Re: [Freesurfer] group level analysis
External Email - Use Caution Now I see. Thank you very much and have a good night! Best, Qi On Mon, Aug 31, 2020 at 11:12 PM Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote: > Let me put it this way. It's possible that your amygdala is bigger than > mine without your brain overall being bigger than mine. But if your corpus > callosum has higher average FA than mine, then your brain overall will have > higher average FA than mine (assuming we don't have a reverse difference > somewhere else). Higher average whole-brain FA doesn’t mean that the FA is > higher *everywhere* in the brain, so it's not a global effect in the way > that a bigger brain would be a global effect. I hope this makes sense! > -- > *From:* Zeng, Qi > *Sent:* Monday, August 31, 2020 10:57 PM > *To:* Yendiki, Anastasia > *Cc:* Freesurfer support list > *Subject:* Re: [Freesurfer] group level analysis > > > External Email - Use Caution > > Hi Anastasia, > > Thank you for the clarification! As you said, if I regress out the global > FA, I could wipe out the regional FA. But what if my question is to find > out exactly which regional FA differentiate the two groups rather than if > global FA is different between groups. In that case, should I control the > global FA when running regional FA between groups? > > Best, > Qi > > On Mon, Aug 31, 2020 at 10:41 PM Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > > Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or > surface area measures. > > In a situation where a regional FA difference is high enough to also cause > a whole brain FA difference, regressing out the latter could wipe out the > former. Not sure why you'd want to do that, unless there's a specific > question you want to ask that requires it. > > Anastasia. > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < > qi.z...@icahn.mssm.edu> > *Sent:* Monday, August 31, 2020 10:03 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] group level analysis > > > External Email - Use Caution > > Hi Anastasia, > > Thank you for your reply. So for segmentation.stats, should I divide the > regional areas by eTIV or treat it as a covariate for a group comparison? > Is it the same with Total cerebral white matter volume for wmparc.stats. > For Diffusion measurement, for example, FA, if a subject has lower FA in > general in the brain, should I adjust the whole brain FA or average FA for > that matter? > > Best, > Qi > > On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > > Hi Qi - Correcting for overall brain size is important when you are > comparing measures of length/area/volume. As in, you want to know if a > region specifically is bigger in population A vs. B, and not just because > the whole brain is bigger. In that case, use eTIV (estimated total > intracranial volume) from the freesurfer segmentation stats. > > FA is not measuring size of a region, so correcting for brain size is less > of an issue there. It's a possibility perhaps that for someone with a > substantially smaller brain there may be more partial voluming affecting > FA, so it can't hurt to check for an effect before including it in your > analysis. > > Anastasia. > ------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < > qi.z...@icahn.mssm.edu> > *Sent:* Monday, August 31, 2020 11:44 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] group level analysis > > > External Email - Use Caution > > Hi, > > When conducting group-level analysis, for example comparing volumetric > differences or tractography FA across subjects between groups. How we > correct for the size of the brain when comparing volumetric differences or > correct for the whole brain FA? > Thank you so much! > > Best, > Qi > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Ph.D. candidate > Icahn School of Medicine at Mount Sinai > > 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/compliance
Re: [Freesurfer] group level analysis
Let me put it this way. It's possible that your amygdala is bigger than mine without your brain overall being bigger than mine. But if your corpus callosum has higher average FA than mine, then your brain overall will have higher average FA than mine (assuming we don't have a reverse difference somewhere else). Higher average whole-brain FA doesn’t mean that the FA is higher *everywhere* in the brain, so it's not a global effect in the way that a bigger brain would be a global effect. I hope this makes sense! From: Zeng, Qi Sent: Monday, August 31, 2020 10:57 PM To: Yendiki, Anastasia Cc: Freesurfer support list Subject: Re: [Freesurfer] group level analysis External Email - Use Caution Hi Anastasia, Thank you for the clarification! As you said, if I regress out the global FA, I could wipe out the regional FA. But what if my question is to find out exactly which regional FA differentiate the two groups rather than if global FA is different between groups. In that case, should I control the global FA when running regional FA between groups? Best, Qi On Mon, Aug 31, 2020 at 10:41 PM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or surface area measures. In a situation where a regional FA difference is high enough to also cause a whole brain FA difference, regressing out the latter could wipe out the former. Not sure why you'd want to do that, unless there's a specific question you want to ask that requires it. Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Zeng, Qi mailto:qi.z...@icahn.mssm.edu>> Sent: Monday, August 31, 2020 10:03 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] group level analysis External Email - Use Caution Hi Anastasia, Thank you for your reply. So for segmentation.stats, should I divide the regional areas by eTIV or treat it as a covariate for a group comparison? Is it the same with Total cerebral white matter volume for wmparc.stats. For Diffusion measurement, for example, FA, if a subject has lower FA in general in the brain, should I adjust the whole brain FA or average FA for that matter? Best, Qi On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Qi - Correcting for overall brain size is important when you are comparing measures of length/area/volume. As in, you want to know if a region specifically is bigger in population A vs. B, and not just because the whole brain is bigger. In that case, use eTIV (estimated total intracranial volume) from the freesurfer segmentation stats. FA is not measuring size of a region, so correcting for brain size is less of an issue there. It's a possibility perhaps that for someone with a substantially smaller brain there may be more partial voluming affecting FA, so it can't hurt to check for an effect before including it in your analysis. Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Zeng, Qi mailto:qi.z...@icahn.mssm.edu>> Sent: Monday, August 31, 2020 11:44 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] group level analysis External Email - Use Caution Hi, When conducting group-level analysis, for example comparing volumetric differences or tractography FA across subjects between groups. How we correct for the size of the brain when comparing volumetric differences or correct for the whole brain FA? Thank you so much! Best, Qi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Ph.D. candidate Icahn School of Medicine at Mount Sinai 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. -- Ph.D. candidate Icahn School of Medicine at Mount Sinai ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] group level analysis
External Email - Use Caution Hi Anastasia, Thank you for the clarification! As you said, if I regress out the global FA, I could wipe out the regional FA. But what if my question is to find out exactly which regional FA differentiate the two groups rather than if global FA is different between groups. In that case, should I control the global FA when running regional FA between groups? Best, Qi On Mon, Aug 31, 2020 at 10:41 PM Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote: > Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or > surface area measures. > > In a situation where a regional FA difference is high enough to also cause > a whole brain FA difference, regressing out the latter could wipe out the > former. Not sure why you'd want to do that, unless there's a specific > question you want to ask that requires it. > > Anastasia. > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < > qi.z...@icahn.mssm.edu> > *Sent:* Monday, August 31, 2020 10:03 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] group level analysis > > > External Email - Use Caution > > Hi Anastasia, > > Thank you for your reply. So for segmentation.stats, should I divide the > regional areas by eTIV or treat it as a covariate for a group comparison? > Is it the same with Total cerebral white matter volume for wmparc.stats. > For Diffusion measurement, for example, FA, if a subject has lower FA in > general in the brain, should I adjust the whole brain FA or average FA for > that matter? > > Best, > Qi > > On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > > Hi Qi - Correcting for overall brain size is important when you are > comparing measures of length/area/volume. As in, you want to know if a > region specifically is bigger in population A vs. B, and not just because > the whole brain is bigger. In that case, use eTIV (estimated total > intracranial volume) from the freesurfer segmentation stats. > > FA is not measuring size of a region, so correcting for brain size is less > of an issue there. It's a possibility perhaps that for someone with a > substantially smaller brain there may be more partial voluming affecting > FA, so it can't hurt to check for an effect before including it in your > analysis. > > Anastasia. > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < > qi.z...@icahn.mssm.edu> > *Sent:* Monday, August 31, 2020 11:44 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] group level analysis > > > External Email - Use Caution > > Hi, > > When conducting group-level analysis, for example comparing volumetric > differences or tractography FA across subjects between groups. How we > correct for the size of the brain when comparing volumetric differences or > correct for the whole brain FA? > Thank you so much! > > Best, > Qi > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Ph.D. candidate > Icahn School of Medicine at Mount Sinai > > 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. > -- Ph.D. candidate Icahn School of Medicine at Mount Sinai ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] group level analysis
Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or surface area measures. In a situation where a regional FA difference is high enough to also cause a whole brain FA difference, regressing out the latter could wipe out the former. Not sure why you'd want to do that, unless there's a specific question you want to ask that requires it. Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zeng, Qi Sent: Monday, August 31, 2020 10:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] group level analysis External Email - Use Caution Hi Anastasia, Thank you for your reply. So for segmentation.stats, should I divide the regional areas by eTIV or treat it as a covariate for a group comparison? Is it the same with Total cerebral white matter volume for wmparc.stats. For Diffusion measurement, for example, FA, if a subject has lower FA in general in the brain, should I adjust the whole brain FA or average FA for that matter? Best, Qi On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Qi - Correcting for overall brain size is important when you are comparing measures of length/area/volume. As in, you want to know if a region specifically is bigger in population A vs. B, and not just because the whole brain is bigger. In that case, use eTIV (estimated total intracranial volume) from the freesurfer segmentation stats. FA is not measuring size of a region, so correcting for brain size is less of an issue there. It's a possibility perhaps that for someone with a substantially smaller brain there may be more partial voluming affecting FA, so it can't hurt to check for an effect before including it in your analysis. Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Zeng, Qi mailto:qi.z...@icahn.mssm.edu>> Sent: Monday, August 31, 2020 11:44 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] group level analysis External Email - Use Caution Hi, When conducting group-level analysis, for example comparing volumetric differences or tractography FA across subjects between groups. How we correct for the size of the brain when comparing volumetric differences or correct for the whole brain FA? Thank you so much! Best, Qi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Ph.D. candidate Icahn School of Medicine at Mount Sinai ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] group level analysis
External Email - Use Caution Hi Anastasia, Thank you for your reply. So for segmentation.stats, should I divide the regional areas by eTIV or treat it as a covariate for a group comparison? Is it the same with Total cerebral white matter volume for wmparc.stats. For Diffusion measurement, for example, FA, if a subject has lower FA in general in the brain, should I adjust the whole brain FA or average FA for that matter? Best, Qi On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia wrote: > Hi Qi - Correcting for overall brain size is important when you are > comparing measures of length/area/volume. As in, you want to know if a > region specifically is bigger in population A vs. B, and not just because > the whole brain is bigger. In that case, use eTIV (estimated total > intracranial volume) from the freesurfer segmentation stats. > > FA is not measuring size of a region, so correcting for brain size is less > of an issue there. It's a possibility perhaps that for someone with a > substantially smaller brain there may be more partial voluming affecting > FA, so it can't hurt to check for an effect before including it in your > analysis. > > Anastasia. > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < > qi.z...@icahn.mssm.edu> > *Sent:* Monday, August 31, 2020 11:44 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] group level analysis > > > External Email - Use Caution > > Hi, > > When conducting group-level analysis, for example comparing volumetric > differences or tractography FA across subjects between groups. How we > correct for the size of the brain when comparing volumetric differences or > correct for the whole brain FA? > Thank you so much! > > Best, > Qi > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Ph.D. candidate Icahn School of Medicine at Mount Sinai ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] group level analysis
Hi Qi - Correcting for overall brain size is important when you are comparing measures of length/area/volume. As in, you want to know if a region specifically is bigger in population A vs. B, and not just because the whole brain is bigger. In that case, use eTIV (estimated total intracranial volume) from the freesurfer segmentation stats. FA is not measuring size of a region, so correcting for brain size is less of an issue there. It's a possibility perhaps that for someone with a substantially smaller brain there may be more partial voluming affecting FA, so it can't hurt to check for an effect before including it in your analysis. Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zeng, Qi Sent: Monday, August 31, 2020 11:44 AM To: Freesurfer support list Subject: [Freesurfer] group level analysis External Email - Use Caution Hi, When conducting group-level analysis, for example comparing volumetric differences or tractography FA across subjects between groups. How we correct for the size of the brain when comparing volumetric differences or correct for the whole brain FA? Thank you so much! Best, Qi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] group level analysis
