External Email - Use Caution
Dear Experts,
I am running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file. I would now like to run a cluster level correction on these data at the level of each individual subject using mri_mcsim followed by mri_surfcluster and I would like to constrain my inference to a ROI. I have a few questions. First of all, is it correct that I should to a -log10(p) transform on my p values before entering them in mri_surfcluster? Second, will the csd generated by mcsim be valid to feed in mri_surfcluster since the values are a -log10(p) transformed? Does mcsim -log transform the gaussian noise it uses at some point or is this not necessary? My calls to the two methods are as follows (for one hemisphere):
First the mcsim:
mri_mcsim --o “${subject}_mcsim_lh_${roi}" --base mc-z --surface ${subject} lh --nreps 10000 --label $roi
Then the mri_surfcluster: mri_surfcluster --in "/${subject}_lh_${roi}_neglog10p_signed.mgh" \ --csd "${subject}_mcsim_lh_${roi}/fwhm05/abs/th30/mc-z.csd" \ --clabel "${subject}/label/lh.${roi}.label" \ --cwsig "${subject}_lh_${roi}_neglog10p_abs_clu05.mgh" \ --vwsig "${subject}_lh_${roi}_neglog10p_abs_vox05.mgh" \ --sum "${subject}_lh_${roi}_neglog10p_abs_summary.txt" \ --thmin 3 \ --surf white \ --subject ${subject } \ --hemi lh \ --ocn “${subject}_lh_${roi}_neglog10p_abs_clu05_clunum.mgh" \ --cwpvalthresh 0.05
In the call of mri_surfcluster, I want a cluster forming threshold of p=0.001, which would correspond to -logp(0.001)=3. Is it correct that the argument --thmin should be expressed as -log10(p) but the parameter cwpvalthresh should be p? The reason why I think I did something wrong is that I get a lot of clusters from this analysis, sometimes >15 per individual. This makes me think that the correction might not be as stringent as I would like to. Thank you,
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edumailto:ltozzi@stanford.edu | (650) 5615738
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Is there a reason that you are not using mri_glmfit-sim to do this? It is fairly complicated, and so I spent a lot of time writing mri_glmfit-sim to make sure it does the right thing.
On 4/29/2021 6:16 PM, Leonardo Tozzi wrote:
External Email - Use Caution
Dear Experts,
I am running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file.
I would now like to run a cluster level correction on these data at the level of each individual subject using mri_mcsim followed by mri_surfcluster and I would like to constrain my inference to a ROI.
I have a few questions. First of all, is it correct that I should to a -log10(p) transform on my p values before entering them in mri_surfcluster?
Second, will the csd generated by mcsim be valid to feed in mri_surfcluster since the values are a -log10(p) transformed? Does mcsim -log transform the gaussian noise it uses at some point or is this not necessary?
My calls to the two methods are as follows (for one hemisphere):
First the mcsim:
mri_mcsim --o“${subject}_mcsim_lh_${roi}"--basemc-z --surface${subject}lh --nreps10000--label$roi
Then the mri_surfcluster:
mri_surfcluster --in "/${subject}_lh_${roi}_neglog10p_signed.mgh" \
--csd "${subject}_mcsim_lh_${roi}/fwhm05/abs/th30/mc-z.csd" \
--clabel "${subject}/label/lh.${roi}.label" \
--cwsig "${subject}_lh_${roi}_neglog10p_abs_clu05.mgh" \
--vwsig "${subject}_lh_${roi}_neglog10p_abs_vox05.mgh" \
--sum "${subject}_lh_${roi}_neglog10p_abs_summary.txt" \
--thmin 3 \
--surf white \
--subject ${subject } \
--hemi lh \
--ocn “${subject}_lh_${roi}_neglog10p_abs_clu05_clunum.mgh" \
--cwpvalthresh 0.05
In the call of mri_surfcluster, I want a cluster forming threshold of p=0.001, which would correspond to -logp(0.001)=3. Is it correct that the argument --thmin should be expressed as -log10(p) but the parameter cwpvalthresh should be p?
