Re: [Freesurfer] Bad vertex in mris_flatten

[Bruce Fischl]

Hi Hiroyuki
What does that mean? How did it fail?
Bruce 



On Oct 28, 2011, at 5:03 PM, "Oya, Hiroyuki (UI Health Care)" 
 wrote:

> Hiroyuki

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Re: [Freesurfer] Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?

[Pedro Paulo de Magalhães Oliveira Junior]

I have one. I'll give you the link

-- iOS 5.0

Em 28/10/2011, às 20:52, Joshua Lee  escreveu:

Are there any existing Amazon EC2 AMI registered publicly that can be used?
I want to analyze a lot of data fast.

Thanks,
-
Joshua Lee

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[Freesurfer] Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?

[Joshua Lee]

Are there any existing Amazon EC2 AMI registered publicly that can be used?
I want to analyze a lot of data fast.

Thanks,
-
Joshua Lee
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[Freesurfer] Bad vertex in mris_flatten

[Oya, Hiroyuki (UI Health Care)]

Dear sir,

Mris_flatten could not be completed due to the fact that only one bad vertex 
was found in the patch.
Is there any quick way to correct the vertex?

Thank you.

Hiroyuki




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[Freesurfer] Sag3D_T1 or Axial_T1

[Antonella Kis]

Dear Freesurfers,

I have a set of MRI data collected in an Axial_T1 and some in Sag3D_T1. I 
wonder if after dcm to nii conversion when I get a 3D or 4D volume (if further 
use for FSL) it really matter how my data was acquired (Axial or Sag) since the 
NIFTI file is in fact a volume. Should I do a conversion for all the files in 
Axial or Sag? I am planning to use this data in Qdec and also in FSL to do some 
DTI studies, so I will need to register this data into MNI space. Also, how I 
can cut from the nii file's slices in order to bring two files to the same 
dimensions (x, Y, Z)?



Many thanks,
Antonella
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Re: [Freesurfer] TRACULA: how to implement DTI repeat sequence?

[Anastasia Yendiki]

Hi Ansgar - If the 2 series are in register with each other, you can just 
concatenate them with mri_concat. You'd also have to concatenate the 
respective bvals and bvecs in the same order.


For average FA, look in the pathstats.overall.txt file of each 
reconstructed pathway. For more on this see the tutorial:


https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics

Hope this helps,
a.y

On Fri, 28 Oct 2011, Ansgar Furst wrote:


Dear Anastasia,
Re-running bedpostX just did it and I didn't encounter the problem on any 
subjects after that.
Everything is running great now. I just had 2 more follow-up questions:
what's the best way to concatenate the 2 repeat DICOM DWI series into 1 NIFTI 
file (you mentioned that
below)?
How do I extract average FA values constrained by the extracted fiber tracts?
Thanks so much for all your help,
Ansgar

On Wed, Sep 28, 2011 at 5:07 PM, Anastasia Yendiki 
 wrote:

  Hi Ansgar - Most likely everything is fine. Sometimes the script that's 
built into bedpost
  to monitor its progress gives this error but in fact everything has ran 
fine. You should
  check that all the outputs are there in the dmri.bedpostX directory. See 
for list of
  bedpost output files:
         http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html

  a.y


On Wed, 28 Sep 2011, Ansgar Furst wrote:

  Hi Anastasia,
  Thanks so much for your message. You were right about the recon 
directory, the
  contents had been accidentally moved elsewhere (sorry!) and once I moved 
them
  back and reran the script everything worked like a charm without any 
errors.
  However, it looks like I'm now stuck at the next processing stage (fsl's
  bedpostX). I pasted the output with the error message below. FYI: I'm
  unfortunately forced to run the bedpostX on a single Linux box (64-bit 
dual core
  with 8GB of RAM) which I hope is OK?
  Thanks so much for all your help,

  Ansgar

  ==
  trac-all -bedp -c scripts/dmrirc_single_subject_1only
  INFO: SUBJECTS_DIR is /home/ajfurst/Data/WRIISC
  INFO: Diffusion root is /home/ajfurst/Data/WRIISC/TRACULA
  Actual FREESURFER_HOME /usr/local/freesurfer
  ln -sf
  