External Email - Use Caution Hi, When conducting group-level analysis, for example comparing volumetric differences or tractography FA across subjects between groups. How we correct for the size of the brain when comparing volumetric differences or correct for the whole brain FA? Thank you so much! Best, Qi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Group level analysis: Specifying contrasts
On 04/12/2016 04:16 PM, Afzal, Afsana wrote: > The source data is from a gambling task that has multiple levels of risk and > reward. The offset refers to the risk level and the slope refers to the > monetary reward for that particular risk level. > > We were doing some parametric modulation in the first level analysis. For the > second levels, currently I'm just looking at the offset values which is why > the slope rows are all zeros. I don't think this makes sense. If you don't want it there, then it must not be in the FSGD file. What are you trying to test at the group level? > > Please let me know if that makes sense, > > Afsana > > __ > Afsana Afzal > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Monday, April 11, 2016 11:19 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts > > What is your source data? It looks like you have two time points per > subject, but the names of "offset" and "slope" suggest some preprocessing? > > Input hc001-lRsk_offset hc001100 > Input hc001-lRsk_slope hc001000 > Input hc001-mRsk_offset hc001010 > Input hc001-mRsk_slope hc001000 > Input hc001-hRsk_offset hc001001 > Input hc001-hRsk_slope hc001000 > > > > On 04/11/2016 10:09 AM, Afzal, Afsana wrote: >> Hi Doug, >> >> I've attached the fsgd file and the contrast matrix file. Thanks for your >> help! >> >> - Afsana >> >> __ >> Afsana Afzal >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> ________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Friday, April 08, 2016 12:07 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts >> >> I don't know what you mean, can you just send the header of the fsgd >> file and the contrast matrix? >> >> On 04/04/2016 11:20 AM, Afzal, Afsana wrote: >>> Hi, >>> >>> I want to perform a linear regression for a task with 3 different risk >>> conditions (low, medium, high) with the following linear trend: low = >>> 1, medium = 2, high = 3. >>> >>> Right now I'm specifying the above weighted under each risk condition >>> in my contrast matrix. Is this the correct approach? I want to make >>> sure I am calculating a regression and not a weighted average. >>> >>> Thank you for your help, >>> >>> Afsana >>> >>> >>> __ >>> *Afsana Afzal* >>> Clinical Research Coordinator >>> Massachusetts General Hospital >>> Division of Neurotherapeutics >>> Department of Psychiatry: Neurosciences >>> 149 13th St, Room 2612 >>> Charlestown, MA 02129 >>> Phone: 617-643-5129 >>> Fax: 617-726-4078 >>> >>> >>> ___ >>> 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 >
Re: [Freesurfer] Group level analysis: Specifying contrasts
The source data is from a gambling task that has multiple levels of risk and reward. The offset refers to the risk level and the slope refers to the monetary reward for that particular risk level. We were doing some parametric modulation in the first level analysis. For the second levels, currently I'm just looking at the offset values which is why the slope rows are all zeros. Please let me know if that makes sense, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, April 11, 2016 11:19 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts What is your source data? It looks like you have two time points per subject, but the names of "offset" and "slope" suggest some preprocessing? Input hc001-lRsk_offset hc001100 Input hc001-lRsk_slope hc001000 Input hc001-mRsk_offset hc001010 Input hc001-mRsk_slope hc001000 Input hc001-hRsk_offset hc001001 Input hc001-hRsk_slope hc001000 On 04/11/2016 10:09 AM, Afzal, Afsana wrote: > Hi Doug, > > I've attached the fsgd file and the contrast matrix file. Thanks for your > help! > > - Afsana > > __ > Afsana Afzal > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, April 08, 2016 12:07 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts > > I don't know what you mean, can you just send the header of the fsgd > file and the contrast matrix? > > On 04/04/2016 11:20 AM, Afzal, Afsana wrote: >> Hi, >> >> I want to perform a linear regression for a task with 3 different risk >> conditions (low, medium, high) with the following linear trend: low = >> 1, medium = 2, high = 3. >> >> Right now I'm specifying the above weighted under each risk condition >> in my contrast matrix. Is this the correct approach? I want to make >> sure I am calculating a regression and not a weighted average. >> >> Thank you for your help, >> >> Afsana >> >> >> __ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> >> ___ >> 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 > > > ___ > 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 ___