The reason why I think I did something wrong is that I get a lot of clusters from this analysis, sometimes >15 per individual. This makes me think that the correction might not be as stringent as I would like to.
Thank you,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Researcher
Stanford University | 401 Quarry Rd
ltozzi@stanford.edu mailto:ltozzi@stanford.edu | (650) 5615738
*/Connect with us!/*
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Dear Douglas,
The reason is that I am running a GLM at the subject level on 4D fMRI timeseries. Thus, I obtain a parameter estimate on each vertex, which I can then enter in a contrast to obtain a p-value per vertex. These are the p-values I want to correct. From what I understand, the mri_glmfit does not work on timeseries data, am I wrong in this? So at the moment I am fitting the GLM in matlab and using the mcsim to correct the p-values I obtain. Best,
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edumailto:ltozzi@stanford.edu | (650) 5615738
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From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, May 10, 2021 at 8:32 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster correction at subject level using -log10(p) values
Is there a reason that you are not using mri_glmfit-sim to do this? It is fairly complicated, and so I spent a lot of time writing mri_glmfit-sim to make sure it does the right thing. On 4/29/2021 6:16 PM, Leonardo Tozzi wrote:
External Email - Use Caution Dear Experts,
I am running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file. I would now like to run a cluster level correction on these data at the level of each individual subject using mri_mcsim followed by mri_surfcluster and I would like to constrain my inference to a ROI. I have a few questions. First of all, is it correct that I should to a -log10(p) transform on my p values before entering them in mri_surfcluster? Second, will the csd generated by mcsim be valid to feed in mri_surfcluster since the values are a -log10(p) transformed? Does mcsim -log transform the gaussian noise it uses at some point or is this not necessary? My calls to the two methods are as follows (for one hemisphere):
First the mcsim:
mri_mcsim --o “${subject}_mcsim_lh_${roi}" --base mc-z --surface ${subject} lh --nreps 10000 --label $roi
Then the mri_surfcluster: mri_surfcluster --in "/${subject}_lh_${roi}_neglog10p_signed.mgh" \ --csd "${subject}_mcsim_lh_${roi}/fwhm05/abs/th30/mc-z.csd" \ --clabel "${subject}/label/lh.${roi}.label" \ --cwsig "${subject}_lh_${roi}_neglog10p_abs_clu05.mgh" \ --vwsig "${subject}_lh_${roi}_neglog10p_abs_vox05.mgh" \ --sum "${subject}_lh_${roi}_neglog10p_abs_summary.txt" \ --thmin 3 \ --surf white \ --subject ${subject } \ --hemi lh \ --ocn “${subject}_lh_${roi}_neglog10p_abs_clu05_clunum.mgh" \ --cwpvalthresh 0.05
In the call of mri_surfcluster, I want a cluster forming threshold of p=0.001, which would correspond to -logp(0.001)=3. Is it correct that the argument --thmin should be expressed as -log10(p) but the parameter cwpvalthresh should be p? The reason why I think I did something wrong is that I get a lot of clusters from this analysis, sometimes >15 per individual. This makes me think that the correction might not be as stringent as I would like to. Thank you,
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edumailto:ltozzi@stanford.edu | (650) 5615738
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when you say time series, do you mean like fMRI? What are you using to do the time series analysis?
On 5/10/2021 12:56 PM, Leonardo Tozzi wrote:
External Email - Use Caution
Dear Douglas,
The reason is that I am running a GLM at the subject level on 4D fMRI timeseries. Thus, I obtain a parameter estimate on each vertex, which I can then enter in a contrast to obtain a p-value per vertex. These are the p-values I want to correct.
From what I understand, the mri_glmfit does not work on timeseries data, am I wrong in this? So at the moment I am fitting the GLM in matlab and using the mcsim to correct the p-values I obtain.
Best,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Researcher
Stanford University | 401 Quarry Rd
ltozzi@stanford.edu mailto:ltozzi@stanford.edu | (650) 5615738
*/Connect with us!/*
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*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, May 10, 2021 at 8:32 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Cluster correction at subject level using -log10(p) values
Is there a reason that you are not using mri_glmfit-sim to do this? It is fairly complicated, and so I spent a lot of time writing mri_glmfit-sim to make sure it does the right thing.
