[Freesurfer] about the ROI
Dear experts I had obtained the ROI label from Freesurfer, the following I want to obtain the FA value from DTI in this ROI, what should I do? Thanks! Bo Xiang___ 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.
Re: [Freesurfer] about the ROI
Dear doug I still do not know how to change the roi label to roi which is used in DTI? Thanks! Bo Xiang At 2012-12-17 02:06:53,"Douglas Greve" wrote: Hi Bo, look at the multimodal integration tutorial on our wiki; there is an example of just this. You will need to register your dti with the anatomical (bbregister), then run mri_segstats using the registration matrix and the FA volume. doug On 12/16/12 12:32 AM, xiangbo_2010 wrote: Dear experts I had obtained the ROI label from Freesurfer, the following I want to obtain the FA value from DTI in this ROI, what should I do? Thanks! Bo Xiang ___ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://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.
Re: [Freesurfer] about the ROI
Dear doug My roi was obtained by drawing after the analysis in freesurfer. Thanks! Bo Xiang At 2012-12-17 02:06:53,"Douglas Greve" wrote: Hi Bo, look at the multimodal integration tutorial on our wiki; there is an example of just this. You will need to register your dti with the anatomical (bbregister), then run mri_segstats using the registration matrix and the FA volume. doug On 12/16/12 12:32 AM, xiangbo_2010 wrote: Dear experts I had obtained the ROI label from Freesurfer, the following I want to obtain the FA value from DTI in this ROI, what should I do? Thanks! Bo Xiang ___ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://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.
[Freesurfer] about ROI
Dear experts I has obtained the ROI by analysis, I want to obtain the label of this ROI, whether has the command to direct keep label, not drawing this ROI? thanks! Bo Xiang___ 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.
[Freesurfer] 回复: about ROI to SPSS
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" 收件人： 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. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 回复: 回复: about ROI to SPSS
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" 收件人： 抄送： "freesurfer" 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" > > 收件人： > > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] 回复: 回复: 回复: about ROI to SPSS
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" 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" >> 收件人： "xiangbo_2010" , "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" 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" >>>>> 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" >>>>> >> 收件人： >>>>> >> 抄送： "freesurfer" >>>>> >> 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
Re: [Freesurfer] 回复: 回复: 回复: about ROI to SPSS
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" 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" 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" >> 收件人： "xiangbo_2010" , "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" 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" >>>>> 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" >>>>> >> 收件人： >>>>> >> 抄送： "freesurfer" >>>>> >> 主题： [Freesurfer] 回复: about ROI to SPSS >>>>> >> 日期： 周六, 1 月 5 日, 2013 年 05:48 >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> >>> That techniqu
[Freesurfer] Analysis ROI between two levels
发送自我的HTC One SU - Forwarded message - 发件人： "xiangbo_2010" 收件人： "MCLAREN, Donald" 抄送： 主题： [Freesurfer] contrast matrix 日期： 周二, 12 月 11 日, 2012 年 20:08 Dear experts I had obtained a ROI through the interaction between factor 1(A,B) and factor 2(C,D,E), the following: I want to detect the difference between C and D in this ROI. Whether it was done using Freesurfer? thanks! Bo Xiang At 2012-12-02 05:24:18,"MCLAREN, Donald" wrote: >Bo Xiang got the following Error Message. Attached are the mtx and >fsgd file. Does anyone what caused the error? > >> >>On Fri, Nov 30, 2012 at 8:28 AM, xiangbo_2010 wrote: >>> Dear Donald McLaren >>> >>>I used the contrast to run, but the error is appear: >>> >>> mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd COMTthreeinteryes.fsgd >>> dods --C COMTthreeinteryes.mtx --surf fsaverage rh --cortex --glmdir >>> lh.COMTthree.glmdir >>> >>> gdfReadHeader: reading COMTthreeinteryes.fsgd >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >>> Continuous Variable Means (all subjects) >>> 0 age 26.2227 11.3891 >>> Class Means of each Continuous Variable >>> 1 MAC 23.9333 >>> 2 MAD 23.5455 >>> 3 MAE 24.5000 >>> 4 MBC 28.6923 >>> 5 MBD 26.3158 >>> 6 MBE 30.3750 >>> 7 FAC 24.1707 >>> 8 FAD 26.4643 >>> 9 FAE 25.0909 >>> 10 FBC 25.9130 >>> 11 FBD 31.5217 >>> 12 FBE 34. >>> INFO: gd2mtx_method is dods >>> Reading source surface /media/freesurfer1/CT/fsaverage/surf/rh.white >>> Number of vertices 163842 >>> Number of faces327680 >>> Total area 65020.765625 >>> AvgVtxArea 0.396850 >>> AvgVtxDist 0.717994 >>> StdVtxDist 0.193566 >>> >>> $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ >>> cwd /media/freesurfer1/CT >>> cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd >>> COMTthreeinteryes.fsgd dods --C COMTthreeinteryes.mtx --surf fsaverage rh >>> --cortex --glmdir lh.COMTthree.glmdir >>> sysname Linux >>> hostname psylab-desktop >>> machine x86_64 >>> user psylab >>> FixVertexAreaFlag = 1 >>> UseMaskWithSmoothing 1 >>> OneSampleGroupMean 0 >>> y/media/freesurfer1/CT/lh.gender_age.thickness.10.mgh >>> logyflag 0 >>> usedti 0 >>> FSGD COMTthreeinteryes.fsgd >>> labelmask /media/freesurfer1/CT/fsaverage/label/rh.cortex.label >>> maskinv 0 >>> glmdir lh.COMTthree.glmdir >>> IllCondOK 0 >>> ReScaleX 1 >>> DoFFx 0 >>> Creating output directory lh.COMTthree.glmdir >>> Loading y from /media/freesurfer1/CT/lh.gender_age.thickness.10.mgh >>> INFO: gd2mtx_method is dods >>> Saving design matrix to lh.COMTthree.glmdir/Xg.dat >>> Normalized matrix condition is 82.694 >>> Matrix condition is 73313.7 >>> Found 149926 points in label. >>> Pruning voxels by thr: 0.00 >>> Found 149926 voxels in mask >>> Saving mask to lh.COMTthree.glmdir/mask.mgh >>> Reshaping mriglm->mask... >>> search space = 74490.928733 >>> MatrixReadTxT: could not scan value [3][1] >>> >>> ERROR: loading C COMTthreeinteryes.mtx >>> >>> thanks! >>> >>> Bo Xiang >>> >>> >>> >>> >>> >>> At 2012-11-30 06:25:12,"MCLAREN, Donald" wrote: >>>>Yes. >>>> >>>>Best Regards, Donald McLaren >>>>= >>>>D.G. McLaren, Ph.D. >>>>Research Fellow, Department of Neurology, Massachusetts General Hospital >>>> and >>>>Harvard Medical School >>>>Postdoctoral Research Fellow, GRECC, Bedford VA >>>>Website: http://www.martinos.org/~mclaren >>>>Office: (773) 406-2464 >>>>= >>>>This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED >>>>HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >>>>intended only for the use of the individual or entity named above. If the >>>>reader of the e-mail is not the intended recipient or the employee or agent >>>>responsible for delivering it to the intended recipient, you are hereby >>>>notified that you are in possession of confidential and privileged >>>>information. Any unauthorized use, disclosure, copying or the
[Freesurfer] mean cluster surface area in qdec
Dear Freesurfer Experts, I would like the mean surface area measures of each cluster i found in qdec. I used qdec for a group comparison in surface area between a patient group and a healthy control group. I found 4 different significant clusters (FDR corrected). I would like to extract the mean surface area of each significant cluster in the patient group and in the healthy control group. Where can i found the file with this information? Many thanks, Bo Xiang ___ 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.
