Re: [Freesurfer] recon-all -s exited with ERRORS

[Leo Souza]

How long does it take to run the test?

Thanks,
Leo Souza

From: Pedro Paulo de Magalhães Oliveira Junior [mailto:p...@netfilter.com.br]
Sent: Monday, June 13, 2011 6:20 PM
To: Leo Souza
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all -s exited with ERRORS

recon-all -s bert -all -use-gpu

-- iOS 4.3

Em 13/06/2011, às 21:30, Leo Souza 
mailto:lso...@nvidia.com>> escreveu:
/recon-all -use-gpu

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Re: [Freesurfer] recon-all -s exited with ERRORS

[Pedro Paulo de Magalhães Oliveira Junior]

recon-all -s bert -all -use-gpu

-- iOS 4.3

Em 13/06/2011, às 21:30, Leo Souza  escreveu:

/recon-all -use-gpu
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Re: [Freesurfer] Pulvinar Segmentation

[Bruce Fischl]

no, sorry, not yet. Maybe in a year or two!
Bruce
On Mon, 13 Jun 2011, Peter J. 
Molfese wrote:

> Hi,
>
> I'm interested in pulling out segmentation stats on the Pulvinar.  I noticed 
> that Pulvinar is listed in the FreeSurferColorLUT.txt but isn't in the 
> aseg.stats.  Is there a way to get segmentation information for the Pulvinar?
>
> best,
> Peter
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>
>
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Re: [Freesurfer] recon-all -s exited with ERRORS

[Leo Souza]

-use-cuda is invalid I think, but I did -use-gpu and see what I get:

[root@cuda-final2 bin]# ./recon-all -use-gpu
Testing for CUDA device:
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2010 NVIDIA Corporation
Built on Thu_Nov__4_12:44:17_PDT_2010
Cuda compilation tools, release 3.2, V0.2.1221

Driver : 4.0
Runtime : 3.20

Acquiring CUDA device
Using default device
CUDA device: Tesla C2050
stable5

NVIDIA driver version info:
NVRM version: NVIDIA UNIX x86_64 Kernel Module  270.41.23  Sun Jun  5 
22:11:38 PDT 2011


ERROR: must specify a subject id
[root@cuda-final2 bin]#


Thanks,
*Leo Souza*

On 06/13/2011 04:10 PM, Douglas N Greve wrote:

Try adding -use-cuda to recon-all

Leo Souza wrote:

Yes, I did that, but it doesn't actually uses the GPU to do that, only
CPU.

GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q
-d UTILIZATION -l 3" if your'e using any recent drivers.


Thanks,
*Leo Souza*

On 06/13/2011 02:44 PM, Douglas N Greve wrote:

When you run recon-all, it will create a recon-all-status file in the
scripts directory. This has the start times of all the processes, so you
can work out how long each took. This will be wall clock time, so take
that into account.

doug

Leo Souza wrote:


Hi Carolina,

Do you know how can I run Freesurfer just to get some Benchmark
Numbers and to Check GPU Performance using Cuda?

Thanks,
*Leo Souza*

On 06/13/2011 07:04 AM, Carolina Valencia wrote:


Thanks a lot, it works.
just waiting 24 hours.

Best regards,

Carolina

2011/6/10mailto:rspr...@nmr.mgh.harvard.edu>>

 Hi Carolina,

 Sorry My bad. I was inaccurate in my previous message.

 -subject should work.

 Assuming that the MPRAGE of your subject is under the following
 directory:

 /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig

 set your SUBJECTS_DIR to
 /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
 before
 running recon-all

 setenv SUBJECTS_DIR
 ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig

 recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
 $SUBJECTS_DIR/hptu_subj001

 This should create a folder where Freesurfer recons will be created:

 cd
 
~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001

 Best,
 Priti

 >  Hi Carolina,
 >
 >  -subject is not recognized by Freesurfer...Use -subjid or -s
 instead.
 >
 >  setenv SUBJECTS_DIR
 >
 >  recon-all -all -i/MPRAGE.nii.gz -s  freesurfer recons>/hptu_subj001
 >
 >  Priti
 >
 >>  Hello Freesurfer's users,
 >>
 >>  I'm starting using FS and I have a problem running recon-all
 >>  I create a folder called hptu_subj001 which contains MPRAGE.nii.gz
 >>  within
 >>  tutorial_subj
 >>  First I convert nii.gz to mgz qith the command:
 >>  recon-all -i MPRAGE.nii.gz -s hptu_subj001
 >>  and then in order to process all, I type:
 >>  recon-all –i 001.mgz –subject hptu_subj001 –all
 >>
 >>
 
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig>
 >>  recon-all –i 001.mgz –subject hptu_subj001 –all
 >>  ERROR: Flag  i unrecognized.
 >>   i 001.mgz  subject hptu_subj001  all
 >>  Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
 >>  #50-Ubuntu
 >>  SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
 >>
 >>  recon-all -s  exited with ERRORS at Fri Jun 10 12:50:04 COT 2011
 >>
 >>  then I tried with:
 >>
 >>
 
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj>
 >>  recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all
 >>  ERROR: Flag  i unrecognized.
 >>   i MPRAGE.nii.gz  subject hptu_subj001  all
 >>  Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
 >>  #50-Ubuntu
 >>  SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
 >>
 >>  recon-all -s  exited with ERRORS at Fri Jun 10 12:36:24 COT 2011
 >>
 >>  How I can fix this error?
 >>
 >>  Thanks a lot,
 >>
 >>  Best regards,
 >>
 >>  Carolina
 >>  ___
 >>  Freesurfer mailing list
 >>  Freesurfer@nmr.mgh.harvard.edu
 
 >>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 >
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 >
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Re: [Freesurfer] Tracula question: trac-all config file and number of B0 specification

[Anastasia Yendiki]

No, if usemaskanat = 1, then the diffusion mask that comes from applying 
bet to the lowb volume will not be used for tractography. A dilated 
version of aparc+aseg will be used as a mask instead, which is typically 
more reliable than trying to find the right bet threshold.


On Fri, 10 Jun 2011, Deryk S. Beal, Ph.D. wrote:


Hi Anastasia
If I have T1 data available in my FS subject directory and I have

Use brain mask extracted from T1 image instead of low-b diffusion image?#
Has no effect if there is no T1 data
# Default: 1 (yes)
#
set usemaskanat = 1

then will the B0 brain mask we spoke of below be used? 

Deryk


On Fri, Jun 10, 2011 at 10:46 AM, Anastasia Yendiki
 wrote:

  Hi Deryk - This variable is only used to average lowb images to
  create a mask, so in your case you can set it to 2 and it'll
  just use the first 2 volumes from your nii file. Sorry for the
  confusion!

  a.y


On Fri, 10 Jun 2011, Deryk S. Beal, Ph.D. wrote:

  Dear Tracula Users

  Does Tracula assume that the number of B0 scans, specified
  in Step 7.3 of
  the config file tutorial (below), are the first X number
  of volumes in the
  4Dnii.gz file or will the Tracula routines know from the
  bvals file where
  the B0 scans are ordered in the file? For example, I have
  two runs of 16
  directions + 2 B0s each for each of my subjects. I have
  merged the two runs
  together and the resulting file has the volumes ordered
  such that the bvals
  are entered into Tracula as follows:

  0
  0
  1000
  1000
  1000
  etc
  0
  0
  1000
  1000
  1000
  etc 

  My question pertains to the following part of the Tracula
  config file:

  Step7.3: Specifying Number Of low-b Images The last step
  to set up if not
  using original DICOMs would be to specify the number of
  low-b images with
  the following variable:

  set nb0 = *No. of low-b images*
  Thank you in advance for your help.
  Cheers,
  Deryk

  Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO
  Speech-Language Pathologist
  C.I.H.R. Post Doctoral Research Fellow
  Department of Cognitive and Neural Systems Speech
  Laboratory
  Boston University, 677 Beacon Street, Boston, MA 02215 
  dsb...@bu.edu
  http://blogs.bu.edu/dsbeal/about/
  *
  This email may contain confidential and/or privileged
  information for the
  sole use of the intended recipient. Any review or
  distribution by others is
  strictly prohibited. If you have received this email in
  error, please
  contact the sender and delete all copies. Opinions,
  conclusions or other
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Re: [Freesurfer] trac-all - bedp errors

[Anastasia Yendiki]

Hi Deryk - Trac-all doesn't call the version of bedpostx under the FSL dir 
but a specially modified version in the freesurfer distribution (called 
bedpostx_seychelles for historical reasons).


It's fine to run bedpostx directly since that works for you. You can also 
upload the data set for us to try to replicate the error.


