If ls still says bvecs.txt then that's what it is, ignore what a Finder or such says… at the command line type "mv bvecs.txt bvecs" and same for bvals.

Hope that does the trick,
Dave

On 9 Sep 2013, at 17:02, Victor DelBene <[log in to unmask]>

 wrote:

> Hi Stam,
>
> We have deleted the .txt file extensions, however, when running the "ls" command, it still lists the bvecs and bvals files as .txt.
>
> What format should these files be saved as?
>
>
> On Mon, Sep 9, 2013 at 10:00 AM, Stamatios Sotiropoulos <[log in to unmask]> wrote:
> Hi
>
> You need a "bvecs" and a "bvals" file. Without any .txt extension.
>
> Cheers
> Stam
>
>
> On 9 Sep 2013, at 14:08, Victor DelBene wrote:
>
>> Hi Saad,
>>
>> copying this line into terminal provides me with the following output (the first part just lists the content of the directory)
>>
>> dyn-077-010:EINSTEIN_Research Albert$ cd DTI
>> dyn-077-010:DTI Albert$ ls
>> bedpostcom_log.tcl                             dti_L2.nii.gz
>> bedpostcom_log.tcl 11.51.40 AM                 dti_L3.nii.gz
>> bedpostcom_log.tcl 11.52.38 AM                dti_MD.nii.gz
>> bedpostcom_log.tcl copy                       dti_MO.nii.gz
>> bvals.txt                                             dti_S0.nii.gz
>> bvecs.txt                                             dti_V1.nii.gz
>> data.nii.gz                                           dti_V2.nii.gz
>> data_ECC.ecclog                               dti_V3.nii.gz
>> dti_FA.nii.gz                                         nodif_brain_mask.nii.gz
>> dti_L1.nii.gz
>>
>> dyn-077-010:DTI Albert$ ls -l
>> total 153920
>> -rw-r--r--  1 Albert  staff        99 Sep  7 12:17 bedpostcom_log.tcl
>> -rw-r--r--  1 Albert  staff        99 Sep  7 11:49 bedpostcom_log.tcl 11.51.40 AM
>> -rw-r--r--  1 Albert  staff        99 Sep  7 11:52 bedpostcom_log.tcl 11.52.38 AM
>> -rw-r--r--  1 Albert  staff        99 Sep  7 11:48 bedpostcom_log.tcl copy
>> -rw-r--r--@ 1 Albert  staff       135 Sep  7 10:54 bvals.txt
>> -rw-r--r--@ 1 Albert  staff       928 Sep  7 10:54 bvecs.txt
>> -rw-r--r--  1 Albert  staff  66300891 Sep  7 11:17 data.nii.gz
>> -rw-r--r--  1 Albert  staff      8756 Sep  7 11:16 data_ECC.ecclog
>> -rw-r--r--  1 Albert  staff    760685 Sep  7 11:24 dti_FA.nii.gz
>> -rw-r--r--  1 Albert  staff    747846 Sep  7 11:24 dti_L1.nii.gz
>> -rw-r--r--  1 Albert  staff    760844 Sep  7 11:24 dti_L2.nii.gz
>> -rw-r--r--  1 Albert  staff    776699 Sep  7 11:24 dti_L3.nii.gz
>> -rw-r--r--  1 Albert  staff    757521 Sep  7 11:24 dti_MD.nii.gz
>> -rw-r--r--  1 Albert  staff    787079 Sep  7 11:24 dti_MO.nii.gz
>> -rw-r--r--  1 Albert  staff    756068 Sep  7 11:24 dti_S0.nii.gz
>> -rw-r--r--  1 Albert  staff   2363428 Sep  7 11:24 dti_V1.nii.gz
>> -rw-r--r--  1 Albert  staff   2360969 Sep  7 11:24 dti_V2.nii.gz
>> -rw-r--r--  1 Albert  staff   2361283 Sep  7 11:24 dti_V3.nii.gz
>> -rw-r--r--  1 Albert  staff     15035 Sep  7 11:21 nodif_brain_mask.nii.gz
>> dyn-077-010:DTI Albert$ bedpostx_datacheck
>>
>> Is this the information you need?
>>
>> Thank you
>>
>> Victor
>>
>>
>> On Sun, Sep 8, 2013 at 9:09 AM, Saad Jbabdi <[log in to unmask]> wrote:
>> Hi Victor
>>
>> Could you CD into your data directory and run the following commands:
>>
>>      ls -l
>>      bedpostx_datacheck .
>>
>> and send the results please?
>>
>> Cheers,
>> Saad
>>
>> On 7 Sep 2013, at 13:49, Victor DelBene <[log in to unmask]> wrote:
>>
>>> Dear FSL experts,
>>> My colleague and I are attempting to analyze DTI data in FSL. The first part ("DTIFIT Reconstruct Diffusion Tensor") worked just fine. I have outlined those steps below, just in case something we did inadvertently caused an issue in our later analysis. Our issue is with the Bedpostx application. This issue is described below, following the DTIFIT Reconstruct Diffusion Tensor steps we followed.
>>>
>>> Step 1:
>>> •   In GUI, we selected "FDT Diffusion"
>>> •   We selected "Eddy Current Correction"
>>> •   Reference volume is 0
>>> Step 2:
>>> •   We then made a brain mask for the DTI data
>>> •   We selected "Binary brain masking image"
>>> •   Fractional Intensity Threshold = 0.3