[Freesurfer] mean cluster surface area in mri_glmfit
Dear Freesurfer Experts, I would like the mean surface area measures of each cluster i found using command line (mri_glmfit). I used mri_glmfit for a group comparison in surface area between a patient group and a healthy control group. I found 4 different significant clusters (using FDR corrected, is not Clusterwise Correction for Multiple Comparisons). I would like to extract the mean surface area of each significant cluster in the patient group and in the healthy control group. Where can i found the file with this information? thanks! Bo Xiang ___ 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.
Re: [Freesurfer] 回复: about ROI to SPSS
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, 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 difference in this ROIs which from region to region, and the other is significant difference between AA and GG, I do not know whether these different result were influenced from region to region? I hope that have experts to help me, thanks! Bo Xiang At 2013-01-05 05:13:21,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" >收件人： >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. >> ___ 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.
[Freesurfer] contrast matrix
Dear Prof Donald McLaren
I am sorry to disturb you! I have four discrete variables {factor 1(A,B),
factor 2(C,D), factor 3(E,F), and gender(M,F)} and a continuous variable (age),
I want to use the GLM to analysis the result of the interaction among factor
1(A,B), factor 2(C,D) and factor 3(E,F) regressing out the effect of gender and
age, and how to make the contrast? thank you very much!
look forward your reply!
Bo Xiang
At 2012-11-21 04:07:37,"MCLAREN, Donald" wrote:
>On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve
> wrote:
>> Thanks Donald. Is this the standard way to do this? I had used 8 rows
>> instead of 4 with the difference being that 8 rows gives you an opportunity
>> to look for an effect in males OR females.
>
>Yes. Having 8 rows would tell you if you have an interaction between
>factor 1 and 2 in either males or females. My 4 rows only tell you if
>the interaction exists. Technically speaking, one would run the
>three-way interaction first. If nothing existed then you do the
>two-way interaction as I suggested. If there is a three-way
>interaction, then you would use Doug's approach of the interaction in
>either males or females.
>
>If there is an effect in both
>> males and females but the effects go in opposite directions, then the 4 row
>> implementation will resolve to 0 (no effect). Or am I misunderstanding
>> something (again:)?
>
>Nope. You are right. If the male and female effects are different,
>then they could cancel each other out. If you suspect this to be the
>case, then you should be able to demonstrate a three-way interaction.
>
>> thanks!
>> doug
>>
>>
>> On 11/20/2012 01:50 PM, MCLAREN, Donald wrote:
>>>
>>> Bo,
>>>
>>> Doug asked me to chime in on your issue. Here are some points that you
>>> (and others) will hopefully find useful.
>>>
>>> (1) Inferences are two-step process. First, you create and estimate
>>> the design matrix. Every column in the design matrix accounts can
>>> account for some of the variance in the data. Second, you have
>>> contrasts that allow you to infer specific effects. Because the model
>>> contains your covariates, you are always controlling for the
>>> covariates and by extension any factor/covariate not in the contrast.
>>>
>>> (2) Forming contrasts is often the most difficult thing to do. I
>>> assume that your three factors (1, 2, and gender) are all
>>> between-subject factors. If one of them is a within-subject factor
>>> please let me know and disregard the rest of the email. The final
>>> F-contrast will have 4 rows (factor 1 levels-1)*(factor 2 levels
>>> -1)=(3-1)*(3-1)=2*2=4
>>>
>>> The following is an outline for creating contrasts:
>>> (a) Start simple - difference between levels of 1 factor
>>> (b) Define your null hypothesis: AO=AP=AQ
>>> (c) Make it equal to 0: AO-AP=0 AND AP-AQ=0
>>> (d) Repeat for the other levels of the factor...
>>> BO-BP=0 AND BP-BQ=0
>>> CO-CP=0 AND CP-CQ=0
>>>
>>> (e) Now combine them AO-AP=BO-BP=CO-CP AND AP-AQ=BP-BQ=CP-CQ
>>>
>>> (f) Make them equal to 0:
>>> AO-AP-BO+BP=0
>>> BO-BP-CO+CP=0
>>> AP-AQ-BP+BQ=0
>>> BP-BQ-CP+CQ=0
>>>
>>> (g) Expand them to include gender, for example:
>>> AO-AP-BO+BP=0 becomes FAO-FAP-FBO+FBP+MAO-MAP-MBO+MBP=0
>>>
>>> Since the contrast now has 2 columns per level, you should divide all
>>> values by 2. This will produce the correct amplitude and statistics.
>>> If you leave the values as 1 and -1, then you will have an incorrect
>>> amplitude, but the statistics will still be correct.
>>>
>>> (h) Fill in the respective columns of your design matrix.
>>>
>>> (3) The degrees of freedom are defined based on the rows of the
>>> F-matrix and the number of rows in the design matrix. The F-test has a
>>> numerator and denominator degrees of freedom. F(n,d).
>>>
>>> Best Regards, Donald McLaren
>>> =
>>> D.G. McLaren, Ph.D.
>>> Research Fellow, Department of Neurology, Massachusetts General Hospital
>>> and
>>> Harvard Medical School
>>> Postdoctoral Research Fellow, GRECC, Bedford VA
>>> Website: http://www.martinos.org/~mclaren
>>> Office: (773) 406-2464
>>> =
>>> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
>>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
>>> intended only for the
[Freesurfer] Linear Mixed modal
Dear experts Whether can the design of contrast in freesurfer 5.2 the same as SPM? it is difficult to make the contrast in freesurfer if the categorical variables were much more, specifically compute the interaction or F-test in study. Thanks！ Bo Xiang ___ 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.
