Hi,
We were hoping to get these labels listed in FreeSurferColorLUT.txt. Does anyone know of any command lines that would get us this data?
100 Left-wm-intensity-abnormality 124 140 178 0 101 Left-caudate-intensity-abnormality 125 140 178 0 102 Left-putamen-intensity-abnormality 126 140 178 0 103 Left-accumbens-intensity-abnormality 127 140 178 0 104 Left-pallidum-intensity-abnormality 124 141 178 0 105 Left-amygdala-intensity-abnormality 124 142 178 0 106 Left-hippocampus-intensity-abnormality 124 143 178 0 107 Left-thalamus-intensity-abnormality 124 144 178 0 108 Left-VDC-intensity-abnormality 124 140 179 0 109 Right-wm-intensity-abnormality 124 140 178 0 110 Right-caudate-intensity-abnormality 125 140 178 0 111 Right-putamen-intensity-abnormality 126 140 178 0 112 Right-accumbens-intensity-abnormality 127 140 178 0 113 Right-pallidum-intensity-abnormality 124 141 178 0 114 Right-amygdala-intensity-abnormality 124 142 178 0 115 Right-hippocampus-intensity-abnormality 124 143 178 0 116 Right-thalamus-intensity-abnormality 124 144 178 0 117 Right-VDC-intensity-abnormality 124 140 179 0
Thanks, Alyssa
________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, August 05, 2013 10:19 AM To: Zhu, Alyssa Subject: RE: [Freesurfer] Segmentation Abnormalities Label
Hi Alyssa
I don't think we label those explicitly. Presumably you could infer the structure from surrounding labels though (or from spatial priors I guess) Bruce On Mon, 5 Aug 2013, Zhu, Alyssa wrote:
Hi Bruce,
Thanks for the reply.
Sorry if I worded my e-mail badly, but I was actually wondering if there was a way to obtain those labels as we haven't seen them in our stats files. We did get some voxels labeled as non-WM hypointensities, but they are in various parts of the basal ganglia and would have to be manually differentiated (e.g. caudate vs. putamen). Is there some way they could be automatically parcellated into the intensity abnormality labels listed in the FreeSurferColorLUT.txt file. In other words, is there a way we can opt for those parcellations/labels in the recon-all or aparcstats2table commands?
Thanks again, Alyssa
From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, August 02, 2013 7:35 PM To: Zhu, Alyssa Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation Abnormalities Label
Hi Alyssa,
the orbital stuff might be fat that has shifted into brain, for which there's really nothing that can be done except fix the acquisition (change the read-out direction or increase the bandwidth or both). Not sure what's up with the other spot. Is the nearby white matter intensity significantly less than 110? If so, some control points in the wm might help. If not you would need to upload the dataset so we can take a look Bruce
On Sat, 3 Aug 2013, Zhu, Alyssa wrote:
Hi,
Is there a way to get the various intensity abnormality labels (100-117) seen in the FreeSurferColorLUT.txt file (e.g. via a different command line option)? Thus far we've only been getting the WM-hypointensities (77) and non-WM-hypointensities (80) labels. I read in another thread that some labels are no longer used in current versions (my lab is using v5.1). Is that the case here?
Thanks, Alyssa
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