mri_segstats also has a --mask option. It will exclude anything not in
the mask. There are a few mask options like setting thresholds, etc
doug
On 1/28/15 4:17 PM, Ben Eliezer, Noam wrote:
Dear Doug —
Your suggestion worked perfectly.
I’ve loaded the segmentation data (aparc+aseg.mgz) and t
Dear Doug —
Your suggestion worked perfectly.
I’ve loaded the segmentation data (aparc+aseg.mgz) and the registered T2 maps
into MATLAB and was able to detect a few outliers that biased the
standard-deviation of the statistics.
I’ll apply the same approach to collect statistics for the rest of
On 1/27/15 1:56 PM, Ben Eliezer, Noam wrote:
The maps were generated by Siemens scanner, fitting a multi-spin-echo
protocol.
I see your point, though. The values should not range between 0 to
4000. The latter 4000 value is the background out-of-brain map value.
But when looking at the T2_siem
The maps were generated by Siemens scanner, fitting a multi-spin-echo protocol.
I see your point, though. The values should not range between 0 to 4000. The
latter 4000 value is the background out-of-brain map value.
But when looking at the T2_siemens_reg.mgz, overlaid on the aparc+aseg.mgz in
f
It is finding 0s in the T2 (the range is 0-4000). I'm not sure about the
4000, but the 0s indicate that something is strange with that image. How
was it created?
On 1/27/15 1:22 PM, Ben Eliezer, Noam wrote:
— I (think that) I am not really interested in converting into rawavg
coordinate syst
— I (think that) I am not really interested in converting into rawavg
coordinate system, but just need to register my T2 maps to the segmentation
maps.
So, I guess that aseg+aparc.mgz will suffice in my case
— Regarding the mean +- std values:
Yes - the T2 maps are whole brain. could that accoun
On 1/27/15 12:38 PM, Ben Eliezer, Noam wrote:
Thanks Doug.
I’ve made two changes to the set of commands.
*1.* Following your suggestion, I’ve shifted from --init-spm to
--init-header and now tkregister2 shows that the registration is OK.
>>tkregister2 --mov T2_siemens.mgz --reg T2_siemens_r
Thanks Doug.
I’ve made two changes to the set of commands.
1. Following your suggestion, I’ve shifted from --init-spm to --init-header and
now tkregister2 shows that the registration is OK.
>> tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf
Thanks!
2. When loading the resul
First off, I would use --init-header instead of --init-spm. Probably
won't make a difference, but it is safer in this case. Second, look at
the registration in tkregister (bbregister prints out the command line,
you can just cut and paste).
doug
ps. Please remember to post the list instead o
On 1/27/15 2:11 AM, Ben Eliezer, Noam wrote:
Hello ---
I'm trying to extract quantitative T2 values for different brain segments.
I've converted my T2 set of DICOMs to .mgz format using mri_convert
and loaded them into freeview.
>> mri_convert -it siemens_dicom -ot mgz
T2_maps_Dir/slice_1_T2_
Hello —
I’m trying to extract quantitative T2 values for different brain segments.
I’ve converted my T2 set of DICOMs to .mgz format using mri_convert and loaded
them into freeview.
>> mri_convert -it siemens_dicom -ot mgz T2_maps_Dir/slice_1_T2_map.dcm
>> T2_in_mgz.mgz
After loading T2_in_mgz.
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