[Freesurfer] contrast matrix
~mclaren >>> Office: (773) 406-2464 >>> = >>> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED >>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >>> intended only for the use of the individual or entity named above. If the >>> reader of the e-mail is not the intended recipient or the employee or >>> agent >>> responsible for delivering it to the intended recipient, you are hereby >>> notified that you are in possession of confidential and privileged >>> information. Any unauthorized use, disclosure, copying or the taking of >>> any >>> action in reliance on the contents of this information is strictly >>> prohibited and may be unlawful. If you have received this e-mail >>> unintentionally, please immediately notify the sender via telephone at >>> (773) >>> 406-2464 or email. >>> >>> >>> On Tue, Nov 20, 2012 at 8:17 AM, xiangbo_2010 >>> wrote: >>>> >>>> Dear doug >>>> Thank you for your reply! >>>> +AOM -BOM -APM -BPM00000 >>>> +AOM -BOM00 -AQM +BQM000 >>>> +AOM0 -APM000 -COM +CPM0 >>>> +AOM000 -AQM -COM0 +CQM >>>> there should be use 1 -1 or 0.5 -0.5? whether the -BPM should be change >>>> BPM? >>>> Thanks >>>> >>>> Bo Xiang >>>> >>>> >>>> >>>> >>>> >>>> >>>> At 2012-11-19 07:23:31,"Douglas Greve" wrote: >>>> >>>> >>>> Hi Bo, you can think of the Ftest as a logical 'OR' between the t-test >>>> contrasts indicated in each row. Each row is a difference of differences, >>>> so >>>> >>>> 1. (A-B)om - (A-B)pm --> Does the difference between A and B differ >>>> between >>>> groups O and P for Males? >>>> 2. (A-B)om - (A-B)qm >>>> 3. (A-C)om - (A-C)pm >>>> 4. (A-C)om - (A-C)qm >>>> 5. (A-B)of - (A-B)pf --> Does the difference between A and B differ >>>> between >>>> groups O and P for Females? >>>> 6. (A-B)of - (A-B)qf >>>> 7. (A-C)of - (A-C)pf >>>> 8. (A-C)of - (A-C)pf >>>> >>>> I've put together the first 9 columns of the first 4 rows. The last 9 >>>> columns are all 0s. For the last for rows, the 0s and below matrix are >>>> swapped to give you the same for the females >>>> >>>> doug >>>> >>>> AOM BOM APM BPM AQM BQM COM CPM CQM >>>> >>>> -- >>>> +AOM -BOM -APM -BPM00000 >>>> +AOM -BOM00 -AQM +BQM000 >>>> +AOM0 -APM000 -COM +CPM0&! nbsp;&nb sp; >>>> >>>> +AOM000 -AQM -COM0 +CQM >>>> >>>> >>>> >>>> On 11/17/12 9:21 PM, xiangbo_2010 wrote: >>>> >>>> Hi Freesurfer experts, >>>> >>>> I'm very sorry to bother you, but I am very confused with the following >>>> questions: >>>> >>>> My experimental design includes three discrete factors: factor 1 with >>>> three >>>> levels (A,B,C ); factor 2 with three levels (O,P,Q); gender (F, M), and >>>> one >>>> covariate. >>>> >>>> So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, >>>> MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the interaction >>>> between >>>> factor 1 and factor 2 regressing out the effect of gender and one >>>> covariate, >>>> but I don't know the rules for setting the contrasts for the F-test. The >>>> contrast matrix I used is: >>>> >>>> 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >>>> 0 >>>> >>>> 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >>>> 0 >>>> >>>> 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >>>> 0 >>>> >>>> 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >>>> 0 >>>> >&
[Freesurfer] The Asymmetry of surface area or thickness
Dear experts I want to analysis the asymmetry of surface area or thickness, what I do next? thanks! Bo Xiang___ 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.
[Freesurfer] 2013年6月15日 20:37:34 自动保存草稿
Dear experts, I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer. Though which was pointed out by reseachers, but I still can not know it. I hope some experts help me, Thanks! Bo Thank you in advance for your help!___ 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.
[Freesurfer] SPM ROI to Cortical Thickness
Dear experts, I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer. Though which was pointed out by reseachers, but I still can not know it. I hope some experts help me, Thanks! Bo Thank you in advance for your help! ___ 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.
Re: [Freesurfer] SPM ROI to Cortical Thickness
Hi Doug I use the MNI space! And what I do is the same with Ola, the following is the exchange of massage, but I still can not know how to do? thanks! Bo MNI space. On Jun 5, 2013, at 11:14 AM, Douglas N Greve wrote: what space is your VBM map in? doug On 06/05/2013 11:06 AM, Ozranov-Palchik, Ola wrote: Hi Doug, Thank you for your response! I am still a bit confused about the vol2surf command. I have a volumetric mask with voxels of interest based on a VBM analysis in SPM. I would like to extract the cortical thickness measurements based on these voxels. I am not clear what specifications I need to include when using vol2surf. For example, what do I use as my registration matrix?Thank you for your help!Ola Ola Ozranov-Palchik M.S. Research Coordinator, Gaab Lab Laboratories of Cognitive Neuroscience Children's Hospital Boston 1 Autumn Street, Mailbox # 713 Boston, MA 02115 olga.ozra...@childrens.harvard.edu phone: (617) 334-5046 main lab: (617) 355-0400 fax: (617) 730-0518 http://www.childrenshospital.org/research/gaablab -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, June 04, 2013 1:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] SPM ROI to Cortical Thickness Make sure that your SPM volume is registered to the anatomical, then use mri_vol2surf to map the volume to the surface, then mri_segstats to extract the mean of the thickness doug On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote: main lab: (617) 355-0400 Dear FreeSurfer Experts, I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer. Thank you in advance for your help! Ola At 2013-06-16 01:31:24,"Douglas Greve" wrote: I don't know anything about XjView. You will need to be very specific and detailed about what you did in order for us to help you. Eg, what space is the ROI in? doug On 6/15/13 8:40 AM, xiangbo_2010 wrote: Dear experts, I was wondering if anyone can advise on the best way to use an ROI mask created in SPM (XjView) to extract cortical thickness values in freesurfer. Though which was pointed out by reseachers, but I still can not know it. I hope some experts help me, Thanks! Bo Thank you in advance for your help! ___ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://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.
Re: [Freesurfer] SPM ROI to Cortical Thickness
Hi doug Thank you for giving this information, I used the command: "/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/to/spm/roi/yourfile.img/", but do not have results for me, and do not know how to do next? thanks! Bo At 2013-06-06 23:04:30,"Douglas N Greve" wrote: >Hi Stephanie, I don't know which recommendation you are referring to. We >get a lot of emails, and I can't remember each one. Can you repost with >the full thread? >doug > > >On 06/06/2013 10:40 AM, McMains, Stephanie wrote: >> I am wondering why you didn't tell them to go through fsvarege space? >> I thought that was an easy way to go from SPM MNI to freesurfer land. >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay >>> /pathname/to/spm/roi/yourfile.img/ >> >> >> I am wondering because when I look at the segmentation for fsaverage, >> it seems like it is missing a lot of the gray matter, particularly in >> the big sulci, most likely from the 'smoothing' that comes with >> averaging subjects together. And therefore I wonder if this is the >> best thing to use as an intermediate step. Are you instead suggesting >> (as it seemed like in this thread), to put the SPM roi into individual >> subject space and then somehow project it to the surface in free surfer? >> >> Thanks, >> Stephanie >> >> >> + >> >> Stephanie McMains >> Neuroimaging Staff Scientist >> Center for Brain Science >> Harvard University >> 52 Oxford Street >> Cambridge, MA 02138 >> >> + >> For answers to frequently asked questions: >> http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information-investigators/faq >> >> >> >> >> >> >> >> >> >> ___ >> 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 > > >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. > ___ 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.
Re: [Freesurfer] SPM ROI to Cortical Thickness
Hi Bruce Thank you for my help, when I use the bbregister, do not know how to choose data for --mov, thanks! Bo At 2013-06-17 20:34:39,"Bruce Fischl" wrote: >Hi Bo, > >tksurfer doesn't take a path to a file. Read the help on it - you need to >reconstrcut the subject with recon-all then give it the subject id. To >project a volumetric map onto the surface use mri_vol2surf, with the >registration typically computed by bbregister. > >cheers >Bruce > > >On Mon, 17 Jun 2013, xiangbo_2010 wrote: > >> Hi dougThank you for giving this information, I used the >command: "/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay >/pathname/to/s >> pm/roi/yourfile.img/", but do not have results for me, and do not know how >> to do next? thanks! >> >> >> Bo >> >> >> >> >> >> At 2013-06-06 23:04:30,"Douglas N Greve" wrote: >> >Hi Stephanie, I don't know which recommendation you are referring to. We >> >get a lot of emails, and I can't remember each one. Can you repost with >> >the full thread? >> >doug >> > >> > >> >On 06/06/2013 10:40 AM, McMains, Stephanie wrote: >> >> I am wondering why you didn't tell them to go through fsvarege space? >> >> I thought that was an easy way to go from SPM MNI to freesurfer land. >> >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathname/to/ >> spm/roi/yourfile.img/ >> >> >> >> >> >> I am wondering because when I look at the segmentation for fsaverage, >> >> it seems like it is missing a lot of the gray matter, particularly in >> >> the big sulci, most likely from the 'smoothing' that comes with >> >> averaging subjects together. And therefore I wonder if this is the >> >> best thing to use as an intermediate step. Are you instead suggesting >> >> (as it seemed like in this thread), to put the SPM roi into individual >> >> subject space and then somehow project it to the surface in free surfer? >> >> >> >> Thanks, >> >> Stephanie >> >> >> >> >> >> + >> >> >> >> Stephanie McMains >> >> Neuroimaging Staff Scientist >> >> Center for Brain Science >> >> Harvard University >> >> 52 Oxford Street >> >> Cambridge, MA 02138 >> >> >> >> + >> >> For answers to frequently asked questions: >> >> http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/informati >> on-investigators/faq >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ___ >> >> 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 >> > >> > >> >The information in this e-mail is intended only for the person to whom it i >> s >> >addressed. If you believe this e-mail was sent to you in error and the e-ma >> il >> >contains patient information, please contact the Partners Compliance HelpLi >> ne at >> >http://www.partners.org/complianceline . If the e-mail was sent to you in e >> rror >> >but does not contain patient information, please contact the sender and pro >> perly >> >dispose of the e-mail. >> > >> >> >> >> ___ 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.