On 4/29/2021 6:16 PM, Leonardo Tozzi wrote:
* External Email - Use Caution * Dear Experts, I am running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file. I would now like to run a cluster level correction on these data at the level of each individual subject using mri_mcsim followed by mri_surfcluster and I would like to constrain my inference to a ROI. I have a few questions. First of all, is it correct that I should to a -log10(p) transform on my p values before entering them in mri_surfcluster? Second, will the csd generated by mcsim be valid to feed in mri_surfcluster since the values are a -log10(p) transformed? Does mcsim -log transform the gaussian noise it uses at some point or is this not necessary? My calls to the two methods are as follows (for one hemisphere): First the mcsim: mri_mcsim --o“${subject}_mcsim_lh_${roi}"--basemc-z --surface${subject}lh --nreps10000--label$roi Then the mri_surfcluster: mri_surfcluster --in "/${subject}_lh_${roi}_neglog10p_signed.mgh" \ --csd "${subject}_mcsim_lh_${roi}/fwhm05/abs/th30/mc-z.csd" \ --clabel "${subject}/label/lh.${roi}.label" \ --cwsig "${subject}_lh_${roi}_neglog10p_abs_clu05.mgh" \ --vwsig "${subject}_lh_${roi}_neglog10p_abs_vox05.mgh" \ --sum "${subject}_lh_${roi}_neglog10p_abs_summary.txt" \ --thmin 3 \ --surf white \ --subject ${subject } \ --hemi lh \ --ocn “${subject}_lh_${roi}_neglog10p_abs_clu05_clunum.mgh" \ --cwpvalthresh 0.05 In the call of mri_surfcluster, I want a cluster forming threshold of p=0.001, which would correspond to -logp(0.001)=3. Is it correct that the argument --thmin should be expressed as -log10(p) but the parameter cwpvalthresh should be p? The reason why I think I did something wrong is that I get a lot of clusters from this analysis, sometimes >15 per individual. This makes me think that the correction might not be as stringent as I would like to. Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edu <mailto:ltozzi@stanford.edu> | (650) 5615738 */Connect with us!/* signature_1075933358 <https://secure-web.cisco.com/154LqJFzFLISeYtGLsUgwToWD-mN0G4thIfubhtThzJ6F9WpZSTHEctacwX441OLHfh0UtXPCqIHTqi5NxPGqT2vUp9CwVwxTzGfBbalFm29WK-Yzcl2RjBUxGhmSPmqPMvC5_lVL--iJnfmI6UeHzCc-S6OiCJlNeTqRnb9_nAuI5_dJET2YyMRosEGTGNbjRv_nVN5ldRMD4kPNEx9WKGBzfYCQ3kDQ-Ra9E218aIcmmCY4JaMtm6GkDjrbqLvcl618Zmp1lMa9iU7tJkHhow/https%3A%2F%2Ftwitter.com%2FStanford_PMHW>signature_1282923475 <http://secure-web.cisco.com/11JA0cps0LSyc_YKkvLkjj53ioS8G144vcOsjQghqMz-F2MNt-O4PUFyL4YII8C5Z9LTyzgqfxbuDRq_46cX1PtKAbMhM4GIHWkkCg-co9I8z5igR2VGlwK_p2gWbca9vQWwDALu4ub97LG4mV0U5oKnD6zvPTZG5f1BRGtbSPj70hUakvd67X8RGEcucVASu9ra_Ek3llRS0AQ5zB6YJJ_MXtuHflVQ%20Lr48It6WMEf-rGUhutwIrS7BOv_XHBjBa81gBLfzG-YreHqzY9a5vMw/http%3A%2F%2Fwww.instagram.com%2Fstanfordpmhw><https://secure-web.cisco.com/1Mkao1uevqs0RL-8o0FG2efSSKGQAOwrHeahbv3dcsTbir-fMSJHMfQqDXmA-tuPwCl7qTwImS5GKeZlsVtpCZp1YhxywSgtJggCNjKUu-B9Duw2r04zO0YxOnZhVWq46szPxGdWR64Tx1C6RpT6TUytcKHDeSjJJVuu5CYeokwKF73Rf3EG3LVwDbQ0F4B4BVIp58hzou_hlElyn3nx-33Rd7og_GmnFjH8uIQmtpJFwMxLIABNV29kr9BdhAFG1MweyTWY7qrle2auQEIPEZg/https%3A%2F%2Fwww.youtube.com%2Fchannel%2FUCN8g9b2eCpSRMs6AyY15U3g> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1rNpkydT6yNRhvVQDXqwJmFoBflgQFLTsOh26W0gU7Jveix-_VmqzGwpyvr_1jILHvCgIQ7hX85Tgr3BSAxjjjxT9C5BzPKnGW7yuOxfbjtUM2LaM42wSu8fwulUpg1BBIOtAc-VQgjqR_soC1wnopnURuJ0HfoFZou533Y2lsObYEj1Emq3GQ-XP-6uMvOPORmJj4zJsibLc5frkersKnVatWpacD7qbLPMYgAOlKytULWvjMf8mOIlE6XT5AZSbUGS5mTOtP3WxoeiVs99DPw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Dear