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r03ert0 / brainspell

brainspell is a web platform to facilitate the creation of an open, human-curated, classification of the neuroimaging literature
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range of nifti volumes #2

Open pbellec opened 9 years ago

pbellec commented 9 years ago

I just downloaded the nifti volume from the "MCI" query, and the range is weird (max is something like 50000). I may not understand what this map represents, but I thought it was a simple average of binary volumes (full of spheres). Is the range right ? Is so, what does it represent ?

r03ert0 commented 9 years ago

what are you using to read the .nii files? the .nii maps are the sum of locations mapping each voxel. I downloaded the one for MCI, which was made out of 63 articles, and the maximum was 74 (remember that there are sometimes >1 experiment per article). For Alzheimer, the max I get 140.

On Mon, Oct 20, 2014 at 9:45 PM, Pierre Bellec notifications@github.com wrote:

I just downloaded the nifti volume from the "MCI" query, and the range is weird (max is something like 50000). I may not understand what this map represents, but I thought it was a simple average of binary volumes (full of spheres). Is the range right ? Is so, what does it represent ?

— Reply to this email directly or view it on GitHub https://github.com/r03ert0/brainspell/issues/2.

pbellec commented 9 years ago

I use MRIcron. The max gets set at around 50000.

Pierre Bellec http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec Telephone (1) 514 713 5596 SIMEXP lab http://simexp-lab.org

On Mon, Oct 20, 2014 at 4:43 PM, Roberto Toro notifications@github.com wrote:

what are you using to read the .nii files? the .nii maps are the sum of locations mapping each voxel. I downloaded the one for MCI, which was made out of 63 articles, and the maximum was 74 (remember that there are sometimes >1 experiment per article). For Alzheimer, the max I get 140.

On Mon, Oct 20, 2014 at 9:45 PM, Pierre Bellec notifications@github.com wrote:

I just downloaded the nifti volume from the "MCI" query, and the range is weird (max is something like 50000). I may not understand what this map represents, but I thought it was a simple average of binary volumes (full of spheres). Is the range right ? Is so, what does it represent ?

— Reply to this email directly or view it on GitHub https://github.com/r03ert0/brainspell/issues/2.

— Reply to this email directly or view it on GitHub https://github.com/r03ert0/brainspell/issues/2#issuecomment-59836399.[image: Web Bug from https://github.com/notifications/beacon/1670887__eyJzY29wZSI6Ik5ld3NpZXM6QmVhY29uIiwiZXhwaXJlcyI6MTcyOTQ1Njk5OCwiZGF0YSI6eyJpZCI6NDYzNjM4Mzh9fQ==--7de7da17be94336545bd6b5470503fee12960e10.gif] {"@context":"http://schema.org","@type":"EmailMessage","description":"View this Issue on GitHub","action":{"@type":"ViewAction","url":" https://github.com/r03ert0/brainspell/issues/2#issuecomment-59836399","name":"View Issue"}}

r03ert0 commented 9 years ago

Hmm. I just checked with MRIcron, and the max was at 54979.109, which I thought was curious because the volume is encoded using shorts (int16 integers) and values can't have decimals. I found that MRICron is changing the 'slope' value for the image intensity to 3118 (I didn't find how to change it). It would be possible that brainspell is writing a bogus slope. To rule out that out, I used fslhd to print the mci.brainspell.nii file, and the slope value is not set. Here's the complete header

sizeof_hdr 348 data_type INT16 dim0 4 dim1 45 dim2 54 dim3 45 dim4 1 dim5 0 dim6 0 dim7 0 vox_units Unknown time_units Unknown datatype 4 nbyper 2 bitpix 16 pixdim0 0.0000000000 pixdim1 4.0000000000 pixdim2 4.0000000000 pixdim3 4.0000000000 pixdim4 1.0000000000 pixdim5 0.0000000000 pixdim6 0.0000000000 pixdim7 0.0000000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 0.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Unknown qform_code 0 qto_xyz:1 4.000000 0.000000 0.000000 0.000000 qto_xyz:2 0.000000 4.000000 0.000000 0.000000 qto_xyz:3 0.000000 0.000000 4.000000 0.000000 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Unknown sform_code 0 sto_xyz:1 0.000000 0.000000 0.000000 0.000000 sto_xyz:2 0.000000 0.000000 0.000000 0.000000 sto_xyz:3 0.000000 0.000000 0.000000 0.000000 sto_xyz:4 0.000000 0.000000 0.000000 0.000000 sform_xorient Unknown sform_yorient Unknown sform_zorient Unknown file_type NIFTI-1+ file_code 1 descrip generated by rto aux_file none

On Mon, Oct 20, 2014 at 10:51 PM, Pierre Bellec notifications@github.com wrote:

I use MRIcron. The max gets set at around 50000.