Re: [Freesurfer] SPM ROI to Cortical Thickness
I have finished the recon-all, and obtained the mask from SPM which include the file with .img and .hdr, whether I should convert the file (.img and .hdr) to file (.nii), and use the command: "bbregister --s bert --mov func.nii --init-spm --reg register.dat tkregister2 --mov func.nii --reg register.dat --surf " to obtain the result? thanks! Bo At 2013-06-17 23:07:19,"Bruce Fischl" wrote: >please cc the list so others can answer. Do you mean get cortical >thickness? If so, then you need to run recon-all on the structural image > > >On Mon, 17 Jun 2013, xiangbo_2010 >wrote: > >> I have obtained the mask from xjview (.img), I want to obtain the CT from >> the mask, thanks! >> Bo >> >> >> >> >> >> At 2013-06-17 22:40:43,"Bruce Fischl" wrote: >> >what are you trying to map to the surface? >> >On Mon, 17 Jun 2013, xiangbo_2010 >> >wrote: >> > >> >> >> >> Hi Bruce >> >> Thank you for my help, when I use the bbregister, do not know how to choo >> se >> >> data for --mov, thanks! >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> At 2013-06-17 20:34:39,"Bruce Fischl" wrote: >> >> >Hi Bo, >> >> > >> >> >tksurfer doesn't take a path to a file. Read the help on it - you need t >> o >> >> >reconstrcut the subject with recon-all then give it the subject id. To >> >> >project a volumetric map onto the surface use mri_vol2surf, with the >> >> >registration typically computed by bbregister. >> >> > >> >> >cheers >> >> >Bruce >> >> > >> >> > >> >> >On Mon, 17 Jun 2013, xiangbo_2010 wrote: >> >> > >> >> >> Hi dougThank you for giving this information, I used the >> >> >command: "/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pa >> thn >> >> ame/to/s >> >> >> pm/roi/yourfile.img/", but do not have results for me, and do not know >> ho >> >> w >> >> >> to do next? thanks! >> >> >> >> >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-06 23:04:30,"Douglas N Greve" w >> rot >> >> e: >> >> >> >Hi Stephanie, I don't know which recommendation you are referring to. >> We >> >> >> >> >> >get a lot of emails, and I can't remember each one. Can you repost wi >> th >> >> >> >the full thread? >> >> >> >doug >> >> >> > >> >> >> > >> >> >> >On 06/06/2013 10:40 AM, McMains, Stephanie wrote: >> >> >> >> I am wondering why you didn't tell them to go through fsvarege spac >> e? >> >> >> >> I thought that was an easy way to go from SPM MNI to freesurfer la >> nd. >> >> >> >> >> >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathna >> me/ >> >> to/ >> >> >> spm/roi/yourfile.img/ >> >> >> >> >> >> >> >> >> >> >> >> I am wondering because when I look at the segmentation for fsaverag >> e, >> >> >> >> it seems like it is missing a lot of the gray matter, particularly >> in >> >> >> >> the big sulci, most likely from the 'smoothing' that comes with >> >> >> >> averaging subjects together. And therefore I wonder if this is the >> >> >> >> >> best thing to use as an intermediate step. Are you instead suggest >> ing >> >> >> >> >> >> (as it seemed like in this thread), to put the SPM roi into individ >> ual >> >> >> >> >> >> subject space and then somehow project it to the surface in free su >> rfe >> >> r? >> >> >> >> >> >> >> >> Thanks, >> >> >> >> Stephanie >> >> >> >> >> >> >> >> >> >> >> >> + >> >> >> >> >> >> >
Re: [Freesurfer] SPM ROI to Cortical Thickness
the mask was obtained from xjview, and use the MNI space in my study, thanks! Bo At 2013-06-17 23:52:33,"Bruce Fischl" wrote: >sorry, the formatting of your emails is lost in my reader and you may >have said this before, but what is the mask of? What space is it in? > >On Mon, 17 Jun 2013, >xiangbo_2010 wrote: > >> I want to get cortical thickness, and have finished the recon-all, and >> obtained the mask from SPM which include the file with .img and .hdr, >> whether I should convert the file (.img and .hdr) to file (.nii), and use >> the command: "bbregister --s bert --mov func.nii --init-spm --reg >> register.dat tkregister2 --mov func.nii --reg register.dat --surf " to >> obtain the result? thanks! >> >> Bo >> >> >> >> >> >> At 2013-06-17 23:07:19,"Bruce Fischl" wrote: >> >please cc the list so others can answer. Do you mean get cortical >> >thickness? If so, then you need to run recon-all on the structural image >> > >> > >> >On Mon, 17 Jun 2013, xiangbo_2010 >> >wrote: >> > >> >> I have obtained the mask from xjview (.img), I want to obtain the CT from >> >> the mask, thanks! >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 22:40:43,"Bruce Fischl" wrote: >> >> >what are you trying to map to the surface? >> >> >On Mon, 17 Jun 2013, xiangbo_2010 >> >> >wrote: >> >> > >> >> >> >> >> >> Hi Bruce >> >> >> Thank you for my help, when I use the bbregister, do not know how to c >> hoo >> >> se >> >> >> data for --mov, thanks! >> >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 20:34:39,"Bruce Fischl" wro >> te: >> >> >> >Hi Bo, >> >> >> > >> >> >> >tksurfer doesn't take a path to a file. Read the help on it - you nee >> d t >> >> o >> >> >> >reconstrcut the subject with recon-all then give it the subject id. >> To >> >> >> >project a volumetric map onto the surface use mri_vol2surf, with the >> >> >> >registration typically computed by bbregister. >> >> >> > >> >> >> >cheers >> >> >> >Bruce >> >> >> > >> >> >> > >> >> >> >On Mon, 17 Jun 2013, xiangbo_2010 wrote: >> >> >> > >> >> >> >> Hi dougThank you for giving this information, I used the >> >> >> >command: "/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay >> /pa >> >> thn >> >> >> ame/to/s >> >> >> >> pm/roi/yourfile.img/", but do not have results for me, and do not k >> now >> >> ho >> >> >> w >> >> >> >> to do next? thanks! >> >> >> >> >> >> >> >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-06 23:04:30,"Douglas N Greve" > > w >> >> rot >> >> >> e: >> >> >> >> >Hi Stephanie, I don't know which recommendation you are referring >> to. >> >> We >> >> >> >> >> >> >> >get a lot of emails, and I can't remember each one. Can you repost >> wi >> >> th >> >> >> >> >the full thread? >> >> >> >> >doug >> >> >> >> > >> >> >> >> > >> >> >> >> >On 06/06/2013 10:40 AM, McMains, Stephanie wrote: >> >> >> >> >> I am wondering why you didn't tell them to go through fsvarege s >> pac >> >> e? >> >> >> >> >> I thought that was an easy way to go from SPM MNI to freesurfer >> la >> >> nd. >> >> >> >> >> >> >> >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pa
Re: [Freesurfer] SPM ROI to Cortical Thickness
