[Freesurfer] problem with generating cesvar.nii
Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: Error: MRInormWeights: values less than or eq to 0 which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] problem with generating cesvar.nii
Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. What you are trying to get is the expected variance of your difference between the ces files (as a variance, it must be positive). To get this you need cesvardiff = (cesvar1+cesvar2)/(2^2) The 2^2 is the number of inputs (2) squared. doug SHAHIN NASR wrote: Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: Error: MRInormWeights: values less than or eq to 0 which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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 ___ 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] problem with generating cesvar.nii
Thanks Doug. Just one related question. Should I also generate a new ffxdof.dat file for this map? I assumed that ffxdof depends on the number of subjects (session) and since number of subjects (sessions) is the same between the two groups then I can use those values, generated by isxconcat-sess for either map1 or map2. Right? On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. What you are trying to get is the expected variance of your difference between the ces files (as a variance, it must be positive). To get this you need cesvardiff = (cesvar1+cesvar2)/(2^2) The 2^2 is the number of inputs (2) squared. doug SHAHIN NASR wrote: Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: Error: MRInormWeights: values less than or eq to 0 which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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/**compliancelinehttp://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. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] problem with generating cesvar.nii
It should be roughly the sum of the dofs of the individual subjects. Why are you using a fixed-effects model? doug SHAHIN NASR wrote: Thanks Doug. Just one related question. Should I also generate a new ffxdof.dat file for this map? I assumed that ffxdof depends on the number of subjects (session) and since number of subjects (sessions) is the same between the two groups then I can use those values, generated by isxconcat-sess for either map1 or map2. Right? On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. What you are trying to get is the expected variance of your difference between the ces files (as a variance, it must be positive). To get this you need cesvardiff = (cesvar1+cesvar2)/(2^2) The 2^2 is the number of inputs (2) squared. doug SHAHIN NASR wrote: Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: Error: MRInormWeights: values less than or eq to 0 which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem with generating cesvar.nii
Do you suggest using random-effect model? Is there any problem with using a fix-effect model (other than the fact that by using this model we can not predict response of subjects outside our population)? On Wed, Oct 19, 2011 at 3:07 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: It should be roughly the sum of the dofs of the individual subjects. Why are you using a fixed-effects model? doug SHAHIN NASR wrote: Thanks Doug. Just one related question. Should I also generate a new ffxdof.dat file for this map? I assumed that ffxdof depends on the number of subjects (session) and since number of subjects (sessions) is the same between the two groups then I can use those values, generated by isxconcat-sess for either map1 or map2. Right? On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. What you are trying to get is the expected variance of your difference between the ces files (as a variance, it must be positive). To get this you need cesvardiff = (cesvar1+cesvar2)/(2^2) The 2^2 is the number of inputs (2) squared. doug SHAHIN NASR wrote: Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: Error: MRInormWeights: values less than or eq to 0 which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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/**compliancelinehttp://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. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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
Re: [Freesurfer] problem with generating cesvar.nii
If you don't care about extending your results beyond your sample, then an FFx is fine. doug SHAHIN NASR wrote: Do you suggest using random-effect model? Is there any problem with using a fix-effect model (other than the fact that by using this model we can not predict response of subjects outside our population)? On Wed, Oct 19, 2011 at 3:07 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It should be roughly the sum of the dofs of the individual subjects. Why are you using a fixed-effects model? doug SHAHIN NASR wrote: Thanks Doug. Just one related question. Should I also generate a new ffxdof.dat file for this map? I assumed that ffxdof depends on the number of subjects (session) and since number of subjects (sessions) is the same between the two groups then I can use those values, generated by isxconcat-sess for either map1 or map2. Right? On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. What you are trying to get is the expected variance of your difference between the ces files (as a variance, it must be positive). To get this you need cesvardiff = (cesvar1+cesvar2)/(2^2) The 2^2 is the number of inputs (2) squared. doug SHAHIN NASR wrote: Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: mris_calc -o diff_map1/rh.cesvar.nii map1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: Error: MRInormWeights: values less than or eq to 0 which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu
