[Freesurfer] How to get transform matrix from Vertex Index to Vertex RAS
Hi all: I am studying the coordinate system transforms within subject across imaging modalities on web page: http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems. I met a problem. First, i run tksurfer : tksurfer subjectname lh inflated -reg register.dat -ov mov.nii , then i chose a point on the surface and save it. There would be Vertex Index value and Vertex RAS value on the panel of TKSurfer Tool. For example: Vertex Index 96063 Vertex RAS (-56.05 0.42 62.6) Now, i want to know how the values between Vertex Index and Vertex RAS transformed each other. I need help. Best wishes!___ 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] How to get surface-based AAL template
Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation? Any suggestions appreciated. Besh wishes.___ 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] How to get surface-based AAL template
Dear Br: Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend toolbox. But I still have some questions about the process. 1. You said I need transform the Colin 27 to the latest FS version (v.5.2). But i don't know how to do this. It is helpful if you can provide some information. 2. How does the Colin 27 space differs from fsaverage MNI305 space? The group analysis of cortical thickness is conducted in fsaverage space, after importing AAL ROI into Colin 27 space, should i transform the obtained ROI into fsaverage space? 3. i don't understand what is the register.dat between COlin 27 and SPM-s single subject t1.nii used for? I have tried the Surfrend, and found there was no entry for input of register file during the processing. Looking forward to your reply. Best wishes. zhiliang At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" wrote: Hi, In my case transformation to fsaverage did not work very well. What I did was: - from Surfrend page download Colin 27 subject and transform it to the latest version (now 5.2) - with bbregister obtain register.dat between this Colin 27 subject and SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined in Colin 27. As they are the same subject, the registering is very good. - now you can import every AAL ROI (in .nii form) to an annotation or in the form of individual labels to your FS Colin 27, using the newly created registering file. - now you can use surf2surf or label2label to go to your subjects and obtain stats. Br! On 27/03/2013, at 05:35, ZhiLiangLong wrote: Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation? Any suggestions appreciated. Besh wishes. ___ 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] FS version of Colin27
Hi FS experts: I am trying to map AAL template onto FS surface to create surface-based AAL template. Several days ago, i asked this question, and Garikoitz Lerma gave me some suggestions. Possibly, i think the process is like as folllows: 1. downloa the Colin27 subject in Surfrend page, and transform it to the latest FS version (5.2 currently). 2. obtain register.dat between Colin27 subject and single_subj_T1.nii under the canonical directory in SPM8 using bbregister. bbregister --s Colin27_subject --mov single_subj_T1.nii --reg register.dat --init-fsl --t1 3. transfrom each AAL ROI to the surface file with register.dat file obtained above using mri_vol2surf. mri_vol2surf --mov AAL_ROI.nii --reg register.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh \ --out lh.Colin27_AALROI.mgh --reshape 4. use mri_label2label or mri_segstat to obtain the cortical thickness of each ROI for individual subject. My question is about the first step. How to transform the Colin27 subject to FS version 5.2? that is to say how can i get the FS version of Colin27 template instead of fsaverage template? Hope someone gives me some suggetions. Besh wishes. ___ 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] How to get surface-based AAL template
Dear Gari: Thank you for give me suggestions patiently. i figured it out as you suggested. it works well. I have one more question: Do you know there are published papers which use the surface-based aal template (or something like this) to do research (e.g. cortical network analysis based on this template)? Best wishes. zhiliang At 2013-03-29 15:34:02,"Garikoitz Lerma-Usabiaga" wrote: Hi Zhiliang, 1- well, I just recon-all-ed their subject again with the newest version. Recon-all -s Colin -all 2- maybe Doug or some other will answer this question better. I don't know the exact differences between fs mni305 and fs mnicolin27. What I know is that going the fsaverage path I couldn't obtain reliable transformations of the AAL labels. I think this was because fsaverage is very smoothed. Spm_register and vol2surf weren't working well. The thing is, for group analysis, you can use Colin (or any