Sorry for the confusion,
a.y

On Mon, 13 Jun 2011, Deryk S. Beal, Ph.D. wrote:


Hi Priti
In addition, if I run bedpostx from the command line as follows:

bedpostx /usr/local/freesurfer/subjects/C001/dmri 

it works just fine without errors.

Deryk

Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO
Speech-Language Pathologist
C.I.H.R. Post Doctoral Research Fellow
Department of Cognitive and Neural Systems Speech Laboratory
Boston University, 677 Beacon Street, Boston, MA 02215 
dsb...@bu.edu
http://blogs.bu.edu/dsbeal/about/
*
This email may contain confidential and/or privileged information for the
sole use of the intended recipient. Any review or distribution by others is
strictly prohibited. If you have received this email in error, please
contact the sender and delete all copies. Opinions, conclusions or other
information expressed or contained in this email are not given or endorsed
by the sender unless otherwise affirmed independently by the sender.


On Mon, Jun 13, 2011 at 1:51 PM, Deryk S. Beal, Ph.D.  wrote:
  Hi Priti
Thank you for your quick replay. The following files / folders are
listed in my dmri.bedpostx directory:

**
/usr/local/freesurfer/subjects/C001/dmri.bedpostX$ ls
commands.txt  diff_slices  logs  monitor  xfms
**

I am able to call bedpostx from the command line without error. It is
worth noting that I am running Ubuntu 10.10 and the Neurodebian distro
of FSL4.1. However, FSL and bedpostx appear to be sourced properly:

**
:/usr/local/freesurfer/subjects/C001/dmri.bedpostX$ bedpostx

Usage: bedpostx  [options]

expects to find bvals and bvecs in subject directory
expects to find data and nodif_brain_mask in subject directory
options:
-n (number of fibres per voxel, default 2)
-w (ARD weight, more weight means less secondary fibres per voxel,
default 1)
-b (burnin period, default 1000)
-j (number of jumps, default 1250)
-s (sample every, default 25)



Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO
Speech-Language Pathologist
C.I.H.R. Post Doctoral Research Fellow
Department of Cognitive and Neural Systems Speech Laboratory
Boston University, 677 Beacon Street, Boston, MA 02215 
dsb...@bu.edu
http://blogs.bu.edu/dsbeal/about/
*
This email may contain confidential and/or privileged information for
the
sole use of the intended recipient. Any review or distribution by
others is
strictly prohibited. If you have received this email in error, please
contact the sender and delete all copies. Opinions, conclusions or
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endorsed
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On Mon, Jun 13, 2011 at 1:25 PM,  wrote:
  Hi Deryk,

  Is bedpostx properly installed in your computer? Can you
  just type
  bedpostx in your terminal to see if it gives this message?

###
  #
  Usage: bedpostx  [options]

  expects to find bvals and bvecs in subject directory
  expects to find data and nodif_brain_mask in subject
  directory
  options:
  -n (number of fibres per voxel, default 2)
  -w (ARD weight, more weight means less secondary fibres
  per voxel, default 1)
  -b (burnin period, default 1000)
  -j (number of jumps, default 1250)
  -s (sample every, default 25)
###
  #

  Also can you let us know if any files are created after
  this error in
  /usr/local/freesurfer/subjects/C001/dmri.bedpostx
  directory ?

  This looks like an error with the bedpostx itself...I've
  used the trac-all
  -bedp on my local machine (instead of a cluster) and it
  seems to work
  fine.

  Priti

> Dear Tracula Users
>
> I completed trac-all -prep -c without difficulty or errors.
However,
> without
> any changes to my director structure or my Tracula config file
I am
> receiving the following errors when running trac-all -bedp -c.
I will copy
> and past my config file contents below the error messages.
Please advise.
>
> trac-all -bedp -c
> /media/5424CE1A24CDFECC/UofT/data/Tracula/tracula_config.txt
-debug
> INFO: SUBJECTS_DIR is /usr/local/freesurfer/s

Re: [Freesurfer] recon-all -s exited with ERRORS

[Leo Souza]

Okay,

Let me see what's gonna happen.

Thanks,
*Leo Souza*

On 06/13/2011 04:10 PM, Douglas N Greve wrote:

Try adding -use-cuda to recon-all

Leo Souza wrote:

Yes, I did that, but it doesn't actually uses the GPU to do that, only
CPU.

GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q
-d UTILIZATION -l 3" if your'e using any recent drivers.


Thanks,
*Leo Souza*

On 06/13/2011 02:44 PM, Douglas N Greve wrote:

When you run recon-all, it will create a recon-all-status file in the
scripts directory. This has the start times of all the processes, so you
can work out how long each took. This will be wall clock time, so take
that into account.

doug

Leo Souza wrote:


Hi Carolina,

Do you know how can I run Freesurfer just to get some Benchmark
Numbers and to Check GPU Performance using Cuda?

Thanks,
*Leo Souza*

On 06/13/2011 07:04 AM, Carolina Valencia wrote:


Thanks a lot, it works.
just waiting 24 hours.

Best regards,

Carolina

2011/6/10mailto:rspr...@nmr.mgh.harvard.edu>>

 Hi Carolina,

 Sorry My bad. I was inaccurate in my previous message.

 -subject should work.

 Assuming that the MPRAGE of your subject is under the following
 directory:

 /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig

 set your SUBJECTS_DIR to
 /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
 before
 running recon-all

 setenv SUBJECTS_DIR
 ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig

 recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
 $SUBJECTS_DIR/hptu_subj001

 This should create a folder where Freesurfer recons will be created:

 cd
 
~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001

 Best,
 Priti

 >  Hi Carolina,
 >
 >  -subject is not recognized by Freesurfer...Use -subjid or -s
 instead.
 >
 >  setenv SUBJECTS_DIR
 >
 >  recon-all -all -i/MPRAGE.nii.gz -s  freesurfer recons>/hptu_subj001
 >
 >  Priti
 >
 >>  Hello Freesurfer's users,
 >>
 >>  I'm starting using FS and I have a problem running recon-all
 >>  I create a folder called hptu_subj001 which contains MPRAGE.nii.gz
 >>  within
 >>  tutorial_subj
 >>  First I convert nii.gz to mgz qith the command:
 >>  recon-all -i MPRAGE.nii.gz -s hptu_subj001
 >>  and then in order to process all, I type:
 >>  recon-all –i 001.mgz –subject hptu_subj001 –all
 >>
 >>
 
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig>
 >>  recon-all –i 001.mgz –subject hptu_subj001 –all
 >>  ERROR: Flag  i unrecognized.
 >>   i 001.mgz  subject hptu_subj001  all
 >>  Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
 >>  #50-Ubuntu
 >>  SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
 >>
 >>  recon-all -s  exited with ERRORS at Fri Jun 10 12:50:04 COT 2011
 >>
 >>  then I tried with:
 >>
 >>
 
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj>
 >>  recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all
 >>  ERROR: Flag  i unrecognized.
 >>   i MPRAGE.nii.gz  subject hptu_subj001  all
 >>  Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
 >>  #50-Ubuntu
 >>  SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
 >>
 >>  recon-all -s  exited with ERRORS at Fri Jun 10 12:36:24 COT 2011
 >>
 >>  How I can fix this error?
 >>
 >>  Thanks a lot,
 >>
 >>  Best regards,
 >>
 >>  Carolina
 >>  ___
 >>  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
 >
 >
 >



 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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and may contain confidential information.  Any unauthorized review,
use, disclosure or distribution is prohibited.  If you are not the
intended recipient, please contact the sender by reply email and
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[Freesurfer] Adding a new measure to the design tab

[Jeanette Berberich]

Hi,

So I'm trying to add new measures, after having run recon-all -qcache, to my 
design tab drop-down menu and it doesn't seem to be working. I was a little 
confused about the .Qdecrc file. I put a file named qdec.Qdecrc file inside my 
$SUBJECTS_DIR/qdec/ and i also have a qdec.fsgd file in the same place. I'm not 
sure what else to do to get my new measurements to show up.

Thank you so much,


Jeanette
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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.

Re: [Freesurfer] recon-all -s exited with ERRORS

[Douglas N Greve]

Try adding -use-cuda to recon-all

Leo Souza wrote:
> Yes, I did that, but it doesn't actually uses the GPU to do that, only 
> CPU.
>
> GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q 
> -d UTILIZATION -l 3" if your'e using any recent drivers.
>
>
> Thanks,
> *Leo Souza*
>
> On 06/13/2011 02:44 PM, Douglas N Greve wrote:
>> When you run recon-all, it will create a recon-all-status file in the 
>> scripts directory. This has the start times of all the processes, so you 
>> can work out how long each took. This will be wall clock time, so take 
>> that into account.
>>
>> doug
>>
>> Leo Souza wrote:
>> 
>>> Hi Carolina,
>>>
>>> Do you know how can I run Freesurfer just to get some Benchmark 
>>> Numbers and to Check GPU Performance using Cuda?
>>>
>>> Thanks,
>>> *Leo Souza*
>>>
>>> On 06/13/2011 07:04 AM, Carolina Valencia wrote:
>>>   
 Thanks a lot, it works.
 just waiting 24 hours.

