>
> On 04/24/2014 09:40 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks again for your help. I had two questions that came up from doing
>> some preliminary analysis with the mri_segstats:
>>
>> 1) When running the mri_segstats command with --seg
>> aparc+aseg_nocortex.mgz (which is the result of the matlab code you
>> provided below) and with --seg wmparc.mgz, even though the average
>> intensity is very close to each other, the individual intensities of
>> same
>> structures are different. For instance
>> Left-Cerebral-White-Matter has an intensity of 145.3869 +/- 21.6883 with
>> --seg aparc+aseg_nocortex.mgz and an intensity of 149.6910 +/- 15.6547
>> with --aseg wmparc.mgz. Also the number of voxels of the same structure
>> is
>> different in each case. Is there a reason why this is happening?
> what are your command lines?
>>
The commands are:
mri_segstats --seg <subj_ID_path>/mri/aparc+aseg_nocortex.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum
<subj_ID_path>/stats/int.aparc+aseg_nocortex.sum --in
<subj_ID_path>/mri/orig.mgz
and
mri_segstats --seg <subj_ID_path>/mri/wmparc.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum
<subj_ID_path>/stats/int.wmparc.sum --in <subj_ID_path>/mri/orig.mgz
>> 2) If I want to include the wm parcellation map to calculate the mean
>> intensity, I am assuming that wmparc.mgz would be the correct
>> segmentation
>> volume to use, right?
> mean intensity of what?
>>
The mean intensity of orig.mgz.
>> 3) If the answer to (2) is yes, and if I wanted to measure the average
>> intensity with --seg wmparc.mgz but after excluding the cortex, should I
>> run with --seg wmparc.mgz and just not take into consideration all the
>> *-ctx-* parcellations that come up in the stats file, or is there a way
>> to
>> remove the cortex from wmparc.mgz and then run mri_segstats with the
>> wmparc_nocortex.mgz file as the --seg (I tried to subtract a binary map
>> of
>> the cortex from wmparc.mgz, but had no luck: maybe I was doing something
>> wrong.)
>>
>> Thanks in advance for your help!
>>
>> Best,
>> Panos
>>
>>
>>
>>
>>> You can just do it in matlab, somethhing like
>>>
>>> a = MRIread('aparc+aseg.mgz');
>>> ind = find(a.vol > 999);
>>> a.vol(ind) = 0;
>>> MRIwrite(a,'nocortex.mgz')
>>>
>>>
>>>
>>> On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
>>>> Hi Doug,
>>>>
>>>> I'm sorry, what I meant to ask in the previous question is whether
>>>> there
>>>> is a way to come up with a segmentation volume for the mri_segstats
>>>> command that is exactly like aseg.mgz but that does not include the
>>>> cortex. The reason I'm asking is because by using the aseg.mgz volume
>>>> in
>>>> the --seg flag, you're also incorporating the intensity of the cortex
>>>> when
>>>> measuring the mean intensity of orig.mgz, but I wanted to see if there
>>>> was
>>>> a way to calculate the mean intensity of orig.mgz but without
>>>> incorporating the intensity of the cortex.
>>>>
>>>> Thanks again,
>>>> Panos
>>>>
>>>>> If you want the volume of cortex, you should definitely not use
>>>>> aseg.mgz. aparc+aseg is better, but the best is to use the
>>>>> surface-based
>>>>> measure found in aseg.stats
>>>>>
>>>>> doug
>>>>>
>>>>> On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote:
>>>>>> Hi Doug,
>>>>>>
>>>>>> Thanks again for your reply. One last question: The aseg.mgz file
>>>>>> includes
>>>>>> the cortex as well. If I want to extract the cortex from the
>>>>>> aseg.mgz
>>>>>> file, should I binarize both the aseg.mgz and aparc_aseg.mgz files
>>>>>> and
>>>>>> subtract them, and then use the result in the mri_segstats command,
>>>>>> or
>>>>>> is
>>>>>> there a different way?
>>>>>>
>>>>>> Thanks,
>>>>>> Panos
>>>>>>
>>>>>>> On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
>>>>>>>> Hi Doug,
>>>>>>>>
>>>>>>>> Thanks for the quick reply! In addition:
>>>>>>>>
>>>>>>>> 1) The average intensity measure in the above example does not
>>>>>>>> include
>>>>>>>> the
>>>>>>>> intensity of the skull, just everything inside, right?
>>>>>>> It includes all the structures that are segmented in seg. If there
>>>>>>> is
>>>>>>> not a skull segmentation, then it will not be in the output list.
>>>>>>>> 2) Just to be clear on the purpose of including the segmentations
>>>>>>>> in
>>>>>>>> the
>>>>>>>> command line: The segmentations only specify the areas of the
>>>>>>>> brain
>>>>>>>> that
>>>>>>>> you would like to measure the intensity on, but besides that they
>>>>>>>> don't
>>>>>>>> provide any intensity info by themselves, would that be correct?
>>>>>>>> That
>>>>>>>> is
>>>>>>>> the purpose of the --i flag, right?
>>>>>>> Correct
>>>>>>> doug
>>>>>>>> Thanks again for your help,
>>>>>>>> Panos
>>>>>>>>
>>>>>>>>> On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote:
>>>>>>>>>> Hi FS community,
>>>>>>>>>>
>>>>>>>>>> I had some questions regarding the mri_segstats command:
>>>>>>>>>>
>>>>>>>>>> 1) In the excludeid flag, are the ids the ones shown in the
>>>>>>>>>> FreeSurferColorLUT.txt?
>>>>>>>>> Yes
>>>>>>>>>> 2) In case I would like to measure the mean intensity of the
>>>>>>>>>> orig
>>>>>>>>>> file
>>>>>>>>>> as
>>>>>>>>>> outlined in the second example in
>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats:
>>>>>>>>>>
>>>>>>>>>> mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg
>>>>>>>>>> --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt
>>>>>>>>>> --nonempty --excludeid 0 --sum bert.aseg.sum
>>>>>>>>>> --in $SUBJECTS_DIR/bert/mri/orig
>>>>>>>>>>
>>>>>>>>>> is the --seg flag necessary in order to calculate only the mean
>>>>>>>>>> intensity
>>>>>>>>>> within the skull, or does it serve another purpose?
>>>>>>>>> The seg defines the segmentations (eg, 17 is hippocampus)
>>>>>>>>>
>>>>>>>>>> Thanks in advance,
>>>>>>>>>> Panos
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Freesurfer mailing list
>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Freesurfer mailing list
>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>> --
>>>>> Douglas N. Greve, Ph.D.
>>>>> MGH-NMR Center
>>>>> gr...@nmr.mgh.harvard.edu
>>>>> Phone Number: 617-724-2358
>>>>> Fax: 617-726-7422
>>>>>
>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>>> Outgoing:
>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