other), as I understood it. When you use -qcache your data goes to fsaverage, but you can do it manually and specify that you want Colin instead (maybe someone can confirm it). If you are going to use just the AAL average CTs, then you just need to use surf2surf or label2label and you won't need fsaverage at all. 3- well, the spm single subject and Colin from Surfrend are the same subject but not exactly the same image. You do bbregister to them and obtain your register.dat matrix (you name it), and it goes from 2mm to 1mm and has some minimal translation. If you see both T1-s with tkregister you will see that they are almost the same (the spm version a little bit blurred, because of the resolution). You use this register.dat when doing vol2surf of the AAL.nii to your AAL.mgh surface ROI. Hope this helps! Gari On 27/03/2013, at 14:06, ZhiLiangLong wrote: Dear Br: Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend toolbox. But I still have some questions about the process. 1. You said I need transform the Colin 27 to the latest FS version (v.5.2). But i don't know how to do this. It is helpful if you can provide some information. 2. How does the Colin 27 space differs from fsaverage MNI305 space? The group analysis of cortical thickness is conducted in fsaverage space, after importing AAL ROI into Colin 27 space, should i transform the obtained ROI into fsaverage space? 3. i don't understand what is the register.dat between COlin 27 and SPM-s single subject t1.nii used for? I have tried the Surfrend, and found there was no entry for input of register file during the processing. Looking forward to your reply. Best wishes. zhiliang At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" wrote: Hi, In my case transformation to fsaverage did not work very well. What I did was: - from Surfrend page download Colin 27 subject and transform it to the latest version (now 5.2) - with bbregister obtain register.dat between this Colin 27 subject and SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined in Colin 27. As they are the same subject, the registering is very good. - now you can import every AAL ROI (in .nii form) to an annotation or in the form of individual labels to your FS Colin 27, using the newly created registering file. - now you can use surf2surf or label2label to go to your subjects and obtain stats. Br! On 27/03/2013, at 05:35, ZhiLiangLong wrote: Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation? Any suggestions appreciated. Besh wishes. ___ 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,
Re: [Freesurfer] How to get surface-based AAL template
Hi Thomas: There are no special reasons why i need the surface-based aal template. my goal is to parcellate surface into thousands of small brain areas, and construct large-scale cortical network. I have no idea how to segment the surface directly in FS. But i know the way to segment AAL template to the specific parcellation level (e.g. AAL-1024 ) i want. that is why i do this. Best. zhiliang At 2013-04-01 12:55:03,"Thomas Yeo" wrote: >Hi Zhi Liang, > >Out of curiosity, why not just use the FreeSurfer parcellations, so >you don't end up with holes in the sulci/gyri? > >--Thomas > >On Sun, Mar 31, 2013 at 8:28 PM, Martijn Steenwijk > wrote: >> I faced this problem a while ago. Both MNI to fsaverage, MNI itself and >> Colin27 didn’t work sufficiently for sampling the labels, all had problems >> with the registration causing holes in the sulci and gyri ending up in the >> wrong label. (That might be ‘good’ since AAL is a volumetric atlas; but >> might also be bad, since you often don’t want to look at an in complete >> label). I ended up making my own gcs fom a training set with mris_ca_train. >> Now I can segment surfaces just by calling mris_ca_label which works >> flawlessly and consistent throughout subjects. >> >> >> >> Best, >> >> Martijn >> >> >> >> Van: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens ZhiLiangLong >> Verzonden: zaterdag 30 maart 2013 16:25 >> Aan: Garikoitz Lerma-Usabiaga >> CC: Freesurfer >> Onderwerp: Re: [Freesurfer] How to get surface-based AAL template >> >> >> >> Dear Gari: >> >> Thank you for give me suggestions patiently. i figured it out as you >> suggested. it works well. I have one more question: Do you know there are >> published papers which use the surface-based aal template (or something like >> this) to do research (e.g. cortical network analysis based on this >> template)? >> >> >> >> Best wishes. >> >> zhiliang >> >> At 2013-03-29 15:34:02,"Garikoitz Lerma-Usabiaga" >> wrote: >> >> Hi Zhiliang, >> >> 1- well, I just recon-all-ed their subject again with the newest version. >> Recon-all -s Colin -all >> >> 2- maybe Doug or some other will answer this question better. I don't know >> the exact differences between fs mni305 and fs