Douglas, Yes, I mean fMRI. I am currently using MATLAB to fit a GLM to the timeseries and then export the p-values as a MGH file of the cortical surface. Best,
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edumailto:ltozzi@stanford.edu | (650) 5615738
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From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, May 10, 2021 at 9:59 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster correction at subject level using -log10(p) values
when you say time series, do you mean like fMRI? What are you using to do the time series analysis? On 5/10/2021 12:56 PM, Leonardo Tozzi wrote:
External Email - Use Caution Dear Douglas,
The reason is that I am running a GLM at the subject level on 4D fMRI timeseries. Thus, I obtain a parameter estimate on each vertex, which I can then enter in a contrast to obtain a p-value per vertex. These are the p-values I want to correct. From what I understand, the mri_glmfit does not work on timeseries data, am I wrong in this? So at the moment I am fitting the GLM in matlab and using the mcsim to correct the p-values I obtain. Best,
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edumailto:ltozzi@stanford.edu | (650) 5615738
Connect with us! [signature_1075933358]https://secure-web.cisco.com/1FKpYRw97JWaPWT3ZAl3Lrox-jM21LmxbF9ZEHeU5qtHK-REW8TIf1MW-5kY8B6dFUSXrgHaf46PyRtQKE8f3gG5AAyxhr6ES4lBT6gXJP6GfDBPiZbxiVXsMDbX5gf1PL_znG0avOIRVijb38ZGIT5OPqbuwZTn6HGzoFTK2qSoWCLAxiZKvfTrjDXknNVHPQxUVmN8igcVPw6-Cb-0RkJKxijEzftxOk0L_iZIIQDonT8C1ts9_WFMMuoLds6Md97O2q0j_9_0PbhbPA4-07w/https%3A%2F%2Ftwitter.com%2FStanford_PMHW [signature_1282923475] http://secure-web.cisco.com/1sx0mz8OLK99iEtgYKvr6T3_J6EjPXUU16knmNMN3b8cwqdKo28zt3WmPEQKJD1R4ybfh_HV2rspULGmh0pFWOlUofYpr7dgO9sgn3N0O1ebPAQ8HshmLGR7VN2Tb9uX5sAFAUe4SmdrbgUDvk4qn70EYfRquPq4Sl0Ggv9Otcl0EZRGZF6OrMkK63So70LW10odUwyQWzzaxDLojNVzG5-s9neWtPL7f%20cX290V7cqgkePcf_X-FBQCO4N_2EU75nypfE_me1wiLrhtRjcTGieA/http%3A%2F%2Fwww.instagram.com%2Fstanfordpmhw [signa! ture_911 042299] https://secure-web.cisco.com/1rFWgvMDaCNKwptwR5qEZMc2o0R1f2IQPHcILZbxp-S3YMOvUqMg_R2_n7y4Vkawe4o4uA-PJ-CV5cowGQasEg3DVF8rRZRNRRc2E77SvL9w_gB0BrCQF9p5k-lqZqg6ok9WLXeubEt9iWVvvsa_Zsvf4OFXpB33Izh4QXizNzewipo9fikUIGu-3tyh_uf15_DYTi0Z-Io4rZbtt3hLE_bf42BNxtiJV_taNlYtz6eL2HnOrg83OLH48xFez2popaRWnjZHgqY4YIY84nv-Esg/https%3A%2F%2Fwww.youtube.com%2Fchannel%2FUCN8g9b2eCpSRMs6AyY15U3g
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, May 10, 2021 at 8:32 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster correction at subject level using -log10(p) values
Is there a reason that you are not using mri_glmfit-sim to do this? It is fairly complicated, and so I spent a lot of time writing mri_glmfit-sim to make sure it does the right thing. On 4/29/2021 6:16 PM, Leonardo Tozzi wrote:
External Email - Use Caution Dear Experts,
I am running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file. I would now like to run a cluster level correction on these data at the level of each individual subject using mri_mcsim followed by mri_surfcluster and I would like to constrain my inference to a ROI. I have a few questions. First of all, is it correct that I should to a -log10(p) transform on my p values before entering them in mri_surfcluster? Second, will the csd generated by mcsim be valid to feed in mri_surfcluster since the values are a -log10(p) transformed? Does mcsim -log transform the gaussian noise it uses at some point or is this not necessary? My calls to the two methods are as follows (for one hemisphere):
First the mcsim:
mri_mcsim --o “${subject}_mcsim_lh_${roi}" --base mc-z --surface ${subject} lh --nreps 10000 --label $roi
Then the mri_surfcluster: mri_surfcluster --in "/${subject}_lh_${roi}_neglog10p_signed.mgh" \ --csd "${subject}_mcsim_lh_${roi}/fwhm05/abs/th30/mc-z.csd" \ --clabel "${subject}/label/lh.${roi}.label" \ --cwsig "${subject}_lh_${roi}_neglog10p_abs_clu05.mgh" \ --vwsig "${subject}_lh_${roi}_neglog10p_abs_vox05.mgh" \ --sum "${subject}_lh_${roi}_neglog10p_abs_summary.txt" \ --thmin 3 \ --surf white \ --subject ${subject } \ --hemi lh \ --ocn “${subject}_lh_${roi}_neglog10p_abs_clu05_clunum.mgh" \ --cwpvalthresh 0.05
In the call of mri_surfcluster, I want a cluster forming threshold of p=0.001, which would correspond to -logp(0.001)=3. Is it correct that the argument --thmin should be expressed as -log10(p) but the parameter cwpvalthresh should be p? The reason why I think I did something wrong is that I get a lot of clusters from this analysis, sometimes >15 per individual. This makes me think that the correction might not be as stringent as I would like to. Thank you,
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edumailto:ltozzi@stanford.edu | (650) 5615738
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If you just have a simple design matrix (not doing any temporal whitening or anything else other than a standard GLM), you can use mri_glmfit. Just pass the design matrix as a text file via --X (instead of using an FSGD). You'll have to pass contrast matrices as well.
On 5/10/2021 2:23 PM, Leonardo Tozzi wrote:
External Email - Use Caution
Dear Douglas,
Yes, I mean fMRI. I am currently using MATLAB to fit a GLM to the timeseries and then export the p-values as a MGH file of the cortical surface.
Best,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Researcher
Stanford University | 401 Quarry Rd
ltozzi@stanford.edu mailto:ltozzi@stanford.edu | (650) 5615738
*/Connect with us!/*
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*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, May 10, 2021 at 9:59 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Cluster correction at subject level using -log10(p) values
when you say time series, do you mean like fMRI? What are you using to do the time series analysis?
