Thanks.
***********************************************
John E. Richards
Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC 29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: [log in to unmask]
<applewebdata:[log in to unmask]>
HTTP: jerlab.psych.sc.edu
*************************************************
On 1/17/13 12:11 PM, "Mark Jenkinson" <[log in to unmask]> wrote:
>Dear John,
>
>Yes, you can just take the unscaled nifti image (the one created by
>fslchfiletype) and multiply the values with fslmaths to scale them
>correctly (this will stored the scaled values directly, and not the
>unscaled ones together with a scaling factor, but I think storing the
>scaled values is less error prone). To figure out the scaling factor you
>should be able to use fslhd on the Analyze file and extract the funused1
>value (if I remember rightly this is what SPM interpreted as the scaling
>slope).
>
>All the best,
> Mark
>
>
>On 17 Jan 2013, at 16:47, "RICHARDS, JOHN" <[log in to unmask]>
> wrote:
>
>> Thanks for the info. However, it appears that fslchfiletype also
>>ignores
>> the scl_ values in the *.hdr and presumes they are 1.0, 0. I am
>> converting them to nifti, but get them from the software in ANALYZE
>>format
>> with no option for nifti output.
>>
>> I am able to modify them with other software, but could these be altered
>> after fslchfiletype conversion by a fsl utility?
>>
>> John
>>
>> ***********************************************
>> John E. Richards
>> Carolina Distinguished Professor
>> Department of Psychology
>> University of South Carolina
>> Columbia, SC 29208
>> Dept Phone: 803 777 2079
>> Fax: 803 777 9558
>> Email: [log in to unmask]
>>
>><applewebdata:[log in to unmask]
>>>
>> HTTP: jerlab.psych.sc.edu
>> *************************************************
>>
>>
>>
>>
>>
>> On 1/17/13 8:55 AM, "Mark Jenkinson" <[log in to unmask]>
>>wrote:
>>
>>> Hi,
>>>
>>> It is definitely the case that Analyze images are not sufficiently
>>> standardised that all packages treat them equally. That is why the
>>>nifti
>>> format was created. We strongly encourage people to use nifti when
>>> possible in order to avoid such trouble. If you are forced to use
>>> Analyze then I would convert them into NIFTI as the first stage in your
>>> FSL processing (you can use fslchfiletype) and correct for the scaling
>>> errors at this stage (if there are any, since it should be consistently
>>> applied or not for all images).
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>>
>>> On 17 Jan 2013, at 01:11, "RICHARDS, JOHN" <[log in to unmask]>
>>> wrote:
>>>
>>>> One further thought on this. Apparently the ANALYZE 7.5 format does
>>>>not
>>>> define the scl_slope and scl_intercept values; these apparently were
>>>> first
>>>> used by SPM and became part of the NIFTI definition. Perhaps when fsl
>>>> utils are using *.hdr/*.img files defined as ANALYZE files, it ignores
>>>> these. I have found the fslmaths will use the scl_slope and
>>>> scl_intercept
>>>> if the file is a nii.gz file.
>>>>
>>>> Is this the reason?
>>>>
>>>> John
>>>>
>>>>
>>>>
>>>>
>>>> On 1/16/13 7:15 PM, "RICHARDS, JOHN" <[log in to unmask]> wrote:
>>>>
>>>>> I have ANALYZE MRI volumes from CURRY that have current density,
>>>>>which
>>>>> are
>>>>> values < 1. The HDR has "calibration scaling" set. When I use
>>>>>fslhd,
>>>>> or
>>>>> fslmaths, or fslmerge, with these files, it appears to not read the
>>>>> calibration scaling. ANALYZE/NIFTII has a calibration intercept and
>>>>> scale that is supposed to be applied to the store values. MRICRON
>>>>> reads
>>>>> these files correctly, shows the calibration scaling, and has voxel
>>>>> values
>>>>> with the scaling. If I use:
>>>>>
>>>>> Fslmaths inputfile.hdr -add 0 outputfile.nii.gz, then the scaling
>>>>> factor
>>>>> is not read; the fslstats -M reports a value that appears to be about
>>>>> x*scale, and when I view this in MRICron the individual voxels in the
>>>>> input file, * scale, are what are shown in the output file.
>>>>>
>>>>> So it appears the fsl utils are not reading the calibration scale.
>>>>>
>>>>> Any help?
>>>>>
>>>>> John
>>>>>
>>>>> ***********************************************
>>>>> John E. Richards
>>>>> Carolina Distinguished Professor
>>>>> Department of Psychology
>>>>> University of South Carolina
>>>>> Columbia, SC 29208
>>>>> Dept Phone: 803 777 2079
>>>>> Fax: 803 777 9558
>>>>> Email: [log in to unmask]
>>>>>
>>>>>
>>>>><applewebdata:[log in to unmask]
>>>>>ed
>>>>> u>
>>>>> HTTP: jerlab.psych.sc.edu
>>>>> *************************************************
>>>>>
>>>>>
>>>>>>
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