I want to get cortical thickness, and have finished the recon-all, and obtained the mask from SPM which include the file with .img and .hdr, whether I should convert the file (.img and .hdr) to file (.nii), and use the command: "bbregister --s bert --mov func.nii --init-spm --reg register.dat tkregister2 --mov func.nii --reg register.dat --surf " to obtain the result? thanks! Bo At 2013-06-17 23:07:19,"Bruce Fischl" wrote: >please cc the list so others can answer. Do you mean get cortical >thickness? If so, then you need to run recon-all on the structural image > > >On Mon, 17 Jun 2013, xiangbo_2010 >wrote: > >> I have obtained the mask from xjview (.img), I want to obtain the CT from >> the mask, thanks! >> Bo >> >> >> >> >> >> At 2013-06-17 22:40:43,"Bruce Fischl" wrote: >> >what are you trying to map to the surface? >> >On Mon, 17 Jun 2013, xiangbo_2010 >> >wrote: >> > >> >> >> >> Hi Bruce >> >> Thank you for my help, when I use the bbregister, do not know how to choo >> se >> >> data for --mov, thanks! >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> At 2013-06-17 20:34:39,"Bruce Fischl" wrote: >> >> >Hi Bo, >> >> > >> >> >tksurfer doesn't take a path to a file. Read the help on it - you need t >> o >> >> >reconstrcut the subject with recon-all then give it the subject id. To >> >> >project a volumetric map onto the surface use mri_vol2surf, with the >> >> >registration typically computed by bbregister. >> >> > >> >> >cheers >> >> >Bruce >> >> > >> >> > >> >> >On Mon, 17 Jun 2013, xiangbo_2010 wrote: >> >> > >> >> >> Hi dougThank you for giving this information, I used the >> >> >command: "/tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pa >> thn >> >> ame/to/s >> >> >> pm/roi/yourfile.img/", but do not have results for me, and do not know >> ho >> >> w >> >> >> to do next? thanks! >> >> >> >> >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-06 23:04:30,"Douglas N Greve" w >> rot >> >> e: >> >> >> >Hi Stephanie, I don't know which recommendation you are referring to. >> We >> >> >> >> >> >get a lot of emails, and I can't remember each one. Can you repost wi >> th >> >> >> >the full thread? >> >> >> >doug >> >> >> > >> >> >> > >> >> >> >On 06/06/2013 10:40 AM, McMains, Stephanie wrote: >> >> >> >> I am wondering why you didn't tell them to go through fsvarege spac >> e? >> >> >> >> I thought that was an easy way to go from SPM MNI to freesurfer la >> nd. >> >> >> >> >> >> >> >>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay /pathna >> me/ >> >> to/ >> >> >> spm/roi/yourfile.img/ >> >> >> >> >> >> >> >> >> >> >> >> I am wondering because when I look at the segmentation for fsaverag >> e, >> >> >> >> it seems like it is missing a lot of the gray matter, particularly >> in >> >> >> >> the big sulci, most likely from the 'smoothing' that comes with >> >> >> >> averaging subjects together. And therefore I wonder if this is the >> >> >> >> >> best thing to use as an intermediate step. Are you instead suggest >> ing >> >> >> >> >> >> (as it seemed like in this thread), to put the SPM roi into individ >> ual >> >> >> >> >> >> subject space and then somehow project it to the surface in free su >> rfe >> >> r? >> >> >> >> >> >> >> >> Thanks, >> >> >> >> Stephanie >> >> >> >> >> >> >> >> >> >> >> >> + >> >> >>
Re: [Freesurfer] SPM ROI to Cortical Thickness
my subject has finished the recon-all on the structural image, whether use the command: "mri_vol2surf --src sig.img --src_type analyze --srcreg register.dat --hemi rh --o ./sig-rh.img --out_type analyze --float2int round --trgsubject ico --icoorder 7" to obtain the result? thanks! Bo At 2013-06-18 00:00:09,"Bruce Fischl" wrote: >and what subject do you wan to obtain thickness measures from? You could >use mri_vol2vol to map your mask to the individual using the MNI >transform >On Mon, 17 Jun 2013, xiangbo_2010 wrote: > >> the mask was obtained from xjview, and use the MNI space in my study, >> thanks! >> Bo >> >> >> >> >> >> At 2013-06-17 23:52:33,"Bruce Fischl" wrote: >> >sorry, the formatting of your emails is lost in my reader and you may >> >have said this before, but what is the mask of? What space is it in? >> > >> >On Mon, 17 Jun 2013, >> >xiangbo_2010 wrote: >> > >> >> I want to get cortical thickness, and have finished the recon-all, and >> >> obtained the mask from SPM which include the file with .img and .hdr, >> >> whether I should convert the file (.img and .hdr) to file (.nii), and use >> >> the command: "bbregister --s bert --mov func.nii --init-spm --reg >> >> register.dat tkregister2 --mov func.nii --reg register.dat --surf " to >> >> obtain the result? thanks! >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 23:07:19,"Bruce Fischl" wrote: >> >> >please cc the list so others can answer. Do you mean get cortical >> >> >thickness? If so, then you need to run recon-all on the structural image >> >> > >> >> > >> >> >On Mon, 17 Jun 2013, xiangbo_2010 >> >> >wrote: >> >> > >> >> >> I have obtained the mask from xjview (.img), I want to obtain the CT f >> rom >> >> >> the mask, thanks! >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 22:40:43,"Bruce Fischl" wro >> te: >> >> >> >what are you trying to map to the surface? >> >> >> >On Mon, 17 Jun 2013, xiangbo_2010 >> >> >> >wrote: >> >> >> > >> >> >> >> >> >> >> >> Hi Bruce >> >> >> >> Thank you for my help, when I use the bbregister, do not know how t >> o c >> >> hoo >> >> >> se >> >> >> >> data for --mov, thanks! >> >> >> >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 20:34:39,"Bruce Fischl" >> wro >> >> te: >> >> >> >> >Hi Bo, >> >> >> >> > >> >> >> >> >tksurfer doesn't take a path to a file. Read the help on it - you >> nee >> >> d t >> >> >> o >> >> >> >> >reconstrcut the subject with recon-all then give it the subject id >> . >> >> To >> >> >> >> >project a volumetric map onto the surface use mri_vol2surf, with t >> he >> >> >> >> >registration typically computed by bbregister. >> >> >> >> > >> >> >> >> >cheers >> >> >> >> >Bruce >> >> >> >> > >> >> >> >> > >> >> >> >> >On Mon, 17 Jun 2013, xiangbo_2010 wrote: >> >> >> >> > >> >> >> >> >> Hi dougThank you for giving this information, I used the >> >> >> >> >command: "/tksurfer fsaverage lh inflated -aparc -mni152reg -overl >> ay >> >> /pa >> >> >> thn >> >> >> >> ame/to/s >> >> >> >> >> pm/roi/yourfile.img/", but do not have results for me, and do no >> t k >> >> now >> >> >> ho >> >> >> >> w >> >> >> >> >> to do next? thanks! >> >> >> >> &g
Re: [Freesurfer] SPM ROI to Cortical Thickness