On 5/10/2021 12:56 PM, Leonardo Tozzi wrote:
* External Email - Use Caution * Dear Douglas, The reason is that I am running a GLM at the subject level on 4D fMRI timeseries. Thus, I obtain a parameter estimate on each vertex, which I can then enter in a contrast to obtain a p-value per vertex. These are the p-values I want to correct. From what I understand, the mri_glmfit does not work on timeseries data, am I wrong in this? So at the moment I am fitting the GLM in matlab and using the mcsim to correct the p-values I obtain. Best, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edu <mailto:ltozzi@stanford.edu> | (650) 5615738 */Connect with us!/* signature_1075933358 <https://secure-web.cisco.com/1FKpYRw97JWaPWT3ZAl3Lrox-jM21LmxbF9ZEHeU5qtHK-REW8TIf1MW-5kY8B6dFUSXrgHaf46PyRtQKE8f3gG5AAyxhr6ES4lBT6gXJP6GfDBPiZbxiVXsMDbX5gf1PL_znG0avOIRVijb38ZGIT5OPqbuwZTn6HGzoFTK2qSoWCLAxiZKvfTrjDXknNVHPQxUVmN8igcVPw6-Cb-0RkJKxijEzftxOk0L_iZIIQDonT8C1ts9_WFMMuoLds6Md97O2q0j_9_0PbhbPA4-07w/https%3A%2F%2Ftwitter.com%2FStanford_PMHW>signature_1282923475 <http://secure-web.cisco.com/1sx0mz8OLK99iEtgYKvr6T3_J6EjPXUU16knmNMN3b8cwqdKo28zt3WmPEQKJD1R4ybfh_HV2rspULGmh0pFWOlUofYpr7dgO9sgn3N0O1ebPAQ8HshmLGR7VN2Tb9uX5sAFAUe4SmdrbgUDvk4qn70EYfRquPq4Sl0Ggv9Otcl0EZRGZF6OrMkK63So70LW10odUwyQWzzaxDLojNVzG5-s9neWtPL7f%20cX290V7cqgkePcf_X-FBQCO4N_2EU75nypfE_me1wiLrhtRjcTGieA/http%3A%2F%2Fwww.instagram.com%2Fstanfordpmhw>signa! ture_911 042299 <https://secure-web.cisco.com/1rFWgvMDaCNKwptwR5qEZMc2o0R1f2IQPHcILZbxp-S3YMOvUqMg_R2_n7y4Vkawe4o4uA-PJ-CV5cowGQasEg3DVF8rRZRNRRc2E77SvL9w_gB0BrCQF9p5k-lqZqg6ok9WLXeubEt9iWVvvsa_Zsvf4OFXpB33Izh4QXizNzewipo9fikUIGu-3tyh_uf15_DYTi0Z-Io4rZbtt3hLE_bf42BNxtiJV_taNlYtz6eL2HnOrg83OLH48xFez2popaRWnjZHgqY4YIY84nv-Esg/https%3A%2F%2Fwww.youtube.com%2Fchannel%2FUCN8g9b2eCpSRMs6AyY15U3g> *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Monday, May 10, 2021 at 8:32 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Cluster correction at subject level using -log10(p) values Is there a reason that you are not using mri_glmfit-sim to do this? It is fairly complicated, and so I spent a lot of time writing mri_glmfit-sim to make sure it does the right thing. On 4/29/2021 6:16 PM, Leonardo Tozzi wrote: * External Email - Use Caution * Dear Experts, I am running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file. I would now like to run a cluster level correction on these data at the level of each individual subject using mri_mcsim followed by mri_surfcluster and I would like to constrain my inference to a ROI. I have a few questions. First of all, is it correct that I should to a -log10(p) transform on my p values before entering them in mri_surfcluster? Second, will the csd generated by mcsim be valid to feed in mri_surfcluster since the values are a -log10(p) transformed? Does mcsim -log transform