 Best regards,

 Carolina

 2011/6/10 >>> >

 Hi Carolina,

 Sorry My bad. I was inaccurate in my previous message.

 -subject should work.

 Assuming that the MPRAGE of your subject is under the following
 directory:

 /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig

 set your SUBJECTS_DIR to
 /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
 before
 running recon-all

 setenv SUBJECTS_DIR
 ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig

 recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
 $SUBJECTS_DIR/hptu_subj001

 This should create a folder where Freesurfer recons will be created:

 cd
 
 ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001

 Best,
 Priti

 > Hi Carolina,
 >
 > -subject is not recognized by Freesurfer...Use -subjid or -s
 instead.
 >
 > setenv SUBJECTS_DIR 
 >
 > recon-all -all -i /MPRAGE.nii.gz -s >>> > freesurfer recons>/hptu_subj001
 >
 > Priti
 >
 >> Hello Freesurfer's users,
 >>
 >> I'm starting using FS and I have a problem running recon-all
 >> I create a folder called hptu_subj001 which contains MPRAGE.nii.gz
 >> within
 >> tutorial_subj
 >> First I convert nii.gz to mgz qith the command:
 >> recon-all -i MPRAGE.nii.gz -s hptu_subj001
 >> and then in order to process all, I type:
 >> recon-all –i 001.mgz –subject hptu_subj001 –all
 >>
 >>
 
 cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig>
 >> recon-all –i 001.mgz –subject hptu_subj001 –all
 >> ERROR: Flag  i unrecognized.
 >>  i 001.mgz  subject hptu_subj001  all
 >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
 >> #50-Ubuntu
 >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
 >>
 >> recon-all -s  exited with ERRORS at Fri Jun 10 12:50:04 COT 2011
 >>
 >> then I tried with:
 >>
 >>
 
 cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj>
 >> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all
 >> ERROR: Flag  i unrecognized.
 >>  i MPRAGE.nii.gz  subject hptu_subj001  all
 >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
 >> #50-Ubuntu
 >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
 >>
 >> recon-all -s  exited with ERRORS at Fri Jun 10 12:36:24 COT 2011
 >>
 >> How I can fix this error?
 >>
 >> Thanks a lot,
 >>
 >> Best regards,
 >>
 >> Carolina
 >> ___
 >> 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
 >
 >
 >



 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
 

Re: [Freesurfer] recon-all -s exited with ERRORS

[Leo Souza]

Sorry my typos, got a weird keyboard here.

Thanks,
*Leo Souza*

On 06/13/2011 03:27 PM, Leo Souza wrote:
Yes, I did that, but it doesn't actually uses the GPU to do that, only 
CPU.


GPU percentage is 0%.  (you can check it by do running: "nvidia-smi -q 
-d UTILIZATION -l 3" if youŕe using any recent drivers.



Thanks,
*Leo Souza*

On 06/13/2011 02:44 PM, Douglas N Greve wrote:

When you run recon-all, it will create a recon-all-status file in the
scripts directory. This has the start times of all the processes, so you
can work out how long each took. This will be wall clock time, so take
that into account.

doug

Leo Souza wrote:

Hi Carolina,

Do you know how can I run Freesurfer just to get some Benchmark
Numbers and to Check GPU Performance using Cuda?

Thanks,
*Leo Souza*

On 06/13/2011 07:04 AM, Carolina Valencia wrote:

Thanks a lot, it works.
just waiting 24 hours.

Best regards,

Carolina

2011/6/10mailto:rspr...@nmr.mgh.harvard.edu>>

 Hi Carolina,

 Sorry My bad. I was inaccurate in my previous message.

 -subject should work.

 Assuming that the MPRAGE of your subject is under the following
 directory:

 /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig

 set your SUBJECTS_DIR to
 /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
 before
 running recon-all

 setenv SUBJECTS_DIR
 ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig

 recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
 $SUBJECTS_DIR/hptu_subj001

 This should create a folder where Freesurfer recons will be created:

 cd
 
~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001

 Best,
 Priti

 >  Hi Carolina,
 >
 >  -subject is not recognized by Freesurfer...Use -subjid or -s
 instead.
 >
 >  setenv SUBJECTS_DIR
 >
 >  recon-all -all -i/MPRAGE.nii.gz -s  freesurfer recons>/hptu_subj001
 >
 >  Priti
 >
 >>  Hello Freesurfer's users,
 >>
 >>  I'm starting using FS and I have a problem running recon-all
 >>  I create a folder called hptu_subj001 which contains MPRAGE.nii.gz
 >>  within
 >>  tutorial_subj
 >>  First I convert nii.gz to mgz qith the command:
 >>  recon-all -i MPRAGE.nii.gz -s hptu_subj001
 >>  and then in order to process all, I type:
 >>  recon-all –i 001.mgz –subject hptu_subj001 –all
 >>
 >>
 
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig>
 >>  recon-all –i 001.mgz –subject hptu_subj001 –all
 >>  ERROR: Flag  i unrecognized.
 >>   i 001.mgz  subject hptu_subj001  all
 >>  Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
 >>  #50-Ubuntu
 >>  SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
 >>
 >>  recon-all -s  exited with ERRORS at Fri Jun 10 12:50:04 COT 2011
 >>
 >>  then I tried with:
 >>
 >>
 
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj>
 >>  recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all
 >>  ERROR: Flag  i unrecognized.
 >>   i MPRAGE.nii.gz  subject hptu_subj001  all
 >>  Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
 >>  #50-Ubuntu
 >>  SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
 >>
 >>  recon-all -s  exited with ERRORS at Fri Jun 10 12:36:24 COT 2011
 >>
 >>  How I can fix this error?
 >>
 >>  Thanks a lot,
 >>
 >>  Best regards,
 >>
 >>  Carolina
 >>  ___
 >>  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
 >
 >
 >



 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.




--

This email message is for the sole use of the intended recipient(s)
and may contain confidential information.  Any unauthorized review,
use, disclosure or distribution is prohibited.  If you are not the
intended recipient, please contact the sender by reply email and
destroy all copies of the original message.
-

Re: [Freesurfer] recon-all -s exited with ERRORS

[Leo Souza]

Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU.

GPU percentage is 0%.  (you can check it by do running: "nvidia-smi -q 
-d UTILIZATION -l 3" if your'e using any recent drivers.



Thanks,
*Leo Souza*

On 06/13/2011 02:44 PM, Douglas N Greve wrote:

When you run recon-all, it will create a recon-all-status file in the
scripts directory. This has the start times of all the processes, so you
can work out how long each took. This will be wall clock time, so take
that into account.

doug

Leo Souza wrote:

Hi Carolina,

Do you know how can I run Freesurfer just to get some Benchmark
Numbers and to Check GPU Performance using Cuda?

Thanks,
*Leo Souza*

On 06/13/2011 07:04 AM, Carolina Valencia wrote:

Thanks a lot, it works.
just waiting 24 hours.

Best regards,

Carolina

2011/6/10mailto:rspr...@nmr.mgh.harvard.edu>>

 Hi Carolina,

 Sorry My bad. I was inaccurate in my previous message.

 -subject should work.

 Assuming that the MPRAGE of your subject is under the following
 directory:

 /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig

 set your SUBJECTS_DIR to
 /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
 before
 running recon-all

 setenv SUBJECTS_DIR
 ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig

 recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
 $SUBJECTS_DIR/hptu_subj001

 This should create a folder where Freesurfer recons will be created:

 cd
 
~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001

 Best,
 Priti

 >  Hi Carolina,
 >
 >  -subject is not recognized by Freesurfer...Use -subjid or -s
 instead.
 >
 >  setenv SUBJECTS_DIR
 >
 >  recon-all -all -i/MPRAGE.nii.gz -s  freesurfer recons>/hptu_subj001
 >
 >  Priti
 >
 >>  Hello Freesurfer's users,
 >>
 >>  I'm starting using FS and I have a problem running recon-all
 >>  I create a folder called hptu_subj001 which contains MPRAGE.nii.gz
 >>  within
 >>  tutorial_subj
 >>  First I convert nii.gz to mgz qith the command:
 >>  recon-all -i MPRAGE.nii.gz -s hptu_subj001
 >>  and then in order to process all, I type:
 >>  recon-all –i 001.mgz –subject hptu_subj001 –all
 >>
 >>
 
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig>
 >>  recon-all –i 001.mgz –subject hptu_subj001 –all
 >>  ERROR: Flag  i unrecognized.
 >>   i 001.mgz  subject hptu_subj001  all
 >>  Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
 >>  #50-Ubuntu
 >>  SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
 >>
 >>  recon-all -s  exited with ERRORS at Fri Jun 10 12:50:04 COT 2011
 >>
 >>  then I tried with:
 >>
 >>
 
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj>
 >>  recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all
 >>  ERROR: Flag  i unrecognized.
 >>   i MPRAGE.nii.gz  subject hptu_subj001  all
 >>  Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
 >>  #50-Ubuntu
 >>  SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
 >>
 >>  recon-all -s  exited with ERRORS at Fri Jun 10 12:36:24 COT 2011
 >>
 >>  How I can fix this error?
 >>
 >>  Thanks a lot,
 >>
 >>  Best regards,
 >>
 >>  Carolina
 >>  ___
 >>  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
 >
 >
 >



 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.