I want to obtain the cortical thickness from a group of subjects, thanks! At 2013-06-18 00:13:08,"Bruce Fischl" wrote: >are you trying to do this for a single subject or for a group of subjects >, or group average data? >On Tue, 18 Jun 2013, xiangbo_2010 wrote: > >> my subject has finished the recon-all on the structural image, whether use >> the command: "mri_vol2surf --src sig.img --src_type analyze --srcreg >> register.dat --hemi rh --o ./sig-rh.img --out_type analyze --float2int round >> --trgsubject ico --icoorder 7" to obtain the result? thanks! >> >> Bo >> >> >> >> >> >> At 2013-06-18 00:00:09,"Bruce Fischl" wrote: >> >and what subject do you wan to obtain thickness measures from? You could >> >use mri_vol2vol to map your mask to the individual using the MNI >> >transform >> >On Mon, 17 Jun 2013, xiangbo_2010 wrote: >> > >> >> the mask was obtained from xjview, and use the MNI space in my study, >> >> thanks! >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 23:52:33,"Bruce Fischl" wrote: >> >> >sorry, the formatting of your emails is lost in my reader and you may >> >> >have said this before, but what is the mask of? What space is it in? >> >> > >> >> >On Mon, 17 Jun 2013, >> >> >xiangbo_2010 wrote: >> >> > >> >> >> I want to get cortical thickness, and have finished the recon-all, and >> >> >> obtained the mask from SPM which include the file with .img and .hdr, >> >> >> whether I should convert the file (.img and .hdr) to file (.nii), and >> use >> >> >> the command: "bbregister --s bert --mov func.nii --init-spm --reg >> >> >> register.dat tkregister2 --mov func.nii --reg register.dat --surf " to >> >> >> obtain the result? thanks! >> >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 23:07:19,"Bruce Fischl" wro >> te: >> >> >> >please cc the list so others can answer. Do you mean get cortical >> >> >> >thickness? If so, then you need to run recon-all on the structural im >> age >> >> >> > >> >> >> > >> >> >> >On Mon, 17 Jun 2013, xiangbo_2010 >> >> >> >wrote: >> >> >> > >> >> >> >> I have obtained the mask from xjview (.img), I want to obtain the C >> T f >> >> rom >> >> >> >> the mask, thanks! >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 22:40:43,"Bruce Fischl" >> wro >> >> te: >> >> >> >> >what are you trying to map to the surface? >> >> >> >> >On Mon, 17 Jun 2013, xiangbo_2010 >> >> >> >> >wrote: >> >> >> >> > >> >> >> >> >> >> >> >> >> >> Hi Bruce >> >> >> >> >> Thank you for my help, when I use the bbregister, do not know ho >> w t >> >> o c >> >> >> hoo >> >> >> >> se >> >> >> >> >> data for --mov, thanks! >> >> >> >> >> >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 20:34:39,"Bruce Fischl" > u> >> >> wro >> >> >> te: >> >> >> >> >> >Hi Bo, >> >> >> >> >> > >> >> >> >> >> >tksurfer doesn't take a path to a file. Read the help on it - y >> ou >> >> nee >> >> >> d t >> >> >> >> o >> >> >> >> >> >reconstrcut the subject with recon-all then give it the subject >> id >> >> . >>
Re: [Freesurfer] SPM ROI to Cortical Thickness
Hi Bruce I use the SPM to analysis my data, and use the xjview to get a mask (have .img and .hdr files) as ROI, use the MNI space in SPM analysis. Following I want to obtain the cortical thickness from this mask in Freesurfer, and I have analyzed all my individual subjects in FreeSurfer(recon-all). thanks! Bo At 2013-06-18 02:35:40,"Bruce Fischl" wrote: >can you give a complete description of your study and what you are trying >to achieve? Have you analyzed all your individual subjects in FreeSurfer >(recon-all)? What is the mask you want to use? > >On Tue, 18 Jun 2013, xiangbo_2010 wrote: > >> I want to obtain the cortical thickness from a group of subjects, thanks! >> >> >> >> >> >> At 2013-06-18 00:13:08,"Bruce Fischl" wrote: >> >are you trying to do this for a single subject or for a group of subjects >> >, or group average data? >> >On Tue, 18 Jun 2013, xiangbo_2010 wrote: >> > >> >> my subject has finished the recon-all on the structural image, whether us >> e >> >> the command: "mri_vol2surf --src sig.img --src_type analyze --srcreg >> >> register.dat --hemi rh --o ./sig-rh.img --out_type analyze --float2int ro >> und >> >> --trgsubject ico --icoorder 7" to obtain the result? thanks! >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-18 00:00:09,"Bruce Fischl" wrote: >> >> >and what subject do you wan to obtain thickness measures from? You could >> >> >> >use mri_vol2vol to map your mask to the individual using the MNI >> >> >transform >> >> >On Mon, 17 Jun 2013, xiangbo_2010 wrote: >> >> > >> >> >> the mask was obtained from xjview, and use the MNI space in my study, >> >> >> thanks! >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 23:52:33,"Bruce Fischl" wro >> te: >> >> >> >sorry, the formatting of your emails is lost in my reader and you may >> >> >> >> >have said this before, but what is the mask of? What space is it in? >> >> >> > >> >> >> >On Mon, 17 Jun 2013, >> >> >> >xiangbo_2010 wrote: >> >> >> > >> >> >> >> I want to get cortical thickness, and have finished the recon-all, >> and >> >> >> >> obtained the mask from SPM which include the file with .img and .hd >> r, >> >> >> >> whether I should convert the file (.img and .hdr) to file (.nii), a >> nd >> >> use >> >> >> >> the command: "bbregister --s bert --mov func.nii --init-spm --reg >> >> >> >> register.dat tkregister2 --mov func.nii --reg register.dat --surf " >> to >> >> >> >> obtain the result? thanks! >> >> >> >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 23:07:19,"Bruce Fischl" >> wro >> >> te: >> >> >> >> >please cc the list so others can answer. Do you mean get cortical >> >> >> >> >thickness? If so, then you need to run recon-all on the structural >> im >> >> age >> >> >> >> > >> >> >> >> > >> >> >> >> >On Mon, 17 Jun 2013, xiangbo_2010 >> >> >> >> >wrote: >> >> >> >> > >> >> >> >> >> I have obtained the mask from xjview (.img), I want to obtain th >> e C >> >> T f >> >> >> rom >> >> >> >> >> the mask, thanks! >> >> >> >> >> Bo >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2013-06-17 22:40:43,"Bruce Fischl" > u> >> >> wro >> >> >> te: >> >> >> >> >> &g
[Freesurfer] contrast matrix
Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: genotype with three levels (GG,GA,AA ); gender (F, M), and one covariate. So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA. 1) I want to perform the difference between any of the genotype leves analysis with regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: [1 -1 0 1 -1 0 0 0 0 0 0 0 ]/2 [1 0 -1 1 0 -1 0 0 0 0 0 0 ]/2 is it correct? Any help will be very appreciated. Best wishes, Meng Li ___ 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.
[Freesurfer] contrast matrix
Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: genotype with three levels (GG,GA,AA ); gender (F, M), and one covariate. So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA. 1) I want to perform the difference between any of the genotype leves analysis with regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: [1 -1 0 1 -1 0 0 0 0 0 0 0 ]/2 [1 0 -1 1 0 -1 0 0 0 0 0 0 ]/2 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang ___ 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.