mnicolin27. What I know is >> that going the fsaverage path I couldn't obtain reliable transformations of >> the AAL labels. I think this was because fsaverage is very smoothed. >> Spm_register and vol2surf weren't working well. >> >> >> >> The thing is, for group analysis, you can use Colin (or any other), as I >> understood it. When you use -qcache your data goes to fsaverage, but you can >> do it manually and specify that you want Colin instead (maybe someone can >> confirm it). If you are going to use just the AAL average CTs, then you just >> need to use surf2surf or label2label and you won't need fsaverage at all. >> >> >> >> 3- well, the spm single subject and Colin from Surfrend are the same subject >> but not exactly the same image. You do bbregister to them and obtain your >> register.dat matrix (you name it), and it goes from 2mm to 1mm and has some >> minimal translation. If you see both T1-s with tkregister you will see that >> they are almost the same (the spm version a little bit blurred, because of >> the resolution). You use this register.dat when doing vol2surf of the >> AAL.nii to your AAL.mgh surface ROI. >> >> >> >> Hope this helps! >> >> Gari >> >> >> On 27/03/2013, at 14:06, ZhiLiangLong wrote: >> >> Dear Br: >> >>Thanks for your help. I have downloaded Colin 27 subject, and the >> Surfrend toolbox. But I still have some questions about the process. >> >>1. You said I need transform the Colin 27 to the latest FS version >> (v.5.2). But i don't know how to do this. It is helpful if you can provide >> some information. >> >> 2. How does the Colin 27 space differs from fsaverage MNI305 space? The >> group analysis of cortical thickness is conducted in fsaverage space, after >> importing AAL ROI into Colin 27 space, should i transform the obtained ROI >> into fsaverage space? >> >> 3. i don't understand what is the register.dat between COlin 27 and SPM-s >> single subject t1.nii used for? I have tried the Surfrend, and found there >> was no entry for input of register file during
[Freesurfer] Confused with Coordinate System in FS
Hi all: I am confused with coordinate systems in FS. I have several questions bellow. 1. when we run recon-all -s subjid -all, Is the individual native space transformed to talairach coordinate system?. when run recon-all -s subjid -qcache, does the talairach system go into MNI system (fsaverage space)? 2. what is the tranformation matrix within the file of /mri/transforms/talairach.xfm?, what is it used for? 3. Does the coordinates within .label files under /label/ belong to the MNI coordinate system? 4. In TkSurfer Tool, does the coordinate of "Vertex RAS" belong to MNI coordinate? Hope someone gives me suggestions. best ___ 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] question about MNI coordinates or talariach coordinate in Qdec
Hi all: In qdec, when i left-clicked on a point of pial surface, there would be a coordinate displayed at the bottom of qdec. my qestion is that does the coordinate belong to the MNI space or talariach space?___ 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] recon-all process on brain regions of interest
Hi everyone: I met problem about the recon-all process. I got some brain regions showing group-differences of activation in task. Now, i want to compare the difference of cortical thickness on these brain regions. I prefer to limit the compution of cortical thickness on my regions of interest rather than the whole brain to reduce compution time. But i do not know how the recon-all works it out. I need your suggestions. In addition, assume that i have finished recon-all process on the whole brain, how can i obtain the cortical thickness of my regions of interest? All the best!___ 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] cortical thickness of ROIs derived from VBM results
Hi all: I got some regions of interest showing significant diffencese in VBM between two groups. Now, i attemp to compare cortical thickness of these ROIs. However, i don't know how to map the ROIs to cortical surface and extract cortical thickness values? I need 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] convert .annot file to lable
Hi all: Are there some FS commands that can convert .annot file to lable file? Thanks!___ 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] ANOVA(analysis of variance)
Hi all: Is there a way that can perform a test to compare the difference of cortical thickness between groups (at least three) using ANOVA (analysis of variance) in FS? If it is how can i do that? Any suggestions will be appreciative___ 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] questions about mapping volume data to brain surface and extracting cortical thickness