--

This email message is for the sole use of the intended recipient(s)
and may contain confidential information.  Any unauthorized review,
use, disclosure or distribution is prohibited.  If you are not the
intended recipient, please contact the sender by reply email and
destroy all copies of the original message.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] recon-all -s exited with ERRORS

[Douglas N Greve]

When you run recon-all, it will create a recon-all-status file in the 
scripts directory. This has the start times of all the processes, so you 
can work out how long each took. This will be wall clock time, so take 
that into account.

doug

Leo Souza wrote:
> Hi Carolina,
>
> Do you know how can I run Freesurfer just to get some Benchmark 
> Numbers and to Check GPU Performance using Cuda?
>
> Thanks,
> *Leo Souza*
>
> On 06/13/2011 07:04 AM, Carolina Valencia wrote:
>> Thanks a lot, it works.
>> just waiting 24 hours.
>>
>> Best regards,
>>
>> Carolina
>>
>> 2011/6/10 > >
>>
>> Hi Carolina,
>>
>> Sorry My bad. I was inaccurate in my previous message.
>>
>> -subject should work.
>>
>> Assuming that the MPRAGE of your subject is under the following
>> directory:
>>
>> /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
>>
>> set your SUBJECTS_DIR to
>> /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
>> before
>> running recon-all
>>
>> setenv SUBJECTS_DIR
>> ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
>>
>> recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
>> $SUBJECTS_DIR/hptu_subj001
>>
>> This should create a folder where Freesurfer recons will be created:
>>
>> cd
>> 
>> ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001
>>
>> Best,
>> Priti
>>
>> > Hi Carolina,
>> >
>> > -subject is not recognized by Freesurfer...Use -subjid or -s
>> instead.
>> >
>> > setenv SUBJECTS_DIR 
>> >
>> > recon-all -all -i /MPRAGE.nii.gz -s > > freesurfer recons>/hptu_subj001
>> >
>> > Priti
>> >
>> >> Hello Freesurfer's users,
>> >>
>> >> I'm starting using FS and I have a problem running recon-all
>> >> I create a folder called hptu_subj001 which contains MPRAGE.nii.gz
>> >> within
>> >> tutorial_subj
>> >> First I convert nii.gz to mgz qith the command:
>> >> recon-all -i MPRAGE.nii.gz -s hptu_subj001
>> >> and then in order to process all, I type:
>> >> recon-all –i 001.mgz –subject hptu_subj001 –all
>> >>
>> >>
>> 
>> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig>
>> >> recon-all –i 001.mgz –subject hptu_subj001 –all
>> >> ERROR: Flag  i unrecognized.
>> >>  i 001.mgz  subject hptu_subj001  all
>> >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
>> >> #50-Ubuntu
>> >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
>> >>
>> >> recon-all -s  exited with ERRORS at Fri Jun 10 12:50:04 COT 2011
>> >>
>> >> then I tried with:
>> >>
>> >>
>> 
>> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj>
>> >> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all
>> >> ERROR: Flag  i unrecognized.
>> >>  i MPRAGE.nii.gz  subject hptu_subj001  all
>> >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
>> >> #50-Ubuntu
>> >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
>> >>
>> >> recon-all -s  exited with ERRORS at Fri Jun 10 12:36:24 COT 2011
>> >>
>> >> How I can fix this error?
>> >>
>> >> Thanks a lot,
>> >>
>> >> Best regards,
>> >>
>> >> Carolina
>> >> ___
>> >> 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
>> >
>> >
>> >
>>
>>
>>
>> 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.
>>
>>
>>
>>
>> -- 
> This email message is for the sole use of the intended recipient(s) 
> and may contain confidential information.  Any unauthorized review, 
> use, disclosure or distribution is prohibited.  If you are not the 
> intended recipient, please contact the sender by reply email and 
> destroy all copies of the original message.
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.ed

Re: [Freesurfer] recon-all -s exited with ERRORS

[Leo Souza]

Hi Carolina,

Do you know how can I run Freesurfer just to get some Benchmark Numbers 
and to Check GPU Performance using Cuda?


Thanks,
*Leo Souza*

On 06/13/2011 07:04 AM, Carolina Valencia wrote:

Thanks a lot, it works.
just waiting 24 hours.

Best regards,

Carolina

2011/6/10 >


Hi Carolina,

Sorry My bad. I was inaccurate in my previous message.

-subject should work.

Assuming that the MPRAGE of your subject is under the following
directory:

/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig

set your SUBJECTS_DIR to
/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
before
running recon-all

setenv SUBJECTS_DIR
~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig

recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
$SUBJECTS_DIR/hptu_subj001

This should create a folder where Freesurfer recons will be created:

cd

~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001

Best,
Priti

> Hi Carolina,
>
> -subject is not recognized by Freesurfer...Use -subjid or -s
instead.
>
> setenv SUBJECTS_DIR 
>
> recon-all -all -i /MPRAGE.nii.gz -s  freesurfer recons>/hptu_subj001
>
> Priti
>
>> Hello Freesurfer's users,
>>
>> I'm starting using FS and I have a problem running recon-all
>> I create a folder called hptu_subj001 which contains MPRAGE.nii.gz
>> within
>> tutorial_subj
>> First I convert nii.gz to mgz qith the command:
>> recon-all -i MPRAGE.nii.gz -s hptu_subj001
>> and then in order to process all, I type:
>> recon-all –i 001.mgz –subject hptu_subj001 –all
>>
>>

cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig>
>> recon-all –i 001.mgz –subject hptu_subj001 –all
>> ERROR: Flag  i unrecognized.
>>  i 001.mgz  subject hptu_subj001  all
>> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
>> #50-Ubuntu
>> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
>>
>> recon-all -s  exited with ERRORS at Fri Jun 10 12:50:04 COT 2011
>>
>> then I tried with:
>>
>>

cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj>
>> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all
>> ERROR: Flag  i unrecognized.
>>  i MPRAGE.nii.gz  subject hptu_subj001  all
>> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
>> #50-Ubuntu
>> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
>>
>> recon-all -s  exited with ERRORS at Fri Jun 10 12:36:24 COT 2011
>>
>> How I can fix this error?
>>
>> Thanks a lot,
>>
>> Best regards,
>>
>> Carolina
>> ___
>> 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
>
>
>



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.




--


---
This email message is for the sole use of the intended recipient(s) and may 
contain
confidential information.  Any unauthorized review, use, disclosure or 
distribution
is prohibited.  If you are not the intended recipient, please contact the 
sender by
reply email and destroy all copies of the original message.
---
___
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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.

[Freesurfer] Pulvinar Segmentation

[Peter J. Molfese]

Hi,

I'm interested in pulling out segmentation stats on the Pulvinar.  I noticed 
that Pulvinar is listed in the FreeSurferColorLUT.txt but isn't in the 
aseg.stats.  Is there a way to get segmentation information for the Pulvinar?  

best,
Peter
___
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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.

Re: [Freesurfer] Whole brain parcellation.

[Sudhin A. Shah]

Hi Sorry for bothering you again, but I am not sure I understand.

I was running whole brain correlation analysis (voxel by voxel). BUT for 
comparison purposes, I want to compute region by region correlation matrix.
So, I want to divide up the brain into freesurfer parcellated regions - i.e. 
with no overlap, but with full coverage of whole brain.

I have looked at FreeSurferColorLUT.txt and am confused because there are 
several sets and overlap (eg. 19 and 55 vs 2035..)

