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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>>>>>
>>>>>
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