yes
On Mon, 15 Oct 2012, Knut J Bjuland wrote:
> Hi
>
> I think i understood it. Should i use mri_convert -rl template input output
>
>
> from mri_convert.c
> printf("reading template info from volume %s...\n",
> reslice_like_name);
> template = MRIreadInfo(reslice_like_name);
> if(template == NULL)
> {
> fprintf(stderr, "error reading from volume %s\n",
> reslice_like_name);
> exit(1);
>
>
>
> Knut J
>
>
>
> On 10/15/2012 02:22 PM, Knut J Bjuland wrote:
>> I am able to convert using mri_convert, but when I try to reslice with
>> mri_convert -rl input output. I get the error message shown below. I
>> according to the documentation I could use mri_convert to reslice, but
>> it does not mention how I should set an vaule for the -rl input. Should
>> I use matlab instead please?
>>
>> http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert
>>
>>
>> mri_convert -rl 001.mgz 001t.mgz
>> mri_convert -rl 001.mgz 001t.mgz
>>
>> mri_convert: missing output volume name
>>
>> type mri_convert -u for usage
>>
>>
>> Knut J
>>
>>
>> On 10/15/2012 01:23 PM, Bruce Fischl wrote:
>>> Don't use the -I, just give it an input (the dicoms) and and output
>>>
>>>
>>>
>>> On Oct 15, 2012, at 1:23 AM, Knut J Bjuland <knut...@hotmail.com> wrote:
>>>
>>>> Hi Bruce
>>>>
>>>> I converted the dicom into 001.mgz. Then I tried to reslice.
>>>>
>>>> mri_convert -rl -i orig/001.mgz -o orig/001.mgz
>>>> mri_convert -rl -i orig/001.mgz -o orig/001.mgz
>>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>>>> reading from orig/001.mgz...
>>>> TR=2730.00, TE=3.45, TI=1000.00, flip angle=7.00
>>>> i_ras = (-0, -1, 0)
>>>> j_ras = (-0, -0, -1)
>>>> k_ras = (-1, 0, 0)
>>>> reading template info from volume -i...
>>>>
>>>> mri_read(): couldn't determine type of file
>>>> /home/knutjb/freesurfer/expo/test/mri/-i
>>>> error reading from volume -i
>>>>
>>>> Could you please give me an example on how to use mri_convert to reslice
>>>> please?
>>>>
>>>>
>>>> Knut J
>>>>
>>>>
>>>>
>>>> On 10/15/2012 12:43 AM, Bruce Fischl wrote:
>>>>> Hi Knut
>>>>>
>>>>> you could mri_convert them into mri/orig/001.mgz and 002.mgz, reslicing
>>>>> the 125 into the 128 geometry (-rl) and go from there.
>>>>>
>>>>> cheers
>>>>> Bruce
>>>>>
>>>>> On Sun, 14 Oct 2012, Knut J Bjuland wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> When I import one subject with recon -i dicom -i dicom -s subjec, I get
>>>>>> this error message ERROR: inputs have mismatched dimensions! I think it
>>>>>> is caused by the fact that there is a different number of slices into
>>>>>> the two series. One series has 256x256x125 white the other has
>>>>>> 256x256x128. How can I detect if there is missing slices in the series
>>>>>> with 125 slices? What would you recommend me to do? Is is possible to
>>>>>> ask recon-all to bypass this error message and import both series?
>>>>>>
>>>>>> Knut J
>>>>>>
>>>>>> output
>>>>>>
>>>>>> k_ras = (-1, 0, 0)
>>>>>> writing to
>>>>>> /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz...
>>>>>> ERROR: inputs have mismatched dimensions!
>>>>>> /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100
>>>>>> is
>>>>>> 256 x 256 x 125 while
>>>>>> /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235
>>>>>> is
>>>>>> 256 x 256 x 128
>>>>>> Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC
>>>>>> 2012 x86_64 x86_64 x86_64 GNU/Linux
>>>>>>
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