If I use the following, can I ensure no overlap and full coverage?
1)Subcortical: 9-13, 16-19, 48-55, 58 - 59, 85,86
2)Cortex: 1002- 1034, 2002- 2034

I am asking if there is an established list of whole brain parcellations before 
I rely on label names to choose the ROIS

On 06/13/11, Douglas N Greve   wrote:
> 
> Anything that is non-0 will cover the whole brain.
> doug
> 
> Sudhin A. Shah wrote:
> > Hi, thank you. Is there a range in the labels that will ensure that I am 
> > including the whole brain? I.e. I see labels for Cx, but not subcortical..
> > If I take labels 1001 to 2001 ( for eg ) will that cover whole brain?
> >
> > Thank you,
> > S
> >
> >
> >
> > On Jun 13, 2011, at 10:59 AM, Douglas N Greve  
> > wrote:
> >
> >   
> >> That is fine, or you can use mri_binarize with the --match option. The 
> >> numbers that correspond to each label can be found in  
> >> $FREESURFER_HOME/FreeSurferColorLUT.txt. You can also get at them visual 
> >> as I described in my previous email with tkmedit:
> >>
> >> tkmedit subject orig.mgz -aux aseg.mgz -aseg
> >>
> >> doug
> >>
> >>
> >> Sudhin A. Shah wrote:
> >> 
> >>> I mean that I am using FSL to create binary masks from freesurfer 
> >>> parcellated regions. Unless there is a better way :)
> >>>
> >>> S
> >>>
> >>>
> >>>
> >>> On Jun 10, 2011, at 7:13 PM, Douglas N Greve  
> >>> wrote:
> >>>
> >>>  
> >>>   
>  What do you mean you are doing it with FEAT?
> 
>  Sudhin A. Shah wrote:
>     
>  
> > Hello,
> >
> > I am a beginner so please bear with me. I want to obtain binary masks 
> > for every region (Cortical + subcortical). I am using FSL(feat) to do 
> > this BUT am not sure what the labels would be.
> >
> > I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz 
> > BUT do not know which labels to use to avoid overlap and ensure full 
> > coverage.
> >
> > Thank you,
> >
> > S
> >
> >
> > 
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> > (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
> >  
> >   
>  -- 
>  Douglas N. Greve, Ph.D.
>  MGH-NMR Center
>  gr...@nmr.mgh.harvard.edu
>  Phone Number: 617-724-2358 Fax: 617-726-7422
> 
>  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>  FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>  ___
>  Freesurfer mailing list
>  Freesurfer@nmr.mgh.harvard.edu
>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>  (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 
>  (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.
> 
>     
>  
> >>>  
> >>>   
> >> -- 
> >> Douglas N. Greve, Ph.D.
> >> MGH-NMR Center
> >> gr...@nmr.mgh.harvard.edu
> >> Phone Number: 617-724-2358 Fax: 617-726-7422
> >>
> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >>
> >> 
> >
> >
> >   
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
> 

-- 
Sudhin A. Shah
Postdoctoral Fellow
Laboratory of Cognitive Neuromodulation
Weill Cornell Medical College, NY,NY
(212) 746-4514


__

[Freesurfer] Resampling from MNI 152 to MNI 305 - Problem with orientation

[Balaji Goparaju]

Hello Freesurfers,

I have Brodmann Area binary masks in the ICBM MNI 152 space, that I acquired
using WFU_PickAtlas toolbox in SPM. These
masks are .nii files, and have a RAS orientation.

I am trying to resample these masks into the fsaverage MNI 305 space,
specifically with the dimensions matching the "mni305.cor.subfov2.mgz"
file found in the $FREESURFER_HOME/average file. This file is in the LIA
orientation.

However, the mni152.register.dat file seems to be transforming volumes from
the MNI 305 space to the MNI 152 Space in LAS orientation (MNI152_T1_2mm.nii
in FSL).

Should I transform my Brodmann Area masks from the RAS orientation to a LAS
orientation? If so, how can I achieve this? The RAS orientation is correct,
so I know using mri_convert --out_dimension is out of the question.

I have tried to use
*mri_label2vol --seg {BA_mask} --temp
{$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o {output_file} --reg
mni152.register.dat --invertmtx*

Also, I have tried to use the inverted matrix from mni152.register.dat and
use it with
*mri_vol2vol -mov {BA_mask} --reg {inverted_mni152.register.dat} --o
{output_file} --tal --talres 2*
However, the output files had interchanged posterior (P) and anterior (A),
and superior (S) and interior (I) orientations.

What is the best way to achieve the resampling? Any guidance is really
appreciated!

Regards,

Balaji Goparaju
___
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] pet partial volume correction

[Douglas N Greve]

A couple of things:
Map aparc+aseg into the PET space:
mri_label2vol --seg aparc+aseg.mgz --reg register.dat --temp 
subject.pet.pvf.nii --o subject_bl.petlabel.nii

Use the PET space aparc+aseg when computing the seg stats:
mri_segstats --seg  subject_bl.petlabel.nii --sum 
/home/corinna/blstats/subject.pvcorr.segstats.csv --i 
subject_bl.petlabel.nii --ctab segments.txt

doug

corinna bauer wrote:
> Hi Doug,
> I tried the partial volume correction method over the weekend and got 
> some unexpected results. Many cortical GM regions were reported as 
> having 0 uptake, left and right hemisphere uptake values for the same 
> ROI were drastically different (i.e. 7 vs 150). Below is my code. 
> Maybe I'm missing something?
>
> mri_compute_volume_fractions register.dat bl_pet.nii subject_bl.pvf
> fscalc --o subject.pet.pvf.nii bl_pet.nii div subject_bl.pvf.gm.mgz
> mri_label2vol --seg aparc+aseg.mgz --reg register.dat --temp orig.mgz 
> --o subject_bl.petlabel.nii
> mri_segstats --seg aparc+aseg.mgz --sum 
> /home/corinna/blstats/subject.pvcorr.segstats.csv --i 
> subject_bl.petlabel.nii --ctab segments.txt 
>
> Corinna
>
> On Fri, Jun 10, 2011 at 11:18 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> No, that will be fine.
> doug
>
> corinna bauer wrote:
>
> Will I need to re-register the pet to the mri?
>
> On Fri, Jun 10, 2011 at 10:58 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>you'll need to get a new version then. You won't need to
> reanalyze
>your anatomicals in the new version, but you will need it
> to run
>these programs.
>
>doug
>
>corinna bauer wrote:
>
>I'm using 4.4.0
>
>On Fri, Jun 10, 2011 at 10:44 AM, Douglas N Greve
> 
>  >
> 
> 
>
>   which version are you using? Both should be in both
> 5.0 and
>5.1.
>   doug
>
>   corinna bauer wrote:
>
>   Hi Doug,
>
>   I used the mri_compute_volume_fractions and
> fscalc commands
>   and got this error message:
>
>   mri_compute_volume_fractions: Command not found.
>   fscalc: Command not found.
>
>   Other FreeSurfer commands, such as mri_segstats
> are working
>   fine in the same batch script.
>
>   Corinna
>
>
>   On Wed, Jun 8, 2011 at 2:30 PM, Douglas N Greve
>
> >
> 
> >>
>    
> >
>    
>  wrote:
>
>
>
>  corinna bauer wrote:
>
>  Alright that should work. So do I use the
>pet.anat.nii
>   files
>  (from mri_vol2vol) as the input pet file
> to the
>  mri_compute_volume_fractions?
>
>  No, use the pet volume. This does everything
> in the
>pet space.
>
>  Also, has anyone published using this pv
>correction method
>  that you know of?
>
>  I don't know. I think this is how they do pvc in
>pet, but I
>   really
>  don't know the lit.
>
>
>  An alternative method that I was thinking
> was to do
>   something
>  similar to the cortical thickness correction
>Salat used and
>  sample on either side of the gray/white
> boundary
>and the
>

Re: [Freesurfer] trac-all - bedp errors

[Deryk S. Beal, Ph.D.]

Hi Priti

In addition, if I run bedpostx from the command line as follows:

bedpostx /usr/local/freesurfer/subjects/C001/dmri

it works just fine without errors.

Deryk

Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO
Speech-Language Pathologist
C.I.H.R. Post Doctoral Research Fellow
Department of Cognitive and Neural Systems Speech Laboratory
Boston University, 677 Beacon Street, Boston, MA 02215
dsb...@bu.edu
http://blogs.bu.edu/dsbeal/about/
*
This email may contain confidential and/or privileged information for the
sole use of the intended recipient. Any review or distribution by others is
strictly prohibited. If you have received this email in error, please
contact the sender and delete all copies. Opinions, conclusions or other
information expressed or contained in this email are not given or endorsed
by the sender unless otherwise affirmed independently by the sender.