Hi FS experts: I have two questions about FS. (1) Is there a way that can map volume data(.hdr and .img file) to brain surface in FS? (2) I find a way that can extract cortical thickness automatically,first,the statistical significant areas derived from group analysis on qdec are converted to annotation file using mri_surfcluster,then i use mri_annotation2label to convert the annotation file to label file,finally, mri_label2label and mri_anatomical_stats are used to map the label file to each subject and obtain cortical thickness. I want to know if the process is correct. any help appreciated___ 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] question about contrast file during group analysis with command line
Hi all : I'm performing general linear model (GLM) analysis in the surface,the attachments above are FSGD file and contrast files(the last three attachments).i wonder if my contrast files are correct. the attachment named diff-C-H-thickness.txt is about difference between C and H and the last two are about difference between C and p and difference between P and H,Here,C H and P represent three groups Any suggestions appreciatedGroupDescriptorFile 1 Title genderage MeasurementName thickness Class C-Male Class C-Female Class P-Male Class P-Female Class H-Male Class H-Female Variables age Input chen_haoC-Female20 Input cui_xi_long C-Female23 Input jiang_xue C-Female24 Input li_qing_jingC-Female24 Input li_ru C-Male 22 Input li_teng_yu C-Male 21 Input liao_yun_feng C-Male 24 Input long_hu C-Male 29 Input long_zhiC-Male 26 Input lv_hai_long C-Male 23 Input peng_chend C-Male 24 Input yue_zhong_wei C-Male 22 Input zhang_qian C-Male 25 Input zhao_ke C-Male 27 Input zhu_min C-Male 21 Input cai_rongP-Female23 Input chen_guo_wu P-Male 23 Input huang_din_qiang P-Male 22 Input kong_fang_fang P-Female24 Input li_guang_yaoP-Male 24 Input liu_zheng_hua P-Male 26 Input long_binP-Male 29 Input qiu_hao P-Male 21 Input quan_su_bin P-Male 22 Input wu_jian_nongP-Male 25 Input wu_li_hui P-Female20 Input xiao_qiao_ling P-Female24 Input xie_gangP-Male 21 Input xu_xian P-Male 24 Input zhang_hai_tao P-Male 27 Input chen_guo_wenH-Male 23 Input chen_hong_liang H-Male 24 Input chen_lu_hua H-Female24 Input kong_san_jian H-Male 21 Input li_you_quan H-Male 21 Input liu_bin H-Male 25 Input long_feng_boH-Male 27 Input qiu_yi H-Male 24 Input tan_zhi_hui H-Male 22 Input wu_xiao_jun H-Male 29 Input wu_yao H-Female20 Input xiao_zhi_ping H-Female23 Input xie_yi_long H-Female24 Input zhi_hui_tao H-Male 26 Input zhou_wei_huaH-Male 22 +1 +1 0 0 -1 -1 0 0 0 0 0 0+1 +1 -1 -1 0 0 0 0 0 0 0 00 0 +1 +1 -1 -1 0 0 0 0 0 0___ 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] question about thickness file
Hi all: After finishing recon-all steps, there are some thickness files generated such as lh.thickness and lh.thickness.fwhm10.fsaverage.mgh which contain cortical thickness values at each vertex. Are the thickness values in lh.thickness file calculated in individual space ,that is , they are absolute values and values in lh.thickness.fwhm10.fsaverage.mgh file computed based on fsaverage template, that is, they represent relative values ? Any suggestions appreciated.___ 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] Does the SurfArea in the lh.aparc.a2009s.stats calculated based on white matter surface or pial surface
Hi, all Does the SurfArea in the lh.aparc.a2009s.stats, as presented below(red color), calculated based on white matter surface or pial surface? any suggestions appreciated. # TableCol 10 Units unitless # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd G_and_S_frontomargin 1518988 2359 2.111 0.655 0.176 0.120 48 7.0 G_and_S_occipital_inf1831 1257 3077 2.091 0.586 0.182 0.077 40 5.8 ___ 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] In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab
Hi freesurfer experts: i'm using qdec to perform statistical analysis in Freesurfer 5.0.0, within 'Measure' menu in 'Design' tab, the default is 'thickness', however, there are other measurements such as 'area' and 'area.pial'. the latter seems meaning area in pial surface. what does the former mean? does it mean area in white matter surface?___ 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] question about FSGD file
Hi, FS experts:
I'm scanning freesurfer pages about FSGD files here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V
and i'm interested in one contrast file(the example of Contrast 5
right-left.intercept.mtx). The original FSGD file is list as follows:
GroupDescriptorFile 1
Title OSGM
Class MaleRight
Class MaleLeft
Class FemaleRight
Class FemaleLeft
Variables Age
Input subject1 MaleRight 30
Input subject2 MaleLeft 40
Input subject3 FemaleRight 50
Input subject4 FemaleLeft 60
The contrast file is : 0.5 -0.5 0.5 -0.5 0 0 0 0, meaning to exame the
difference between Righties and Lefties regressing out the effects of gender
and age.
