Re: [Freesurfer] pre-processing functional data error

/Run this command line instead mri_convert.linux I0001.dcm s105.run1.nii/ doug

On 11/09/2012 01:57 PM, Yangmei LUO wrote:

Hi Dr, Douglas,

I attached the capture of the result using fslview.

Thanks very much!

Yangmei

On Fri, Nov 9, 2012 at 12:51 PM, Yangmei LUO <yangmeiluo@gmail.com mailto:yangmeiluo@gmail.com> wrote:

Hi Dr.Douglas,

Thanks very much for your patient help. MRI_convert can work. It
is great. However, there was another problem about the convert.
The results of the convert is unknown file and there is a warning.
Could you help me again?

This the command :
//usr/local/freesurfer/bin/mri_convert.linux --in_type dicom
--out_type nii I0001.dcm s105.run1.nii/

The result is:

//usr/local/freesurfer/bin/mri_convert.linux --in_type dicom
--out_type nii I0001.dcm s105.run1.nii
$Id: mri_convert.c,v 1.196 2012/07/11 17:50:50 fischl Exp $
reading from I0001.dcm...
Starting DICOMRead2()
dcmfile = /home/fsl/data/emotion/s105/run1/I0001.dcm
dcmdir = /home/fsl/data/emotion/s105/run1
Ref Series No = 3
Found 231 files, checking for dicoms
Found 228 dicom files in series.
First Sorting
Computing Slice Direction


 WARNING: it appears that the image position for all slices is the
same.
 This is a problem with the DICOM file. Using direction cosines
from col and row
 to compute slice direction, but the output may be misoriented.

Vs: 0 -0.0104718 0.999945
Vs: 0 -0.0104718 0.999945
Second Sorting
Counting frames
nframes = 228
nslices = 1
ndcmfiles = 228
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2--
Loading pixel data
TR=2000.00, TE=30.00, TI=0.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -0.999945, 0.0104718)
k_ras = (-0, 0.0104718, 0.999945)
writing to s105.run1.nii.../


Thank you so much!

Best regards,
Yangmei





On Fri, Nov 9, 2012 at 12:29 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    run these two lines then try again
    chmod a+x mri_convert
    reshash.


    On 11/09/2012 01:04 PM, Yangmei LUO wrote:

        Hi Dr. Douglas,

        Thanks for your kind help. The version of freesurfer is
        stable v5.1.0 on CentOS 4 (32b). When I download the
        updated version you provided and switch the file in the
        bin( I do not know what I did is correct). When I run the
        command, the terminal appeared "permission denied".

        What can I do next?

        Thanks so much!

        Best,
        Yangmei




        On Fri, Nov 9, 2012 at 11:29 AM, Douglas N Greve
        <greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>
        <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

            The name is not important. I was able to convert all
        of those
            files without a problem. What version are you using?
        Maybe try an
            updated version of mri_convert
        ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.linux

            Also, please remember to include previous
        correspondences in your
            email to me. I always delete the emails once I answer
        them.
            thanks
            doug



            On 11/09/2012 12:19 PM, Yangmei LUO wrote:


                Hi Douglas,

                Thank you for your help. I change the name of the
        dicom file
                in order to process conveniently. So, I attached
        two files of
                with origin name and two files with the changed
        name. I wish
                it could help you figure out the problem.


                Thanks a million!


                Best,


                Yangmei


            --     Douglas N. Greve, Ph.D.
            MGH-NMR Center
        greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>
        <mailto:greve@nmr.mgh.harvard.edu
        <mailto:greve@nmr.mgh.harvard.edu>>
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        <tel:617-726-7422>>

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    -- 
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:617-724-2358>
    Fax: 617-726-7422 <tel:617-726-7422>

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>