On Mon, Jun 13, 2011 at 1:51 PM, Deryk S. Beal, Ph.D.  wrote:

> Hi Priti
>
> Thank you for your quick replay. The following files / folders are listed
> in my dmri.bedpostx directory:
>
> **
> /usr/local/freesurfer/subjects/C001/dmri.bedpostX$ ls
> commands.txt  diff_slices  logs  monitor  xfms
> **
>
> I am able to call bedpostx from the command line without error. It is worth
> noting that I am running Ubuntu 10.10 and the Neurodebian distro of FSL4.1.
> However, FSL and bedpostx appear to be sourced properly:
>
> **
> :/usr/local/freesurfer/subjects/C001/dmri.bedpostX$ bedpostx
>
> Usage: bedpostx  [options]
>
> expects to find bvals and bvecs in subject directory
> expects to find data and nodif_brain_mask in subject directory
> options:
> -n (number of fibres per voxel, default 2)
> -w (ARD weight, more weight means less secondary fibres per voxel, default
> 1)
> -b (burnin period, default 1000)
> -j (number of jumps, default 1250)
> -s (sample every, default 25)
>
> 
>
> Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO
> Speech-Language Pathologist
> C.I.H.R. Post Doctoral Research Fellow
> Department of Cognitive and Neural Systems Speech Laboratory
> Boston University, 677 Beacon Street, Boston, MA 02215
> dsb...@bu.edu
> http://blogs.bu.edu/dsbeal/about/
> *
> This email may contain confidential and/or privileged information for the
> sole use of the intended recipient. Any review or distribution by others is
> strictly prohibited. If you have received this email in error, please
> contact the sender and delete all copies. Opinions, conclusions or other
> information expressed or contained in this email are not given or endorsed
> by the sender unless otherwise affirmed independently by the sender.
>
>
> On Mon, Jun 13, 2011 at 1:25 PM,  wrote:
>
>> Hi Deryk,
>>
>> Is bedpostx properly installed in your computer? Can you just type
>> bedpostx in your terminal to see if it gives this message?
>>
>>
>> 
>> Usage: bedpostx  [options]
>>
>> expects to find bvals and bvecs in subject directory
>> expects to find data and nodif_brain_mask in subject directory
>> options:
>> -n (number of fibres per voxel, default 2)
>> -w (ARD weight, more weight means less secondary fibres per voxel, default
>> 1)
>> -b (burnin period, default 1000)
>> -j (number of jumps, default 1250)
>> -s (sample every, default 25)
>>
>> 
>>
>> Also can you let us know if any files are created after this error in
>> /usr/local/freesurfer/subjects/C001/dmri.bedpostx directory ?
>>
>> This looks like an error with the bedpostx itself...I've used the trac-all
>> -bedp on my local machine (instead of a cluster) and it seems to work
>> fine.
>>
>> Priti
>>
>> > Dear Tracula Users
>> >
>> > I completed trac-all -prep -c without difficulty or errors. However,
>> > without
>> > any changes to my director structure or my Tracula config file I am
>> > receiving the following errors when running trac-all -bedp -c. I will
>> copy
>> > and past my config file contents below the error messages. Please
>> advise.
>> >
>> > trac-all -bedp -c
>> > /media/5424CE1A24CDFECC/UofT/data/Tracula/tracula_config.txt -debug
>> > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
>> > INFO: Diffusion root is /usr/local/freesurfer/subjects
>> > Actual FREESURFER_HOME /usr/local/freesurfer
>> > ln -sf
>> >
>> /usr/local/freesurfer/subjects/C001/dlabel/diff/anat_brain_mask.bbr.nii.gz
>> > /usr/local/freesurfer/subjects/C001/dmri/nodif_brain_mask.nii.gz
>> > ln -sf /usr/local/freesurfer/subjects/C001/dmri/dwi.nii.gz
>> > /usr/local/freesurfer/

Re: [Freesurfer] trac-all - bedp errors

[Deryk S. Beal, Ph.D.]

Hi Priti

Thank you for your quick replay. The following files / folders are listed in
my dmri.bedpostx directory:

**
/usr/local/freesurfer/subjects/C001/dmri.bedpostX$ ls
commands.txt  diff_slices  logs  monitor  xfms
**

I am able to call bedpostx from the command line without error. It is worth
noting that I am running Ubuntu 10.10 and the Neurodebian distro of FSL4.1.
However, FSL and bedpostx appear to be sourced properly:

**
:/usr/local/freesurfer/subjects/C001/dmri.bedpostX$ bedpostx

Usage: bedpostx  [options]

expects to find bvals and bvecs in subject directory
expects to find data and nodif_brain_mask in subject directory
options:
-n (number of fibres per voxel, default 2)
-w (ARD weight, more weight means less secondary fibres per voxel, default
1)
-b (burnin period, default 1000)
-j (number of jumps, default 1250)
-s (sample every, default 25)



Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO
Speech-Language Pathologist
C.I.H.R. Post Doctoral Research Fellow
Department of Cognitive and Neural Systems Speech Laboratory
Boston University, 677 Beacon Street, Boston, MA 02215
dsb...@bu.edu
http://blogs.bu.edu/dsbeal/about/
*
This email may contain confidential and/or privileged information for the
sole use of the intended recipient. Any review or distribution by others is
strictly prohibited. If you have received this email in error, please
contact the sender and delete all copies. Opinions, conclusions or other
information expressed or contained in this email are not given or endorsed
by the sender unless otherwise affirmed independently by the sender.


On Mon, Jun 13, 2011 at 1:25 PM,  wrote:

> Hi Deryk,
>
> Is bedpostx properly installed in your computer? Can you just type
> bedpostx in your terminal to see if it gives this message?
>
>
> 
> Usage: bedpostx  [options]
>
> expects to find bvals and bvecs in subject directory
> expects to find data and nodif_brain_mask in subject directory
> options:
> -n (number of fibres per voxel, default 2)
> -w (ARD weight, more weight means less secondary fibres per voxel, default
> 1)
> -b (burnin period, default 1000)
> -j (number of jumps, default 1250)
> -s (sample every, default 25)
>
> 
>
> Also can you let us know if any files are created after this error in
> /usr/local/freesurfer/subjects/C001/dmri.bedpostx directory ?
>
> This looks like an error with the bedpostx itself...I've used the trac-all
> -bedp on my local machine (instead of a cluster) and it seems to work
> fine.
>
> Priti
>
> > Dear Tracula Users
> >
> > I completed trac-all -prep -c without difficulty or errors. However,
> > without
> > any changes to my director structure or my Tracula config file I am
> > receiving the following errors when running trac-all -bedp -c. I will
> copy
> > and past my config file contents below the error messages. Please advise.
> >
> > trac-all -bedp -c
> > /media/5424CE1A24CDFECC/UofT/data/Tracula/tracula_config.txt -debug
> > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> > INFO: Diffusion root is /usr/local/freesurfer/subjects
> > Actual FREESURFER_HOME /usr/local/freesurfer
> > ln -sf
> >
> /usr/local/freesurfer/subjects/C001/dlabel/diff/anat_brain_mask.bbr.nii.gz
> > /usr/local/freesurfer/subjects/C001/dmri/nodif_brain_mask.nii.gz
> > ln -sf /usr/local/freesurfer/subjects/C001/dmri/dwi.nii.gz
> > /usr/local/freesurfer/subjects/C001/dmri/data.nii.gz
> > WARN: Running FSL's bedbost locally - this might take a while
> > WARN: It is recommended to run this step on a cluster
> > bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri
> > subjectdir is /usr/local/freesurfer/subjects/C001/dmri
> > Making bedpostx directory structure
> > Queuing preprocessing stages
> > [: 223: NONE: unexpected operator
> > [: 314: NONE: unexpected operator
> > [: 327: xbedpostx_pre: unexpected operator
> > [: 486: x: unexpected operator
> > [: 486: -le: argument expected
> > Queuing parallel processing stage
> > [: 223: NONE: unexpected operator
> > [: 327: xbedpostx: unexpected operator
> > [: 486: x53: unexpected operator
> > 0 slices processed
> > Queuing post processing stage
> > [: 223: NONE: unexpected operator
> > [: 314: NONE: unexpected operator
> > [: 327: xbedpostx_post: unexpected operator
> > [: 486: x: unexpected operator
> > [: 486: -le: argument expected
> >
> > CONFIG FILE CONTENTS:
> > #
> > # dmrirc.example
> > #
> > # This file contains commands that will be run by trac-all before an
> > analysis.
> > # It is used to set all parameters needed for the analysis.
> >

Re: [Freesurfer] trac-all - bedp errors

[rspriti]

Hi Deryk,

Is bedpostx properly installed in your computer? Can you just type
bedpostx in your terminal to see if it gives this message?