the gaussian noise it uses at some point or is this not necessary? My calls to the two methods are as follows (for one hemisphere): First the mcsim: mri_mcsim --o“${subject}_mcsim_lh_${roi}"--basemc-z --surface${subject}lh --nreps10000--label$roi Then the mri_surfcluster: mri_surfcluster --in "/${subject}_lh_${roi}_neglog10p_signed.mgh" \ --csd "${subject}_mcsim_lh_${roi}/fwhm05/abs/th30/mc-z.csd" \ --clabel "${subject}/label/lh.${roi}.label" \ --cwsig "${subject}_lh_${roi}_neglog10p_abs_clu05.mgh" \ --vwsig "${subject}_lh_${roi}_neglog10p_abs_vox05.mgh" \ --sum "${subject}_lh_${roi}_neglog10p_abs_summary.txt" \ --thmin 3 \ --surf white \ --subject ${subject } \ --hemi lh \ --ocn “${subject}_lh_${roi}_neglog10p_abs_clu05_clunum.mgh" \ --cwpvalthresh 0.05 In the call of mri_surfcluster, I want a cluster forming threshold of p=0.001, which would correspond to -logp(0.001)=3. Is it correct that the argument --thmin should be expressed as -log10(p) but the parameter cwpvalthresh should be p? The reason why I think I did something wrong is that I get a lot of clusters from this analysis, sometimes >15 per individual. This makes me think that the correction might not be as stringent as I would like to. Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edu <mailto:ltozzi@stanford.edu> | (650) 5615738 */Connect with us!/* signature_1075933358 <https://secure-web.cisco.com/154LqJFzFLISeYtGLsUgwToWD-mN0G4thIfubhtThzJ6F9WpZSTHEctacwX441OLHfh0UtXPCqIHTqi5NxPGqT2vUp9CwVwxTzGfBbalFm29WK-Yzcl2RjBUxGhmSPmqPMvC5_lVL--iJnfmI6UeHzCc-S6OiCJlNeTqRnb9_nAuI5_dJET2YyMRosEGTGNbjRv_nVN5ldRMD4kPNEx9WKGBzfYCQ3kDQ-Ra9E218aIcmmCY4JaMtm6GkDjrbqLvcl618Zmp1lMa9iU7tJkHhow/https%3A%2F%2Ftwitter.com%2FStanford_PMHW>signature_1282923475 <http://secure-web.cisco.com/11JA0cps0LSyc_YKkvLkjj53ioS8G144vcOsjQghqMz-F2MNt-O4PUFyL4YII8C5Z9LTyzgqfxbuDRq_46cX1PtKAbMhM4GIHWkkCg-co9I8z5igR2VGlwK_p2gWbca9vQWwDALu4ub97LG4mV0U5oKnD6zvPTZG5f1BRGtbSPj70hUakvd67X8R%20GEcucVASu9ra_Ek3llRS0AQ5zB6YJJ_MXtuHflVQ%20Lr48It6WMEf-rGUhutwIrS7BOv_XHBjBa81gBLfzG-YreHqzY9a5vMw/http%3A%2F%2Fwww.instagram.com%2Fstanfordpmhw> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1rNpkydT6yNRhvVQDXqwJmFoBflgQFLTsOh26W0gU7Jveix-_VmqzGwpyvr_1jILHvCgIQ7hX85Tgr3BSAxjjjxT9C5BzPKnGW7yuOxfbjtUM2LaM42wSu8fwulUpg1BBIOtAc-VQgjqR_soC1wnopnURuJ0HfoFZou533Y2lsObYEj1Emq3GQ-XP-6uMvOPORmJj4zJsibLc5frkersKnVatWpacD7qbLPMYgAOlKytULWvjMf8mOIlE6XT5AZSbUGS5mTOtP3WxoeiVs99DPw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1bsgMGXqQ2kebwMHYGFdV-M2PForDtUV7a_EIrgAIaJpXVMuQQUtPPmkSLymhU2VMBbhp7gS1-25EQ-tGNiM5_rjELF2DxAzRkmuc3cza39vZCDYW1k7RFlQa27UO9yI8hzSXiSqz73uZ79LeLroQLDaUrB2d7Cj-I-XOgbwVh8V6b-FMB026B2m35O61_gIX1DF__aVmywt84NpDC6vtROktjtwMXdVQk6hSKPgZ92WTZ65lcDXv1lSiWlALmdhc/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Dear Douglas,
Very good to know this is possible, thank you!
