_PP rh.slft_PP )

set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)


Please advise. Thanks.



Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@labiomed.org<mailto:jason.lede...@labiomed.org>



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XXX7.24.14Configfile.rtf
Description: XXX7.24.14Configfile.rtf
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Re: [Freesurfer] Tracula Inquiry

2020-03-05 Thread Paul Wighton

External Email - Use Caution

Hi Jason,

Tracula depends on FSL.  If you have FSL installed, all that should be
needed is to define FSL_DIR before sourcing
`$FREESURFER_HOME/SetUpFreeSurfer.sh`

So using your example above, you could go

```
export FREESURFER_HOME=/Applications/freesurfer
export FSL_DIR=/location/of/fsl/binaries
source $FREESURFER_HOME/SetUpFreeSurfer.sh
```

-Paul


On Thu, Mar 5, 2020 at 12:45 PM Ledesma, Jason 
wrote:

> External Email - Use Caution
>
> Hello,
>
>
> I am having trouble carrying out Tracula on Freesurfer. See the following
> script (for confidentiality, patient's name has been replaced by XXX):
>
>
> Admins-iMac:~ neurology$ export FREESURFER_HOME=/Applications/freesurfer
>
> Admins-iMac:~ neurology$
>
> Admins-iMac:~ neurology$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
>  freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>
> FREESURFER_HOME   /Applications/freesurfer
>
> FSFAST_HOME   /Applications/freesurfer/fsfast
>
> FSF_OUTPUT_FORMAT nii.gz
>
> SUBJECTS_DIR  /Applications/freesurfer/subjects
>
> MNI_DIR   /Applications/freesurfer/mni
>
> Admins-iMac:~ neurology$ export
> SUBJECTS_DIR=/Applications/freesurfer/subjects/XXX
>
> Admins-iMac:~ neurology$ cd /Applications/freesurfer/subjects/XXX
>
> Admins-iMac:XXX neurology$ trac-all -prep -c XXX7.24.14Configfile
>
> FSLDIR: Undefined variable.
>
> Admins-iMac:XXX neurology$
>
> My Config text file has the following info:
>
>
> setenv SUBJECTS_DIR Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri
>
> set dtroot = Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri
>
> set subjlist = (XXX7.24.14)
>
> set dcmroot = Applications/freesurfer/subjects/XXX/XXX7.24.14AXDWI
>
> set dcmlist = ( MR0001.dcm )
>
> set bvecfile =
> (Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bvec.txt)
>
> set bvalfile =
> (Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bval.txt)
>
> set doeddy = 1
>
> set dorotbvecs = 1
>
> set usemaskanat = 1
>
> set threat = 0.3
>
> set doregflt = 0
>
> set doregbbr = 1
>
> set doregmni = 1
>
> set doregcvs = 0
>
> set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
>
> set pathlist = ( lh.cst_AS rh.cst_AS \
>
>lh.ilf_AS rh.ilf_AS \
>
>lh.unc_AS rh.unc_AS \
>
>fmajor_PP fminor_PP \
>
>lh.atr_PP rh.atr_PP \
>
>lh.cab_PP rh.cab_PP \
>
>lh.ccg_PP rh.ccg_PP \
>
>lh.slfp_PP rh.slfp_PP \
>
>lh.slft_PP rh.slft_PP )
>
> set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
>
> Please advise. Thanks.
>
>
> Sincerely,
>
> Jason Ledesma
> Staff Research Associate
> Phone: 1(424)571-7755
> E-mail: jason.lede...@labiomed.org
>
>
>
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[Freesurfer] Tracula Inquiry

2020-03-05 Thread Ledesma, Jason

External Email - Use Caution

Hello,


I am having trouble carrying out Tracula on Freesurfer. See the following 
script (for confidentiality, patient's name has been replaced by XXX):


Admins-iMac:~ neurology$ export FREESURFER_HOME=/Applications/freesurfer

Admins-iMac:~ neurology$

Admins-iMac:~ neurology$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME   /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  /Applications/freesurfer/subjects

MNI_DIR   /Applications/freesurfer/mni

Admins-iMac:~ neurology$ export 
SUBJECTS_DIR=/Applications/freesurfer/subjects/XXX

Admins-iMac:~ neurology$ cd /Applications/freesurfer/subjects/XXX

Admins-iMac:XXX neurology$ trac-all -prep -c XXX7.24.14Configfile

FSLDIR: Undefined variable.

Admins-iMac:XXX neurology$


My Config text file has the following info:


setenv SUBJECTS_DIR Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri

set dtroot = Applications/freesurfer/subjects/XXX/XXX7.24.2014/mri

set subjlist = (XXX7.24.14)

set dcmroot = Applications/freesurfer/subjects/XXX/XXX7.24.14AXDWI

set dcmlist = ( MR0001.dcm )

set bvecfile = 
(Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bvec.txt)

set bvalfile = 
(Applications/freesurfer/subjects/XXX/20140724_132003HNSBRAINMSREVISEDs005a1001.bval.txt)

set doeddy = 1

set dorotbvecs = 1

set usemaskanat = 1

set threat = 0.3

set doregflt = 0

set doregbbr = 1

set doregmni = 1

set doregcvs = 0

set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

set pathlist = ( lh.cst_AS rh.cst_AS \

   lh.ilf_AS rh.ilf_AS \

   lh.unc_AS rh.unc_AS \

   fmajor_PP fminor_PP \

   lh.atr_PP rh.atr_PP \

   lh.cab_PP rh.cab_PP \

   lh.ccg_PP rh.ccg_PP \

   lh.slfp_PP rh.slfp_PP \

   lh.slft_PP rh.slft_PP )

set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)


Please advise. Thanks.



Sincerely,

Jason Ledesma
Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.lede...@labiomed.org



___
LUNDQUIST Institute Warning: This email (and any attachments) is intended for 
the use of the person to which it is addressed. It may contain information that 
is privileged and confidential. As the recipient, you are obligated to maintain 
it in a safe, secure and confidential manner. Unauthorized disclosure or 
failure to maintain confidentiality may subject you to governmental penalties. 
Should you not be the intended recipient, please notify us by return email, and 
delete this message from your computer at once. 
___
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Re: [Freesurfer] Tracula Inquiry

[Freesurfer] Tracula Inquiry

Re: [Freesurfer] Tracula Inquiry

Re: [Freesurfer] Tracula Inquiry

[Freesurfer] Tracula Inquiry

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