Usage: bedpostx  [options]

expects to find bvals and bvecs in subject directory
expects to find data and nodif_brain_mask in subject directory
options:
-n (number of fibres per voxel, default 2)
-w (ARD weight, more weight means less secondary fibres per voxel, default 1)
-b (burnin period, default 1000)
-j (number of jumps, default 1250)
-s (sample every, default 25)


Also can you let us know if any files are created after this error in
/usr/local/freesurfer/subjects/C001/dmri.bedpostx directory ?

This looks like an error with the bedpostx itself...I've used the trac-all
-bedp on my local machine (instead of a cluster) and it seems to work
fine.

Priti

> Dear Tracula Users
>
> I completed trac-all -prep -c without difficulty or errors. However,
> without
> any changes to my director structure or my Tracula config file I am
> receiving the following errors when running trac-all -bedp -c. I will copy
> and past my config file contents below the error messages. Please advise.
>
> trac-all -bedp -c
> /media/5424CE1A24CDFECC/UofT/data/Tracula/tracula_config.txt -debug
> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> INFO: Diffusion root is /usr/local/freesurfer/subjects
> Actual FREESURFER_HOME /usr/local/freesurfer
> ln -sf
> /usr/local/freesurfer/subjects/C001/dlabel/diff/anat_brain_mask.bbr.nii.gz
> /usr/local/freesurfer/subjects/C001/dmri/nodif_brain_mask.nii.gz
> ln -sf /usr/local/freesurfer/subjects/C001/dmri/dwi.nii.gz
> /usr/local/freesurfer/subjects/C001/dmri/data.nii.gz
> WARN: Running FSL's bedbost locally - this might take a while
> WARN: It is recommended to run this step on a cluster
> bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri
> subjectdir is /usr/local/freesurfer/subjects/C001/dmri
> Making bedpostx directory structure
> Queuing preprocessing stages
> [: 223: NONE: unexpected operator
> [: 314: NONE: unexpected operator
> [: 327: xbedpostx_pre: unexpected operator
> [: 486: x: unexpected operator
> [: 486: -le: argument expected
> Queuing parallel processing stage
> [: 223: NONE: unexpected operator
> [: 327: xbedpostx: unexpected operator
> [: 486: x53: unexpected operator
> 0 slices processed
> Queuing post processing stage
> [: 223: NONE: unexpected operator
> [: 314: NONE: unexpected operator
> [: 327: xbedpostx_post: unexpected operator
> [: 486: x: unexpected operator
> [: 486: -le: argument expected
>
> CONFIG FILE CONTENTS:
> #
> # dmrirc.example
> #
> # This file contains commands that will be run by trac-all before an
> analysis.
> # It is used to set all parameters needed for the analysis.
> #
> # Remove a parameter from your dmrirc file if you want use the default
> value.
> # Parameters that don't have default values must be specified.
> #
> # Any other commands that you might want to run before an analysis can be
> added
> # to this file.
> #
> # Original Author: Anastasia Yendiki
> # CVS Revision Info:
> #$Author: ayendiki $
> #$Date: 2011/05/24 06:47:12 $
> #$Revision: 1.3.2.3 $
> #
> # Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
> #
> # Terms and conditions for use, reproduction, distribution and
> contribution
> # are found in the 'FreeSurfer Software License Agreement' contained
> # in the file 'LICENSE' found in the FreeSurfer distribution, and here:
> #
> # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
> #
> # Reporting: freesurfer@nmr.mgh.harvard.edu
> #
> #
>
> # FreeSurfer SUBJECTS_DIR
> # T1 images and FreeSurfer segmentations are expected to be found here
> #
> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
>
> # Output directory where trac-all results will be saved
> # Default: Same as SUBJECTS_DIR
> #
> set dtroot = /usr/local/freesurfer/subjects
>
> # Subject IDs
> #
> set subjlist = (C001 C002 C003 C004 C005 C006 C007 C008 C009 C010 C011
> S001
> S002 S003 S004 S005 S006 S007 S008 S009 S010 S011)
>
> # In case you want to analyze only Huey and Louie
> # Default: Run analysis on all subjects
> #
> set runlist = (1)
> # 2 3 4 5 6 7 8 9 10 11)
> #12 13 14 15 16 17 18 19 20 21 22)
>
> # Input diffusion DICOMs (file names relative to dcmroot)
> # If original DICOMs don't exist, these can be in other image format
> # but then bvecfile, bvalfile, and nb0 must be specified (see below)
> #
> set dcmroot = /media/5424CE1A24CDFECC/UofT/data/Tracula
> set dcmlist = (C001_merged.nii.gz \ C002_merged.nii.gz \
> C003_merged.nii.gz
> C004_merged.nii.gz \ C005_merged.nii.gz \ C006_merged.nii.gz \
> C007_merged.nii.gz \ C008_merged.nii.gz \ C009_merged.nii.gz \
> C010_merged.nii.gz \ C011_merged.nii.gz \ S001_merged.nii.gz \
> S002_merged.nii.gz \ S003_merged.nii.gz \ S004_merged.nii.gz \
> S005_merged.nii

[Freesurfer] trac-all - bedp errors

[Deryk S. Beal, Ph.D.]

Dear Tracula Users

I completed trac-all -prep -c without difficulty or errors. However, without
any changes to my director structure or my Tracula config file I am
receiving the following errors when running trac-all -bedp -c. I will copy
and past my config file contents below the error messages. Please advise.

trac-all -bedp -c
/media/5424CE1A24CDFECC/UofT/data/Tracula/tracula_config.txt -debug
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
INFO: Diffusion root is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
ln -sf
/usr/local/freesurfer/subjects/C001/dlabel/diff/anat_brain_mask.bbr.nii.gz
/usr/local/freesurfer/subjects/C001/dmri/nodif_brain_mask.nii.gz
ln -sf /usr/local/freesurfer/subjects/C001/dmri/dwi.nii.gz
/usr/local/freesurfer/subjects/C001/dmri/data.nii.gz
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri
subjectdir is /usr/local/freesurfer/subjects/C001/dmri
Making bedpostx directory structure
Queuing preprocessing stages
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_pre: unexpected operator
[: 486: x: unexpected operator
[: 486: -le: argument expected
Queuing parallel processing stage
[: 223: NONE: unexpected operator
[: 327: xbedpostx: unexpected operator
[: 486: x53: unexpected operator
0 slices processed
Queuing post processing stage
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_post: unexpected operator
[: 486: x: unexpected operator
[: 486: -le: argument expected

CONFIG FILE CONTENTS:
#
# dmrirc.example
#
# This file contains commands that will be run by trac-all before an
analysis.
# It is used to set all parameters needed for the analysis.
#
# Remove a parameter from your dmrirc file if you want use the default
value.
# Parameters that don't have default values must be specified.
#
# Any other commands that you might want to run before an analysis can be
added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
#$Author: ayendiki $
#$Date: 2011/05/24 06:47:12 $
#$Revision: 1.3.2.3 $
#
# Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#

# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /usr/local/freesurfer/subjects

# Subject IDs
#
set subjlist = (C001 C002 C003 C004 C005 C006 C007 C008 C009 C010 C011 S001
S002 S003 S004 S005 S006 S007 S008 S009 S010 S011)

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
#
set runlist = (1)
# 2 3 4 5 6 7 8 9 10 11)
#12 13 14 15 16 17 18 19 20 21 22)

# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then bvecfile, bvalfile, and nb0 must be specified (see below)
#
set dcmroot = /media/5424CE1A24CDFECC/UofT/data/Tracula
set dcmlist = (C001_merged.nii.gz \ C002_merged.nii.gz \ C003_merged.nii.gz
C004_merged.nii.gz \ C005_merged.nii.gz \ C006_merged.nii.gz \
C007_merged.nii.gz \ C008_merged.nii.gz \ C009_merged.nii.gz \
C010_merged.nii.gz \ C011_merged.nii.gz \ S001_merged.nii.gz \
S002_merged.nii.gz \ S003_merged.nii.gz \ S004_merged.nii.gz \
S005_merged.nii.gz \ S006_merged.nii.gz \ S007_merged.nii.gz \
S008_merged.nii.gz \ S009_merged.nii.gz \ S010_merged.nii.gz \
S011_merged.nii.gz)

# Diffusion gradient table
# Must be specified if inputs are not MGH DICOMs
# Three-column format, one row for each volume in the diffusion data set
# Default: Read from DICOM header
#
set bvecfile = /media/5424CE1A24CDFECC/UofT/data/Tracula/bvecs.txt

# Diffusion b-value table
# Must be specified if inputs are not MGH DICOMs
# Single-column format, one value for each volume in the diffusion data set
# Default: Read from DICOM header
#
set bvalfile = /media/5424CE1A24CDFECC/UofT/data/Tracula/bvals.txt

# Number of low-b images
# Must be specified if inputs are not DICOM
# Default: Read from DICOM header
#
set nb0 = 2

# Perform registration-based B0-inhomogeneity compensation?
# Default: 0 (no)
#
set dob0 = 0

# Input B0 field map magnitude DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
# set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm
louie/fmag/XXX-1.dcm)

# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
# set b0plist = 

Re: [Freesurfer] Whole brain parcellation.