Now i consider gender as the covariate variable ('1' represents the Male and
'2' represents the Female), and i setup a new FSGD file:
GroupDescriptorFile 2
Title OSGM
Class Right
Class Left
Variables Age gender
Input subject1 Right 30 1
Input subject2 Left 402
I also want to exame the difference as suggested above, and I setup the new
contrast file as :1 -1 0 0 0 0.
My question is that : are the new FSGD and contrast files correct to exame the
difference as suggested by original FSGD and contrast files?___
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[Freesurfer] question about Cluster-wise Correction for Multiple Comparisions
Hi all: I'm performing the group analysis on my own data using command line on FS5.1.0 and i'm a little confused about the Clusterwise Correction for Multiple Comparisions. the command is as follows: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 1 4 mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite In this command, does the vertex-wise threshold (here, '4') mean that the vertex whose p value is lower than 0.0001 can be considered to used for the Correction for Multiple Comparisions ? likewise, does the sign (here,'neg') mean that only negtive vertexs can be considered? Is there a criterion which vertex-wise threshold and sign i should choose? Hope you can give me some suggestions !___ 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] question about Correction for Multiple Comparison
Hi all: A few days ago, i have asked about some questions about Correction for Multiple Comparison. But i'm still confused about it. The version of FS is 5.1.0. when i performed Correction for Multiple Comparison using command line with 'mris_glmfit-sim', it usually took many hours to complete. However, when i performed this in qdec, it only took a few seconds. Moreover, i couldn't find command with ''mris_glmfit-sim' in the terminal except for the 'mri_surfcluster' command. I wander whether the 'mri_surfcluster' command can be used for the Correction for Multiple Comparison? Any suggestions will be appreciated. Thank you!___ 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] How to obtain cortical thickness in fsaverage space
Hi all: After finishing group analysis, how can i obtain the thickness value of each ROIs showing significant group-difference in fsaverage space? That is to say, how i get the value of each ROIs which have been normalized to the fsaverage template. The method suggested in tutorials page(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis) just tells the way to get the thickness values in individual space.___ 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] Question about DODS model and DOSS model
Hi all: I'm a little confused about the DODS model and DOSS model. I have two groups (patient and control) and one covariate (age), and I want to compare the diffirence of thickness between the groups with age as the covariate. In DODS model, is the process the analysis of variance substantially (group is a factor and age is another factor)? Generally, if there is no interaction between age and group, then i can re-run with the DOSS model to increase the statistical power.But i don't know how to determine whether there is no interaction . I hope someone give me some suggestions.___ 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] Does the fsaverage template belong to MNI space or Talairach space
Hi all: In FS, does the fsaverage template belong to MNI space or Talairach space? Thanks!___ 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] qustions about contents of label file