/home/ajfurst/Data/WRIISC/TRACULA/015/dlabel/diff/anat_brain_mask.bbr.nii.gz
  /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/nodif_brain_mask.nii.gz
  ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/dwi.nii.gz
  /home/ajfurst/Data/WRIISC/TRACULA/015/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 /home/ajfurst/Data/WRIISC/TRACULA/015/dmri
  subjectdir is /home/ajfurst/Data/WRIISC/TRACULA/015/dmri
  Making bedpostx directory structure
  Queuing preprocessing stages
  Queuing parallel processing stage
  0 slices processed
  5 slices processed
  6 slices processed
  7 slices processed
  8 slices processed
  9 slices processed
  9 slices processed
  10 slices processed
  11 slices processed
  11 slices processed
  12 slices processed
  12 slices processed
  13 slices processed
  14 slices processed
  14 slices processed
  14 slices processed
  15 slices processed
  15 slices processed
  16 slices processed
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  18 slices processed
  18 slices processed
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  28 slices processed
  29 slices processed
  29

Re: [Freesurfer] TRACULA: how to implement DTI repeat sequence?

[Ansgar Furst]

Dear Anastasia,
Re-running bedpostX just did it and I didn't encounter the problem on any
subjects after that. Everything is running great now. I just had 2 more
follow-up questions:
what's the best way to concatenate the 2 repeat DICOM DWI series into 1
NIFTI file (you mentioned that below)?
How do I extract average FA values constrained by the extracted fiber
tracts?
Thanks so much for all your help,
Ansgar

On Wed, Sep 28, 2011 at 5:07 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Ansgar - Most likely everything is fine. Sometimes the script that's
> built into bedpost to monitor its progress gives this error but in fact
> everything has ran fine. You should check that all the outputs are there in
> the dmri.bedpostX directory. See for list of bedpost output files:
>
> http://www.fmrib.ox.ac.uk/fsl/**fdt/fdt_bedpostx.html
>
> a.y
>
>
> On Wed, 28 Sep 2011, Ansgar Furst wrote:
>
> Hi Anastasia,
>> Thanks so much for your message. You were right about the recon directory,
>> the
>> contents had been accidentally moved elsewhere (sorry!) and once I moved
>> them
>> back and reran the script everything worked like a charm without any
>> errors.
>> However, it looks like I'm now stuck at the next processing stage (fsl's
>> bedpostX). I pasted the output with the error message below. FYI: I'm
>> unfortunately forced to run the bedpostX on a single Linux box (64-bit
>> dual core
>> with 8GB of RAM) which I hope is OK?
>> Thanks so much for all your help,
>>
>> Ansgar
>>
>> ==**
>> trac-all -bedp -c scripts/dmrirc_single_subject_**1only
>> INFO: SUBJECTS_DIR is /home/ajfurst/Data/WRIISC
>> INFO: Diffusion root is /home/ajfurst/Data/WRIISC/**TRACULA
>> Actual FREESURFER_HOME /usr/local/freesurfer
>> ln -sf
>> /home/ajfurst/Data/WRIISC/**TRACULA/015/dlabel/diff/anat_**
>> brain_mask.bbr.nii.gz
>> /home/ajfurst/Data/WRIISC/**TRACULA/015/dmri/nodif_brain_**mask.nii.gz
>> ln -sf /home/ajfurst/Data/WRIISC/**TRACULA/015/dmri/dwi.nii.gz
>> /home/ajfurst/Data/WRIISC/**TRACULA/015/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 /home/ajfurst/Data/WRIISC/**TRACULA/015/dmri
>> subjectdir is /home/ajfurst/Data/WRIISC/**TRACULA/015/dmri
>> Making bedpostx directory structure
>> Queuing preprocessing stages
>> Queuing parallel processing stage
>> 0 slices processed
>> 5 slices processed
>> 6 slices processed
>> 7 slices processed
>> 8 slices processed
>> 9 slices processed
>> 9 slices processed
>> 10 slices processed
>> 11 slices processed
>> 11 slices processed
>> 12 slices processed
>> 12 slices processed
>> 13 slices processed
>> 14 slices processed
>> 14 slices processed
>> 14 slices processed
>> 15 slices processed
>> 15 slices processed
>> 16 slices processed
>> 16 slices processed
>> 16 slices processed
>> 17 slices processed
>> 17 slices processed
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>> 18 slices processed
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