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edumailto:ltozzi@stanford.edu | (650) 5615738
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From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, May 10, 2021 at 12:36 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster correction at subject level using -log10(p) values
If you just have a simple design matrix (not doing any temporal whitening or anything else other than a standard GLM), you can use mri_glmfit. Just pass the design matrix as a text file via --X (instead of using an FSGD). You'll have to pass contrast matrices as well. On 5/10/2021 2:23 PM, Leonardo Tozzi wrote:
External Email - Use Caution Dear Douglas, Yes, I mean fMRI. I am currently using MATLAB to fit a GLM to the timeseries and then export the p-values as a MGH file of the cortical surface. Best,
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edumailto:ltozzi@stanford.edu | (650) 5615738
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From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, May 10, 2021 at 9:59 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster correction at subject level using -log10(p) values
when you say time series, do you mean like fMRI? What are you using to do the time series analysis? On 5/10/2021 12:56 PM, Leonardo Tozzi wrote:
External Email - Use Caution Dear Douglas,
The reason is that I am running a GLM at the subject level on 4D fMRI timeseries. Thus, I obtain a parameter estimate on each vertex, which I can then enter in a contrast to obtain a p-value per vertex. These are the p-values I want to correct. From what I understand, the mri_glmfit does not work on timeseries data, am I wrong in this? So at the moment I am fitting the GLM in matlab and using the mcsim to correct the p-values I obtain. Best,
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edumailto:ltozzi@stanford.edu | (650) 5615738
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From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Monday, May 10, 2021 at 8:32 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cluster correction at subject level using -log10(p) values
Is there a reason that you are not using mri_glmfit-sim to do this? It is fairly complicated, and so I spent a lot of time writing mri_glmfit-sim to make sure it does the right thing. On 4/29/2021 6:16 PM, Leonardo Tozzi wrote:
External Email - Use Caution Dear Experts,
I am running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file. I would now like to run a cluster level correction on these data at the level of each individual subject using mri_mcsim followed by mri_surfcluster and I would like to constrain my inference to a ROI. I have a few questions. First of all, is it correct that I should to a -log10(p) transform on my p values before entering them in mri_surfcluster? Second, will the csd generated by mcsim be valid to feed in mri_surfcluster since the values are a -log10(p) transformed? Does mcsim -log transform the gaussian noise it uses at some point or is this not necessary? My calls to the two methods are as follows (for one hemisphere):
First the mcsim:
mri_mcsim --o “${subject}_mcsim_lh_${roi}" --base mc-z --surface ${subject} lh --nreps 10000 --label $roi
Then the mri_surfcluster: mri_surfcluster --in "/${subject}_lh_${roi}_neglog10p_signed.mgh" \ --csd "${subject}_mcsim_lh_${roi}/fwhm05/abs/th30/mc-z.csd" \ --clabel "${subject}/label/lh.${roi}.label" \ --cwsig "${subject}_lh_${roi}_neglog10p_abs_clu05.mgh" \ --vwsig "${subject}_lh_${roi}_neglog10p_abs_vox05.mgh" \ --sum "${subject}_lh_${roi}_neglog10p_abs_summary.txt" \ --thmin 3 \ --surf white \ --subject ${subject } \ --hemi lh \ --ocn “${subject}_lh_${roi}_neglog10p_abs_clu05_clunum.mgh" \ --cwpvalthresh 0.05
In the call of mri_surfcluster, I want a cluster forming threshold of p=0.001, which would correspond to -logp(0.001)=3. Is it correct that the argument --thmin should be expressed as -log10(p) but the parameter cwpvalthresh should be p? The reason why I think I did something wrong is that I get a lot of clusters from this analysis, sometimes >15 per individual. This makes me think that the correction might not be as stringent as I would like to. Thank you,
Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd ltozzi@stanford.edumailto:ltozzi@stanford.edu | (650) 5615738
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Douglas N. Greve -
Leonardo Tozzi