[Douglas N Greve]

Anything that is non-0 will cover the whole brain.
doug

Sudhin A. Shah wrote:
> Hi, thank you. Is there a range in the labels that will ensure that I am 
> including the whole brain? I.e. I see labels for Cx, but not subcortical..
> If I take labels 1001 to 2001 ( for eg ) will that cover whole brain?
>
> Thank you,
> S
>
>
>
> On Jun 13, 2011, at 10:59 AM, Douglas N Greve  
> wrote:
>
>   
>> That is fine, or you can use mri_binarize with the --match option. The 
>> numbers that correspond to each label can be found in  
>> $FREESURFER_HOME/FreeSurferColorLUT.txt. You can also get at them visual as 
>> I described in my previous email with tkmedit:
>>
>> tkmedit subject orig.mgz -aux aseg.mgz -aseg
>>
>> doug
>>
>>
>> Sudhin A. Shah wrote:
>> 
>>> I mean that I am using FSL to create binary masks from freesurfer 
>>> parcellated regions. Unless there is a better way :)
>>>
>>> S
>>>
>>>
>>>
>>> On Jun 10, 2011, at 7:13 PM, Douglas N Greve  
>>> wrote:
>>>
>>>  
>>>   
 What do you mean you are doing it with FEAT?

 Sudhin A. Shah wrote:

 
> Hello,
>
> I am a beginner so please bear with me. I want to obtain binary masks for 
> every region (Cortical + subcortical). I am using FSL(feat) to do this 
> BUT am not sure what the labels would be.
>
> I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz BUT 
> do not know which labels to use to avoid overlap and ensure full coverage.
>
> Thank you,
>
> S
>
>
> 
>
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>  
>   
 -- 
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 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>>>  
>>>   
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>> 
>
>
>   

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] qustions about contents of label file

[Douglas N Greve]

That interpretation is correct. The MNI coords are MNI305. The last 
field is to hold a statistic. If it is 0, it means that the field was 
not filled with anything.

doug

ZhiLiangLong wrote:

Hello:
I use qdec to generate statistical significant areas and draw ROI and 
map the ROI to each subject ,finally i get a label file of each 
subject called lh.supriorfrontal.label which can be seen in attachment 
below.But i'm a little confused with content of the label file, Is it 
correct that,take the third row as an example,the first number 66847 
means vertex index and -10.184 -3.059 74.153 means coordinate which 
belongs to MNI coordinate system? Besides,what does the last number 
0.00 mean?

Any help will be appreciative,Thanks




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Re: [Freesurfer] A question about the coords of the vertex

[Douglas N Greve]

They are in our own coordinate system, documented on our wiki. Do a 
search for  coordinates to find the page.
doug

soft.join Huang wrote:
> Hi all,
>  
> I have a question about the coords of vertex in ?h.white file.
> I load the ?h.white file in Matlab and get a variable called 
> vertex_coords, and I'm wondering what kind of coords they are, MNI or 
> something else?
> Also how can I get the MNI coords of the vertex?
>  
> Thank in advance,
>  
> Best Regards,
>  
> Lijie Huang
> 
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz

[Douglas N Greve]

Do you mean your individual subject after running through FS has a file
called t1.mgz and not T1.mgz? Something is definitely wrong there. Can
you send the log file?
doug

t...@ms36.hinet.net wrote:
>
> Dear FS experts,
> I use FS5.1 and previous data run on other machine. When I try to
> make_average_subjects program, I get error message that it can not get
> T1.mgz data from subject folder. When I check my dataset, actually it
> has t1.mgz rather than T1.mgz. how could I change the setting from
> T1.mgz to t1.mgz
> thanks help
> JLH
>
> 
>
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Fax: 617-726-7422

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Re: [Freesurfer] aseg labels 96 and 97

[Douglas N Greve]

Hi Andy, I don't think that we ever labeled those regions. Or did you do 
these by hand? If you have a label that you want to see the code for, 
you can load it into tkmedit like

tkmedit subject orig.mgz -aux aseg.mgz -aseg

when you click on a label, you can see its number in the aux value.
doug

Andrew Ward wrote:
> Hi FS experts,
>
> We have some legacy code (in a BASH script) that uses mri_cor2label to  
> convert what it is calling the anterior amygdala to volumetric labels.  
> However, we get the error that these values (96 and 97) do not exist.  
> Have the label IDs changed? We are using stable5.1. Our call looks  
> like this:
>
> mri_cor2label --c ${FSDIR}/${SUBJID}/mri/aseg.mgz --id 96 --l ${FSDIR}/ 
> ${SUBJID}/label2/lh.amygdala_ant_vol.label
>
> Does anyone know what is going on with this?
>
> Thank you for your help,
>
>
> Andrew Ward
> Brigham and Women's Hospital (BBNG)
> Massachusetts General Hospital (GRU)
> Athinoula A. Martinos Center for Biomedical Imaging
> 149 13th St., Rm 2689C
> Charlestown, MA 02129
> Phone: 617-726-6211
> Fax: 617-726-5760
>
>
>
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>
>   

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MGH-NMR Center
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Fax: 617-726-7422

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Re: [Freesurfer] recon-all -s exited with ERRORS

[Carolina Valencia]

Thanks a lot, it works.
just waiting 24 hours.

Best regards,

Carolina

2011/6/10 

> Hi Carolina,
>
> Sorry My bad. I was inaccurate in my previous message.
>
> -subject should work.
>
> Assuming that the MPRAGE of your subject is under the following directory:
>
> /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
>
> set your SUBJECTS_DIR to
> /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig before
> running recon-all
>
> setenv SUBJECTS_DIR
> ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
>
> recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
> $SUBJECTS_DIR/hptu_subj001
>
> This should create a folder where Freesurfer recons will be created:
>
> cd
>
> ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001
>
> Best,
> Priti
>
> > Hi Carolina,
> >
> > -subject is not recognized by Freesurfer...Use -subjid or -s instead.
> >
> > setenv SUBJECTS_DIR 
> >
> > recon-all -all -i /MPRAGE.nii.gz -s  > freesurfer recons>/hptu_subj001
> >
> > Priti
> >
> >> Hello Freesurfer's users,
> >>
> >> I'm starting using FS and I have a problem running recon-all
> >> I create a folder called hptu_subj001 which contains MPRAGE.nii.gz
> >> within
> >> tutorial_subj
> >> First I convert nii.gz to mgz qith the command:
> >> recon-all -i MPRAGE.nii.gz -s hptu_subj001
> >> and then in order to process all, I type:
> >> recon-all –i 001.mgz –subject hptu_subj001 –all
> >>
> >>
> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig>
> >> recon-all –i 001.mgz –subject hptu_subj001 –all
> >> ERROR: Flag  i unrecognized.
> >>  i 001.mgz  subject hptu_subj001  all
> >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
> >> #50-Ubuntu
> >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
> >>
> >> recon-all -s  exited with ERRORS at Fri Jun 10 12:50:04 COT 2011
> >>
> >> then I tried with:
> >>
> >>
> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj>
> >> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all
> >> ERROR: Flag  i unrecognized.
> >>  i MPRAGE.nii.gz  subject hptu_subj001  all
> >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae
> >> #50-Ubuntu
> >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
> >>
> >> recon-all -s  exited with ERRORS at Fri Jun 10 12:36:24 COT 2011
> >>
> >> How I can fix this error?
> >>
> >> Thanks a lot,
> >>
> >> Best regards,
> >>
> >> Carolina
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> >
>
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[Freesurfer] interpretation of qdec results

[tulu]

Dear FS experts,
I use qdec to do two group study. in QDEC, 
it set Normal = 1 and Disease = 2, use AGE as covariate and 
apply DODS model, after analyze group cortical thickness, it showed significant 
negative T value (blue color) in some brain areas. I have two questions in 
qdec
1. the contrast  set as 1 -1 0 0 but I don't know 
if it represents as Normal - Disease (normal group is thinner than Disease) or 
Disease - Normal (disease group is thinner than normal) ?
2. is this 
results come from correction of multiple comparison ? or I still need to re-set 
FDR level (default is 0.05) and re-run it ?
thanks in advance
JLH
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