>>> •   We then unchecked "output brain-extracted image"
>>> Step 3:
>>> •   This was followed by DTIFIT Reconstruct Diffusion Tensor
>>> •   We added the diffusion weighted data, BET Binary Mask, the bvec and bval files
>>> •   This ran without any difficulty
>>> Step 4:
>>> •   We then viewed that data in FSL View without any difficulty. Everything worked as it should.
>>>
>>> We now want to run bedpostx. We went back to FDT Diffusion, and then selected the Bedpostx option. We selected the folder with the participant's DTI data. The following are the contents of the folder:
>>>
>>> dti_L2.nii.gz
>>> dti_L3.nii.gz
>>> dti_MD.nii.gz
>>> dti_L1.nii.gz
>>> dti_V2.nii.gz
>>> dti_V3.nii.gz
>>> dti_FA.nii.gz
>>> dti_MO.nii.gz
>>> dti_S0.nii.gz
>>> dti_V1.nii.gz
>>> nodif_brain_mask.nii.gz
>>> data.nii.gz
>>> data_ECC.ecclog
>>> bvals - tried with and without text extension
>>> bvecs - tried with and without text extension
>>>
>>> The nii.gz files are from the DTIFIT Reconstruct Steps. Bvals and bvecs were included both with, and without the .txt extension (based on a possible lead we got from the mailing list - https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;60cb0eb.0812 ).
>>>
>>> We then ran bedpostx and received a message "Child process ended abnormally." In OS X terminal, we see a message "bvecs not found" but this is odd because the bvecs file is in the directory.
>>>
>>> Here is the content of the bvecs file:
>>> 0 -1 -1.41656e-05 1.00762e-06 0.0424009 -0.174908 -0.23229 -0.367522 -0.190198 0.116788 0.200486 0.495781 0.0141082 0.744492 0.760875 0.18088 0.679633 -0.777106 -0.924162 -0.468478 -0.881688 -0.690413 -0.239108 0.0577864 0.536766 0.991788 0.996763 0.872422 0.248702 -0.11831 -0.33761 -0.528597 -0.996853 0
>>>
>>> 0 -5.29348e-06 1 3.43559e-06 -0.114604 -0.200515 -0.162597 0.0260962 0.374378 0.833393 0.252684 0.134495 -0.628105 -0.147695 0.320392 0.924661 -0.422413 0.470692 -0.103601 -0.76738 -0.189303 0.706195 0.757082 0.983697 0.836063 -0.120693 0.0709022 0.478117 0.933555 0.991859 0.841492 0.840869 0.0549916 0
>>>
>>> 0 1.05469e-06 -3.44006e-06 1 -0.992506 -0.963951 -0.95896 -0.929649 -0.90756 -0.540201 -0.94655 -0.85797 -0.778001 -0.65109 -0.564286 -0.33509 -0.599722 -0.417799 -0.367683 -0.437784 -0.432193 -0.156902 -0.607992 0.170297 -0.113498 -0.0422999 -0.0378998 -0.101406 0.258112 -0.0471015 0.421794 0.116294 -0.0570967 0
>>>
>>> We are running FSL on an iMac 10.8.2, with two memory slots (8 gb each). We are using FSL version 5.0.2.
>>>
>>> What is preventing FSL from reading in the bvecs file? Also, would I be correct in assuming that this "child process ended abnormally" error would be the result of a "missing" bvecs file?
>>>
>>> Thank you!
>>>
>>> Best,
>>> Victor DelBene
>>>
>>
>> --
>> Saad Jbabdi
>> University of Oxford, FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> (+44)1865-222466  (fax 717)
>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi
>>
>>
>>
>>
>> --
>> Victor A. DelBene
>> Campus Representative, Advocacy Coordinating Team (ACT)
>> American Psychological Association of Graduate Students (APAGS)
>> Doctoral Candidate
>> Department of Clinical Psychology, Health Emphasis
>> Neuropsychology Minor
>> Ferkauf Graduate School of Psychology, Yeshiva University
>>
>> Pre-doctoral Research Assistant
>> The Sherly and Daniel R. Tishman Cognitive Neurophysiology Laboratory
>> Department of Pediatrics and Neuroscience
>> Albert Einstein College of Medicine, Yeshiva University
>>
>>
>
>
>
>
> --
> Victor A. DelBene
> Campus Representative, Advocacy Coordinating Team (ACT)
> American Psychological Association of Graduate Students (APAGS)
> Doctoral Candidate
> Department of Clinical Psychology, Health Emphasis
> Neuropsychology Minor
> Ferkauf Graduate School of Psychology, Yeshiva University
>
> Pre-doctoral Research Assistant
> The Sherly and Daniel R. Tishman Cognitive Neurophysiology Laboratory
> Department of Pediatrics and Neuroscience
> Albert Einstein College of Medicine, Yeshiva University
>
>

--
Dave Flitney - IT Manager
Oxford Centre for Functional MRI of the Brain
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