[Freesurfer] contrast matrix
Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: genotype with three levels (GG,GA,AA ); gender (F, M), and one covariate. So I can get 6 classes: MGG, MGA,MAA, FGG,FGA,FAA. 1) I want to perform the difference between any of the genotype leves analysis with regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: [1 -1 0 1 -1 0 0 0 0 0 0 0 ]/2 [1 0 -1 1 0 -1 0 0 0 0 0 0 ]/2 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang ___ 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.
[Freesurfer] Defining a region of interest
Dear experts: I used the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization?highlight=%28ROI%29 to defining a region of interest, but when I make a series of left clicks on the surface， then click the "Make Closed Fill Boundary" icon in the tools window. howevre, there has no connect the points my clicked, and drawing a yellow or red line between them. 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 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.
[Freesurfer] Defining a region of interest
. done At 2012-11-16 22:07:16,"Bruce Fischl" wrote: >can you respond to the list? Not sure what's going on... >Bruce > > >On Fri, 16 Nov 2012, xiangbo_2010 wrote: > >> >> Thank you for my reply, when I check the button, the points have no change. >> Before check the button, these points are white, and have no bright colors, >> Thanks! >> >> >> >> >> At 2012-11-16 21:58:28,"Bruce Fischl" wrote: >> >sorry, not sure I understand. After you click "make closed fill boundary" >> >what happens? Before you click do you see the points hilighted on the >> >surface? >> >On Fri, 16 Nov 2012, xiangbo_2010 wrote: >> > >> >> Dear experts: >> >>I used the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial >> /Visualization?highligh >> >> t=%28ROI%29 to defining a region of interest, but when I make a series of >> >> left clicks on the surface? then click the "Make Closed Fill Boundary" i >> con >> >> in the tools window. howevre, there has no connect the points my >> >> clicked, and drawing a yellow or red line between them. I hope that have >> >> experts to help me. Thanks! >> >> >> >> >> >> >> >> Bo Xiang >> >> >> >> >> >> >> >> >> >> >> >> > > >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. ___ 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.
[Freesurfer] contrast matrix
Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes three discrete factors: factor 1 with three levels (A,B,C ); factor 2 with three levels (O,P,Q); gender (F, M), and one covariate. So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the interaction between factor 1 and factor 2 regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang ___ 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.
[Freesurfer] contrast matrix
Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes three discrete factors: factor 1 with three levels (A,B,C ); factor 2 with three levels (O,P,Q); gender (F, M), and one covariate. So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the interaction between factor 1 and factor 2 regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang ___ 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.
Re: [Freesurfer] contrast matrix
Dear Cherry I our analysis, the gender as a Covariate, so all female groups assigned 0 in the matrix, following is new matrix: 1 -1 -1 -1 -1 -1 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1-1 -1 0 -1 -1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 -1 -1 -1 -1 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1-1 -1 0 -1 -1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang At 2012-11-18 10:51:07,"Yizhou Ma" wrote: Hi Bo, I'm definitely not an expert of this, but I see that you really nead some help, so I tried to look at your matrix. From my humble opinion it doesn't look correct. Firstly, the first 9 groups are male groups and the last 9 are female groups. Then why are all female groups assigned 0 in the matrix? Secondly, since the interaction you are interested in have a df of 4, do you think maybe you should have 4 rows rather than 8 in your matrix? Cherry On Sat, Nov 17, 2012 at 9:21 PM, xiangbo_2010 wrote: Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes three discrete factors: factor 1 with three levels (A,B,C ); factor 2 with three levels (O,P,Q); gender (F, M), and one covariate. So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the interaction between factor 1 and factor 2 regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang ___ 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. ___ 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.
[Freesurfer] variable
Dear experts: I want to ask the question: the gender (1;2) can be as a continuous variable? 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 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.
Re: [Freesurfer] variable
if the gender (1;2) can be as a continuous variable ,can reduce the trouble about the set of contrast,thanks! Bo Xiang At 2012-11-18 22:48:36,"Bruce Fischl" wrote: >sorry, not sure I understand. Why would you want it to be continuous? >On >Sun, 18 Nov 2012, xiangbo_2010 wrote: > >> Dear experts: >>I want to ask the question: the gender (1;2) can be as a >> continuous variable? I hope that have experts to help me. Thanks! >> >> >> >> Bo Xiang >> >> >> >> >> >> > > >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. ___ 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.
Re: [Freesurfer] contrast matrix
Dear doug Thank you for your reply! +AOM -BOM -APM -BPM00000 +AOM -BOM00 -AQM +BQM000 +AOM0 -APM000 -COM +CPM0 +AOM000 -AQM -COM0 +CQM there should be use 1 -1 or 0.5 -0.5? whether the -BPM should be change BPM? Thanks Bo Xiang At 2012-11-19 07:23:31,"Douglas Greve" wrote: Hi Bo, you can think of the Ftest as a logical 'OR' between the t-test contrasts indicated in each row. Each row is a difference of differences, so 1. (A-B)om - (A-B)pm --> Does the difference between A and B differ between groups O and P for Males? 2. (A-B)om - (A-B)qm 3. (A-C)om - (A-C)pm 4. (A-C)om - (A-C)qm 5. (A-B)of - (A-B)pf --> Does the difference between A and B differ between groups O and P for Females? 6. (A-B)of - (A-B)qf 7. (A-C)of - (A-C)pf 8. (A-C)of - (A-C)pf I've put together the first 9 columns of the first 4 rows. The last 9 columns are all 0s. For the last for rows, the 0s and below matrix are swapped to give you the same for the females doug AOM BOM APM BPM AQM BQM COM CPM CQM -- +AOM -BOM -APM -BPM00000 +AOM -BOM00 -AQM +BQM000 +AOM0 -APM000 -COM +CPM0 +AOM000 -AQM -COM0 +CQM On 11/17/12 9:21 PM, xiangbo_2010 wrote: Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes three discrete factors: factor 1 with three levels (A,B,C ); factor 2 with three levels (O,P,Q); gender (F, M), and one covariate. So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO, MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ. I want to perform the interaction between factor 1 and factor 2 regressing out the effect of gender and one covariate, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 1 0 -1 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? Any help will be very appreciated. Best wishes, Bo Xiang ___ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://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.
