Dear doug
I used the command: mri_segstats --i y.mgh --slabel fsaverage lh
yourlabel.label > --avgwf avg.dat --id 1, and the terminal is
following:
cmdline mri_segstats --i
/media/freesurfer1/CT/qdec/Untitled/y.mgh --slabel fsaverage rh
control_AA_GG_ba.label --avgwf avg.dat --id 1
sysname Linux
hostname psylab-desktop
machine x86_64
user psylab
Constructing seg from label
Loading /media/freesurfer1/CT/qdec/Untitled/y.mgh
Vertex Area is 0.501505 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
0 1 19 6.91357
Reporting on 1 segmentations
Computing spatial average of each frame
0
Writing to avg.dat
From the above result, can be show 'Vertex Area is 0.501505 mm^3'
and the value of my result were 0.752064
0.773072 0.800245, should be the size of volume, not the surface
area. these were my opinion, hope you give me some advice, thanks!
Bo Xiang
At 2013-01-08 09:25:05,"Douglas N Greve"<gr...@nmr.mgh.harvard.edu> wrote:
>
>How do you know it is the volume and not surface area? The values will
>be whatever are in y.mgh, so if y.mgh has surface area, then the output
>will be surface area.
>
>
>On 01/07/2013 07:38 PM,xiangbo_2...@126.com wrote:
>>
>> I used the command:
>> mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label > --avgwf
avg.dat --id 1. Thanks!
>>
>> Bo Xiang
>> 送自我的HTC One SU
>>
>> ----- Reply message -----
>> 发件人： "Douglas N Greve"<gr...@nmr.mgh.harvard.edu>
>> 收件人： "xiangbo_2010"<xiangbo_2...@126.com>,"Freesurfer@nmr.mgh.harvard.edu"
<Freesurfer@nmr.mgh.harvard.edu>
>> 主题： [Freesurfer] 回复: 回复: about ROI to SPSS
>> 日期： 周二, 1 月 8 日, 2013 年 01:51
>>
>>
>>
>>
>>> what was your command line?
>>>
>>> On 01/05/2013 01:43 AM, xiangbo_2010 wrote:
>>>> Dear doug
>>>> Using the command to only obtain the size of volume from every
>>>> subject, however, I want to obtain the size of surface area from every
>>>> subject, what should I do? thanks!
>>>> Bo Xiang
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> At 2013-01-05 13:12:18,"Douglas Greve"<gr...@nmr.mgh.harvard.edu>
wrote:
>>>>
>>>>
>>>> Drawing the ROI as a label is fine. Just don't transfer the label
>>>> to each individual subject. The y.mgh is all the data for all the
>>>> subjects in the fsaverage space (where the label is defined). You
>>>> can use mri_segstats, something like
>>>>
>>>> mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label
>>>> --avgwf avg.dat --id 1
>>>>
>>>> avg.dat will have one column and number of rows equal to the
>>>> number of subjects
>>>>
>>>> doug
>>>>
>>>>
>>>> On 1/4/13 11:20 PM, xiangbo_2010 wrote:
>>>>> Dear doug
>>>>> I am sorry to disturb you again, I still do not know how to
>>>>> direct obtain the label of two significant clusters, is not to
>>>>> draw the ROI? thanks!
>>>>> Bo Xiang
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> At 2013-01-05 06:49:14,"Douglas N
Greve"<gr...@nmr.mgh.harvard.edu> wrote:
>>>>> >yes y.mgh
>>>>> >On 01/04/2013 05:13 PM,xiangbo_2...@126.com wrote:
>>>>> >> Do you mean input the file of y.mgh to mri_glmfit and run?
Thanks!
>>>>> >> Bo Xiang
>>>>> >> 发送自我的HTC One SUJ
>>>>> >>
>>>>> >> ----- Reply message -----
>>>>> >> 发件人： "Douglas N Greve"<gr...@nmr.mgh.harvard.edu>
>>>>> >> 收件人：<xiangbo_2...@126.com>
>>>>> >> 抄送： "freesurfer"<freesurfer@nmr.mgh.harvard.edu>
>>>>> >> 主题： [Freesurfer] 回复: about ROI to SPSS
>>>>> >> 日期： 周六, 1 月 5 日, 2013 年 05:48
>>>>> >>
>>>>> >>
>>>>> >>
>>>>> >>
>>>>> >>> That technique can yield inconsistent results when the ROI
is small (as
>>>>> >>> in your case). You are better off extracting the data
directly from the
>>>>> >>> input to mri_glmfit. This is created by QDEC and is called
y.mgh. This
>>>>> >>> will be a file with number of frames equal to the number of
subjects.
>>>>> >>>
>>>>> >>> doug
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>>>> >>> On 01/04/2013 04:13 PM,xiangbo_2...@126.com wrote:
>>>>> >>>> I drawing two ROIs in two clusters, and mapping two labels
to all subjects, following extract the average surface area of two ROIs from every subject. Anyway,
whether have command to direct obtain the label of two clusters, not to drawing the ROIs from these
clusters, then there have exactly data to be obtained. Thanks!
>>>>> >>>> Ho Xiang
>>>>> >>>>
>>>>> >>>> 发送自我的HTC One SU
>>>>> >>>>
>>>>> >>>> ----- Reply message -----
>>>>> >>>> 发件人： "Douglas N Greve"<gr...@nmr.mgh.harvard.edu>
>>>>> >>>> 收件人：<freesurfer@nmr.mgh.harvard.edu>
>>>>> >>>> 主题： [Freesurfer] about ROI to SPSS
>>>>> >>>> 日期： 周六, 1 月 5 日, 2013 年 02:42
>>>>> >>>>
>>>>> >>>>
>>>>> >>>>
>>>>> >>>>
>>>>> >>>>> Hi Bo, you need to make sure that you have exactly the
same design
>>>>> >>>>> matrix in SPSS. The design matrix for qdec is Xg.dat in
the output
>>>>> >>>>> directory. How did you extract the data out of the ROIs?
>>>>> >>>>>
>>>>> >>>>> doug
>>>>> >>>>>
>>>>> >>>>>
>>>>> >>>>>
>>>>> >>>>> On 01/02/2013 11:46 PM, xiangbo_2010 wrote:
>>>>> >>>>>> Dear experts
>>>>> >>>>>> I has obtained two ROIs (corrected FDR) difference
between AA and
>>>>> >>>>>> GG regressing out the effect of age and gender using the
QDEC with
>>>>> >>>>>> attachment, following extract the average surface area of
two ROIs to
>>>>> >>>>>> analysis using SPSS, in which I used the
>>>>> >>>>>> Univariate Analysis of Variance to find the difference
between AA and
>>>>> >>>>>> GG, gender and age as covariates, but find that there no
significant
>>>>> >>>>>> in these ROIs, I want to know why there were significant
difference in
>>>>> >>>>>> QDEC, but no significant difference in SPSS? I hope that
have experts
>>>>> >>>>>> to help me, thanks!
>>>>> >>>>>> Bo Xiang
>>>>> >>>>>>
>>>>> >>>>>>
>>>>> >>>>>>
>>>>> >>>>>>
>>>>> >>>>>>
>>>>> >>>>>>
>>>>> >>>>>> _______________________________________________
>>>>> >>>>>> 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: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
>>>>> >>>>>
>>>>> >>>>>
>>>>> >>>>> 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.
>>>>> >>>>>
>>>>> >>>>
>>>>> >>> --
>>>>> >>> 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: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
>>>>> >>
>>>>> >>
>>>>> >
>>>>> >--
>>>>> >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:www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>>>
>Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>>> >
>>>>>
>>>>>
>>>>
>>>>
>>> --
>>> 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: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
>>
>>
>
>--
>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: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