Hello: I use qdec to generate statistical significant areas and draw ROI and map the ROI to each subject ,finally i get a label file of each subject called lh.supriorfrontal.label which can be seen in attachment below.But i'm a little confused with content of the label file, Is it correct that,take the third row as an example,the first number 66847 means vertex index and -10.184 -3.059 74.153 means coordinate which belongs to MNI coordinate system? Besides,what does the last number 0.00 mean? Any help will be appreciative,Thanks#!ascii label , from subject NC001_R_F vox2ras=TkReg 538 66847 -10.184 -3.059 74.153 0.00 81214 -5.985 9.777 79.988 0.00 70369 -6.045 -1.003 70.503 0.00 62209 -3.632 -8.143 69.280 0.00 76787 -9.605 6.072 79.923 0.00 81186 -3.308 9.202 83.766 0.00 75659 -5.300 4.339 77.346 0.00 87742 -3.387 15.165 76.966 0.00 68014 -9.321 -2.567 71.315 0.00 64564 -5.955 -5.627 67.998 0.00 63308 -6.715 -6.715 70.826 0.00 72441 -10.990 2.207 77.064 0.00 75642 -7.627 5.043 78.336 0.00 72489 -9.493 1.337 74.370 0.00 73546 -6.718 1.928 73.747 0.00 82323 -4.862 10.406 82.019 0.00 86560 -4.074 14.339 82.167 0.00 85443 -5.798 13.640 79.396 0.00 78916 -6.586 7.805 83.501 0.00 81179 -3.831 9.351 85.033 0.00 77843 -5.115 6.503 82.305 0.00 77857 -3.665 6.189 81.723 0.00 78953 -2.699 7.223 80.223 0.00 76840 -2.894 4.990 77.493 0.00 74576 -3.457 3.157 74.126 0.00 64428 -7.243 -5.364 74.475 0.00 62173 -4.158 -7.189 72.089 0.00 59911 -1.004 -9.745 70.622 0.00 85410 -3.035 13.508 84.531 0.00 66857 -10.073 -2.523 72.737 0.00 64504 -8.664 -5.054 70.679 0.00 64471 -8.770 -4.994 72.543 0.00 71392 -10.661 0.122 75.952 0.00 73523 -10.067 1.920 75.679 0.00 70331 -10.328 -0.467 73.758 0.00 70330 -9.713 -0.398 73.133 0.00 81204 -5.051 9.754 81.029 0.00 83359 -5.362 11.402 82.004 0.00 84378 -6.318 12.229 80.608 0.00 85453 -5.925 13.761 78.183 0.00 83385 -6.801 11.382 79.304 0.00 82349 -6.680 10.543 78.971 0.00 70378 -3.872 -1.236 69.634 0.00 69242 -5.132 -1.875 69.183 0.00 61116 -4.285 -7.933 68.678 0.00 64563 -5.544 -5.391 67.391 0.00 61127 -4.025 -7.887 68.109 0.00 61137 -2.651 -8.655 67.337 0.00 61125 -2.458 -8.592 68.171 0.00 77861 -8.022 6.944 81.097 0.00 78930 -6.295 7.115 82.395 0.00 77860 -7.025 6.811 81.069 0.00 75641 -6.563 4.816 78.257 0.00 76803 -6.331 5.362 79.564 0.00 76801 -4.213 5.197 79.427 0.00 78941 -2.580 7.228 80.953 0.00 76800 -3.132 5.684 79.551 0.00 77886 -2.443 6.530 79.057 0.00 75638 -3.735 4.588 77.848 0.00 71434 -6.859 0.619 72.173 0.00 73544 -5.041 2.288 73.598 0.00 72527 -5.190 0.883 71.811 0.00 63245 -5.893 -6.295 73.236 0.00 63243 -4.171 -6.505 73.796 0.00 81178 -3.448 9.033 84.367 0.00 82297 -3.616 10.564 84.986 0.00 84341 -3.626 11.963 84.502 0.00 87722 -3.922 15.377 78.739 0.00 87706 -3.379 15.228 81.535 0.00 69229 -8.155 -1.877 70.932 0.00 66873 -6.245 -3.056 68.754 0.00 65703 -7.474 -4.235 69.097 0.00 63329 -6.708 -6.670 69.177 0.00 62196 -4.439 -7.706 70.240 0.00 75645 -10.454 4.293 78.081 0.00 76805 -8.067 5.547 79.461 0.00 74531 -9.966 3.224 76.746 0.00 73508 -8.833 2.990 76.008 0.00 74547 -7.707 3.240 75.824 0.00 73520 -6.741 2.987 74.948 0.00 72487 -7.983 1.820 73.974 0.00 71436 -8.428 0.307 72.560 0.00 81187 -3.552 9.631 83.278 0.00 83350 -3.959 11.254 83.753 0.00 83358 -4.665 11.292 82.748 0.00 86569 -4.842 13.969 81.244 0.00 87723 -4.595 15.061 78.265 0.00 86598 -4.698 14.528 76.199 0.00 66883 -5.379 -2.949 68.116 0.00 81168 -4.623 9.704 85.474 0.00 80038 -5.124 8.421 84.623 0.00 78901 -3.733 7.793 84.204 0.00 78913 -3.515 7.590 83.362 0.00 77875 -6.365 6.002 80.624 0.00 77858 -4.731 6.105 81.763 0.00 78927 -3.350 7.555 82.587 0.00 80070 -3.422 8.074 82.287 0.00 80075 -4.237 8.435 80.985 0.00 80078 -4.422 8.408 80.142 0.00 80086 -5.277 8.836 78.954 0.00 78969 -4.037 7.888 78.953 0.00 78967 -2.655 7.055 78.314 0.00 77903 -1.808 6.438 76.467 0.00 74544 -4.919 3.815 75.357 0.00 75699 -3.350 4.243 75.464 0.00 67942 -10.460 -2.375 75.890 0.00 65676 -9.205 -4.206 74.390 0.00 71354 -10.832 0.215 76.894 0.00 64469 -7.084 -5.910 72.895 0.00 62184 -4.894 -7.287 71.417 0.00 62194 -2.854 -8.154 70.292 0.00 62171 -1.963 -7.554 72.200 0.00 61094 -1.840 -8.104 70.778 0.00 61112 -1.904 -8.926 69
[Freesurfer] How to obtain volume of specific structure