Re: [Freesurfer] contrast matrix
Dear Donald McLaren Thank you for your reply! I make the contrast according to your method is following，but I want to make interaction between factor 1 (A,B)and factor 2(C,D,E), gender (M,F) and one continuous variable (age) as covariates, the following contrast: 2 -2 0 -2 2 0 2 -2 0 -2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 -2 0 -2 2 0 2 -2 0 -2 2 0 0 0 0 0 0 0 0 0 0 0 0 is correct? Thanks! Bo Xiang At 2012-11-21 04:07:37,"MCLAREN, Donald" wrote: >On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve > wrote: >> Thanks Donald. Is this the standard way to do this? I had used 8 rows >> instead of 4 with the difference being that 8 rows gives you an opportunity >> to look for an effect in males OR females. > >Yes. Having 8 rows would tell you if you have an interaction between >factor 1 and 2 in either males or females. My 4 rows only tell you if >the interaction exists. Technically speaking, one would run the >three-way interaction first. If nothing existed then you do the >two-way interaction as I suggested. If there is a three-way >interaction, then you would use Doug's approach of the interaction in >either males or females. > >If there is an effect in both >> males and females but the effects go in opposite directions, then the 4 row >> implementation will resolve to 0 (no effect). Or am I misunderstanding >> something (again:)? > >Nope. You are right. If the male and female effects are different, >then they could cancel each other out. If you suspect this to be the >case, then you should be able to demonstrate a three-way interaction. > >> thanks! >> doug >> >> >> On 11/20/2012 01:50 PM, MCLAREN, Donald wrote: >>> >>> Bo, >>> >>> Doug asked me to chime in on your issue. Here are some points that you >>> (and others) will hopefully find useful. >>> >>> (1) Inferences are two-step process. First, you create and estimate >>> the design matrix. Every column in the design matrix accounts can >>> account for some of the variance in the data. Second, you have >>> contrasts that allow you to infer specific effects. Because the model >>> contains your covariates, you are always controlling for the >>> covariates and by extension any factor/covariate not in the contrast. >>> >>> (2) Forming contrasts is often the most difficult thing to do. I >>> assume that your three factors (1, 2, and gender) are all >>> between-subject factors. If one of them is a within-subject factor >>> please let me know and disregard the rest of the email. The final >>> F-contrast will have 4 rows (factor 1 levels-1)*(factor 2 levels >>> -1)=(3-1)*(3-1)=2*2=4 >>> >>> The following is an outline for creating contrasts: >>> (a) Start simple - difference between levels of 1 factor >>> (b) Define your null hypothesis: AO=AP=AQ >>> (c) Make it equal to 0: AO-AP=0 AND AP-AQ=0 >>> (d) Repeat for the other levels of the factor... >>> BO-BP=0 AND BP-BQ=0 >>> CO-CP=0 AND CP-CQ=0 >>> >>> (e) Now combine them AO-AP=BO-BP=CO-CP AND AP-AQ=BP-BQ=CP-CQ >>> >>> (f) Make them equal to 0: >>> AO-AP-BO+BP=0 >>> BO-BP-CO+CP=0 >>> AP-AQ-BP+BQ=0 >>> BP-BQ-CP+CQ=0 >>> >>> (g) Expand them to include gender, for example: >>> AO-AP-BO+BP=0 becomes FAO-FAP-FBO+FBP+MAO-MAP-MBO+MBP=0 >>> >>> Since the contrast now has 2 columns per level, you should divide all >>> values by 2. This will produce the correct amplitude and statistics. >>> If you leave the values as 1 and -1, then you will have an incorrect >>> amplitude, but the statistics will still be correct. >>> >>> (h) Fill in the respective columns of your design matrix. >>> >>> (3) The degrees of freedom are defined based on the rows of the >>> F-matrix and the number of rows in the design matrix. The F-test has a >>> numerator and denominator degrees of freedom. F(n,d). >>> >>> Best Regards, Donald McLaren >>> = >>> D.G. McLaren, Ph.D. >>> Research Fellow, Department of Neurology, Massachusetts General Hospital >>> and >>> Harvard Medical School >>> Postdoctoral Research Fellow, GRECC, Bedford VA >>> Website: http://www.martinos.org/~mclaren >>> Office: (773) 406-2464 >>> = >>> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED >>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >>> intended only for the use of the individual or en
Re: [Freesurfer] contrast matrix
No, I want to compute the interaction between factor 1 and factor 2 , gender and age as covariates. thanks Bo Xiang 在 2012-11-22 04:22:06，"Douglas N Greve" 写道： >Hi Bo, I don't understand the contrast you are trying to make. Are you >really trying to compute the interaction between four variables (factor >1, factor 2, gender, and age)? >doug > >On 11/21/2012 10:49 AM, xiangbo_2010 wrote: >> Dear Donald McLaren >> Thank you for your reply! I make the contrast according to your method >> is following，but I want to make interaction between factor 1 (A,B)and >> factor 2(C,D,E), gender (M,F) and one continuous variable (age) as >> covariates, the following contrast: >> 2 -2 0 -2 2 0 2 -2 0 -2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 >> 0 2 -2 0 -2 2 0 2 -2 0 -2 2 0 0 0 0 0 0 0 0 0 0 0 0 >> >> is correct? Thanks! >> Bo Xiang >> >> >> >> >> >> At 2012-11-21 04:07:37,"MCLAREN, Donald"> <mailto:mclaren.don...@gmail.com>> wrote: >> >On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve >> >mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> Thanks Donald. Is this the standard way to do this? I had used 8 rows >> >> instead of 4 with the difference being that 8 rows gives you an >> >> opportunity >> >> to look for an effect in males OR females. >> > >> >Yes. Having 8 rows would tell you if you have an interaction between >> >factor 1 and 2 in either males or females. My 4 rows only tell you if >> >the interaction exists. Technically speaking, one would run the >> >three-way interaction first. If nothing existed then you do the >> >two-way interaction as I suggested. If there is a three-way >> >interaction, then you would use Doug's approach of the interaction in >> >either males or females. >> > >> >If there is an effect in both >> >> males and females but the effects go in opposite directions, then the 4 >> >> row >> >> implementation will resolve to 0 (no effect). Or am I misunderstanding >> >> something (again:)? >> > >> >Nope. You are right. If the male and female effects are different, >> >then they could cancel each other out. If you suspect this to be the >> >case, then you should be able to demonstrate a three-way interaction. >> > >> >> thanks! >> >> doug >> >> >> >> >> >> On 11/20/2012 01:50 PM, MCLAREN, Donald wrote: >> >>> >> >>> Bo, >> >>> >> >>> Doug asked me to chime in on your issue. Here are some points that you >> >>> (and others) will hopefully find useful. >> >>> >> >>> (1) Inferences are two-step process. First, you create and estimate >> >>> the design matrix. Every column in the design matrix accounts can >> >>> account for some of the variance in the data. Second, you have >> >>> contrasts that allow you to infer specific effects. Because the model >> >>> contains your covariates, you are always controlling for the >> >>> covariates and by extension any factor/covariate not in the contrast. >> >>> >> >>> (2) Forming contrasts is often the most difficult thing to do. I >> >>> assume that your three factors (1, 2, and gender) are all >> >>> between-subject factors. If one of them is a within-subject factor >> >>> please let me know and disregard the rest of the email. The final >> >>> F-contrast will have 4 rows (factor 1 levels-1)*(factor 2 levels >> >>> -1)=(3-1)*(3-1)=2*2=4 >> >>> >> >>> The following is an outline for creating contrasts: >> >>> (a) Start simple - difference between levels of 1 factor >> >>> (b) Define your null hypothesis: AO=AP=AQ >> >>> (c) Make it equal to 0: AO-AP=0 AND AP-AQ=0 >> >>> (d) Repeat for the other levels of the factor... >> >>> BO-BP=0 AND BP-BQ=0 >> >>> CO-CP=0 AND CP-CQ=0 >> >>> >> >>> (e) Now combine them AO-AP=BO-BP=CO-CP AND AP-AQ=BP-BQ=CP-CQ >> >>> >> >>> (f) Make them equal to 0: >> >>> AO-AP-BO+BP=0 >> >>> BO-BP-CO+CP=0 >> >>> AP-AQ-BP+BQ=0 >> >>> BP-BQ-CP+CQ=0 >> >>> >> >>> (g) Expand them to include gender, for example: >> >>> AO-AP-BO+BP=0 becomes FAO-FAP-FBO+FBP+MAO-MAP-MBO+MBP=0 >> >
[Freesurfer] error
Dear experts, when I run the "qdec", and the wrong information appear in following: qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory I hope some experts to help me ,thank you very much! -- Bo Xiang State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China The Mental Health Center and the Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China Phone: +8615281056345 QQ: 529111494 Skype: xiang.bo3 向波 四川大学华西医院生物治疗国家重点实验室，华西医院精神医学研究室 成都市武侯区人民南路三段中四川大学华西校区，610041 E-mail: xiangbo_2...@126.com / xiangboyulan2...@gmail.com 电话：15281056345 QQ：529111494 Skype：xiang.bo3 ___ 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.