Re: [Freesurfer] Group level analysis: Specifying contrasts
What is your source data? It looks like you have two time points per subject, but the names of "offset" and "slope" suggest some preprocessing? Input hc001-lRsk_offset hc001100 Input hc001-lRsk_slope hc001000 Input hc001-mRsk_offset hc001010 Input hc001-mRsk_slope hc001000 Input hc001-hRsk_offset hc001001 Input hc001-hRsk_slope hc001000 On 04/11/2016 10:09 AM, Afzal, Afsana wrote: > Hi Doug, > > I've attached the fsgd file and the contrast matrix file. Thanks for your > help! > > - Afsana > > __ > Afsana Afzal > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, April 08, 2016 12:07 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts > > I don't know what you mean, can you just send the header of the fsgd > file and the contrast matrix? > > On 04/04/2016 11:20 AM, Afzal, Afsana wrote: >> Hi, >> >> I want to perform a linear regression for a task with 3 different risk >> conditions (low, medium, high) with the following linear trend: low = >> 1, medium = 2, high = 3. >> >> Right now I'm specifying the above weighted under each risk condition >> in my contrast matrix. Is this the correct approach? I want to make >> sure I am calculating a regression and not a weighted average. >> >> Thank you for your help, >> >> Afsana >> >> >> __ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> >> >> ___ >> 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 > > > ___ > 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.
Re: [Freesurfer] Group level analysis: Specifying contrasts
Hi Doug, I've attached the fsgd file and the contrast matrix file. Thanks for your help! - Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, April 08, 2016 12:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts I don't know what you mean, can you just send the header of the fsgd file and the contrast matrix? On 04/04/2016 11:20 AM, Afzal, Afsana wrote: > Hi, > > I want to perform a linear regression for a task with 3 different risk > conditions (low, medium, high) with the following linear trend: low = > 1, medium = 2, high = 3. > > Right now I'm specifying the above weighted under each risk condition > in my contrast matrix. Is this the correct approach? I want to make > sure I am calculating a regression and not a weighted average. > > Thank you for your help, > > Afsana > > > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > ___ > 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 avg.risk.mod.fsgd Description: avg.risk.mod.fsgd weight_avg.mtx Description: weight_avg.mtx ___ 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] Group level analysis: Specifying contrasts
I don't know what you mean, can you just send the header of the fsgd file and the contrast matrix? On 04/04/2016 11:20 AM, Afzal, Afsana wrote: > Hi, > > I want to perform a linear regression for a task with 3 different risk > conditions (low, medium, high) with the following linear trend: low = > 1, medium = 2, high = 3. > > Right now I'm specifying the above weighted under each risk condition > in my contrast matrix. Is this the correct approach? I want to make > sure I am calculating a regression and not a weighted average. > > Thank you for your help, > > Afsana > > > __ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > > > ___ > 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] Group level analysis: Specifying contrasts
Hi, I want to perform a linear regression for a task with 3 different risk conditions (low, medium, high) with the following linear trend: low = 1, medium = 2, high = 3. Right now I'm specifying the above weighted under each risk condition in my contrast matrix. Is this the correct approach? I want to make sure I am calculating a regression and not a weighted average. Thank you for your help, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ___ 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] group level analysis
Use mri_vol2surf to convert the individual vols to surface overlays, then use mri_concat to put them together as a multi-frame file. Or you can use mris_preproc to do all of this. They both have --help with more info. doug On Mon, 27 Nov 2006, Emily Cooper wrote: Hi, I have functional datasets (.HEAD and .BRIK) from Afni that I'm trying to analyze in the surface domain using Freesurfer. I have Freesurfer anatomical surfaces for all my subjects, and have managed to use the tkmedit and tksurfer gui's to map my functional overlays (using the calculate identity matrix option) onto the volume and surface. What I'd like to do now is map the functional data onto a surface with a common number of nodes so that I can extract a matrix of beta values and do group level analysis using R. Tksurfer seems to be able to do this with the Save plotted data to table option (greyed over right now), however, I've read in other messages on the mail archive that the sphere.reg surface is not in common space. I've been trying to use func2sph-sess, but I seem to be missing something, getting ERROR: cannot find any sessions. Maybe that's the wrong way to go about it? Thanks, Emily -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