Hi all: After all "recon-all -all" processing has been completed for all subjects ,I want to obtain volume of specific structure of each subject(e.g., the volume of Caudate Nucleus). But i have no idea about it,Are there some tools or commands that can help? I hope you can give me some suggestions . Thanks! ___ 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] correct mris_anatomical_stats syntax for lgi
Hi FS experts: I have run a group analysis with Local Gyrification Index (LGI) and obtained some statistical significant areas.Now I want to extract the information (lgi) of each area.Based on the QDec Group Analysis page, the following command is ran to examine cortical thickness: mris_anatomical_stats -l rh.test.label -t rh.thickness -b -f subject/stats/rh.test.stats subject rh Is it possible that i can adjust this for lgi ? If so,would i just replace the rh.thickness above with rh.pial_lgi ? many thanks for any 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] question about qdec
Hi all: I have three groups of subjects (major depression disorder,slight depression disorder and contrast),i want to use qdec to obtain the statistical significant areas containing difference of cortical thickness measurment among them. But there are some errors appearing when i run the group analysis: ERROR: QdecGlmDesign::GenerateContrasts: factor 2 must have 2 levels I think the error is related to the diagnosis.levels file which has 3 levels because i can run it successfully after removing any one of them.But i don't know why. Can you give me some help or suggestions? I have saved error information into the error.log file(see attachments) HP MD DXReading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Loading data table qdec.table.dat... Number of columns: 4 fsid column:1 Number of factors: 3 Number of subjects: 59 Reading discrete factor levels from config file ./sex.levels 'Male','Female', done Reading discrete factor levels from config file ./diagnosis.levels 'HP','MD','DX', done Data table qdec.table.dat loaded. sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n001_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d20' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n003_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd01' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n004_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d02' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n005_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd07' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n009_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd30' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n011_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd15' in SUBJECTS_DIR sh: Syntax error: Bad fd number sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n012_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_19' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n013_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d21' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n014_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d28' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n015_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d22' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n016_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d10' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n017_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d11' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n019_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d16' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n020_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd04' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n021_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d14' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n022_3_a' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't fi
