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_2010@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" greve@nmr.mgh.harvard.edu 收件人： "xiangbo_2010" xiangbo_2010@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" greve@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"<greve@nmr.mgh.harvard.edu> wrote: >yes y.mgh >On 01/04/2013 05:13 PM,xiangbo_2010@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"<greve@nmr.mgh.harvard.edu> >> 收件人：<xiangbo_2010@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_2010@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"<greve@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 >>>>>greve@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 >>>greve@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 >greve@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 greve@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
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" greve@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_2010@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" greve@nmr.mgh.harvard.edu 收件人： "xiangbo_2010" xiangbo_2010@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" greve@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"<greve@nmr.mgh.harvard.edu> wrote: >yes y.mgh >On 01/04/2013 05:13 PM,xiangbo_2010@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"<greve@nmr.mgh.harvard.edu> >> 收件人：<xiangbo_2010@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_2010@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"<greve@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 >>>>>greve@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 >>>greve@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 >greve@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 greve@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 greve@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
Are those 3 numbers the values in the avg.dat file? Why do you think they are volume? In any event, they have the same interpretation as the values in y.mgh
On 1/8/13 8:43 PM, xiangbo_2010 wrote:
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" greve@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_2010@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" greve@nmr.mgh.harvard.edu 收件人： "xiangbo_2010" xiangbo_2010@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" greve@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"<greve@nmr.mgh.harvard.edu> wrote: >yes y.mgh >On 01/04/2013 05:13 PM,xiangbo_2010@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"<greve@nmr.mgh.harvard.edu> >> 收件人：<xiangbo_2010@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_2010@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"<greve@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 >>>>>greve@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 >>>greve@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 >greve@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 greve@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 greve@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
Dear doug In the avg.dat file, where have 61 values which were equal with number of my subjects, however, I used these values in SPSS, there still no signifiant difference, thanks!
Bo Xiang
At 2013-01-09 11:53:15,"Douglas Greve" greve@nmr.mgh.harvard.edu wrote: Are those 3 numbers the values in the avg.dat file? Why do you think they are volume? In any event, they have the same interpretation as the values in y.mgh
On 1/8/13 8:43 PM, xiangbo_2010 wrote:
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" greve@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_2010@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" greve@nmr.mgh.harvard.edu 收件人： "xiangbo_2010" xiangbo_2010@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" greve@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"<greve@nmr.mgh.harvard.edu> wrote: >yes y.mgh >On 01/04/2013 05:13 PM,xiangbo_2010@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"<greve@nmr.mgh.harvard.edu> >> 收件人：<xiangbo_2010@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_2010@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"<greve@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 >>>>>greve@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 >>>greve@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 >greve@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 greve@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/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
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are you positive that the SPSS model is exactly the same as the model in QDEC? You can get the design matrix from Xg.dat
On 1/8/13 11:15 PM, xiangbo_2010 wrote:
Dear doug In the avg.dat file, where have 61 values which were equal with number of my subjects, however, I used these values in SPSS, there still no signifiant difference, thanks! Bo Xiang
At 2013-01-09 11:53:15,"Douglas Greve" greve@nmr.mgh.harvard.edu wrote:
Are those 3 numbers the values in the avg.dat file? Why do you think they are volume? In any event, they have the same interpretation as the values in y.mgh On 1/8/13 8:43 PM, xiangbo_2010 wrote: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"<greve@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_2010@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"<greve@nmr.mgh.harvard.edu> >> 收件人： "xiangbo_2010"<xiangbo_2010@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"<greve@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"<greve@nmr.mgh.harvard.edu> wrote: >>>>> >yes y.mgh >>>>> >On 01/04/2013 05:13 PM,xiangbo_2010@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"<greve@nmr.mgh.harvard.edu> >>>>> >> 收件人：<xiangbo_2010@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_2010@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"<greve@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 >>>>> >>>>>greve@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 >>>>> >>>greve@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 >>>>> >greve@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 >>>greve@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 >greve@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
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xiangbo_2010