External Email - Use Caution
Hi all,
I am doing an analysis and generating the FSGD. I understand sex and race are classes in this context, but something I was also hoping to regress out is the effects of scanner/sequences. We have a large participant size, so we have around 10+ scanner/sequences, which makes for a large amount of classes combinations, with some having just 1 (if not zero) fitting into a class.
Would you proceed with this nonetheless? If not, should scanner/sequence be something that we consider? Should we find some other way to adjust site (I don't think we can z-score...). Or can we consider site/scanner as a continuous variable
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
It is probably not going to work very well if you have some classes that only have one member. You can eliminate members of classes that only have a few members. If you really need to have those cases, there are hybrid ways to analyze the data (but you can't use an FSGD at that point)
On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi all,
I am doing an analysis and generating the FSGD. I understand sex and race are classes in this context, but something I was also hoping to regress out is the effects of scanner/sequences. We have a large participant size, so we have around 10+ scanner/sequences, which makes for a large amount of classes combinations, with some having just 1 (if not zero) fitting into a class.
Would you proceed with this nonetheless? If not, should scanner/sequence be something that we consider? Should we find some other way to adjust site (I don't think we can z-score...). Or can we consider site/scanner as a continuous variable
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Do you have a Freesurfer page I can read up on those hybrid ways just to see whether that could be an option?
Also, although its a binary, you would recommend against have sex be a continuous measurement like age, due to the design of how the contrasts are determined? I.e continuous measurements aren't treated like integers
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Sunday, February 13, 2022 12:24 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] classes for GLM analysis
It is probably not going to work very well if you have some classes that only have one member. You can eliminate members of classes that only have a few members. If you really need to have those cases, there are hybrid ways to analyze the data (but you can't use an FSGD at that point)
On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi all,
I am doing an analysis and generating the FSGD. I understand sex and race are classes in this context, but something I was also hoping to regress out is the effects of scanner/sequences. We have a large participant size, so we have around 10+ scanner/sequences, which makes for a large amount of classes combinations, with some having just 1 (if not zero) fitting into a class.
Would you proceed with this nonetheless? If not, should scanner/sequence be something that we consider? Should we find some other way to adjust site (I don't think we can z-score...). Or can we consider site/scanner as a continuous variable
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1lNoxYAd17Vg3XrVRX1z0ckNTWUKKuu5TPNUHh0E3g3yFlu...https://secure-web.cisco.com/1e58fbAB8bqm7NyMtK8bHh7_ADs4rJ1eJVjFa6RmNOqRvv5vg65kchIzr15LWl7zHaU-d2Q-sk_kxMV3GrldfYKVX5nxsInjHqrZW5hXBohWIbe9tDyDc8fVZUJ_v1KTsJLUnQP04g79MxnlFuKNxknOo-IqbpEzNKBQao0B2ALpLzqZON9xwp1VX53Bc4yDM--1gAyd6ocwWVK7WpTGxyHY3x7zXw_Vd5o2M5RHxlrL-8Q5CcJLyFT9V2-J6GASLNz0kNV16joDe-ehG7a5_cnxuKyq5RIgWDIUsENquGg2IrEYV6H0ZFo2qnNVk9drS/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21CvMGjuU%21oWSHsHxjED1I9do4R5UyRdbrrRZ0JwASmA6lT5nMBEMbU4m_jfTGWrhBU-2K4sn01nxIwg%24
On 2/21/2022 6:50 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Do you have a Freesurfer page I can read up on those hybrid ways just to see whether that could be an option?
No, this is a general statistics question, not something FS-specific.
Also, although its a binary, you would recommend against have sex be a continuous measurement like age, due to the design of how the contrasts are determined? I.e continuous measurements aren't treated like integers
It is not that. It is that when you say that M=1 and F=2, you are expecting F to be twice that of M (or half). This usually does not make sense.
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab
--
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Sunday, February 13, 2022 12:24 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] classes for GLM analysis It is probably not going to work very well if you have some classes that only have one member. You can eliminate members of classes that only have a few members. If you really need to have those cases, there are hybrid ways to analyze the data (but you can't use an FSGD at that point)
On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi all,
I am doing an analysis and generating the FSGD. I understand sex and race are classes in this context, but something I was also hoping to regress out is the effects of scanner/sequences. We have a large participant size, so we have around 10+ scanner/sequences, which makes for a large amount of classes combinations, with some having just 1 (if not zero) fitting into a class.
Would you proceed with this nonetheless? If not, should scanner/sequence be something that we consider? Should we find some other way to adjust site (I don't think we can z-score...). Or can we consider site/scanner as a continuous variable
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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/1e58fbAB8bqm7NyMtK8bHh7_ADs4rJ1eJVjFa6RmNOqRvv5vg65kchIzr15LWl7zHaU-d2Q-sk_kxMV3GrldfYKVX5nxsInjHqrZW5hXBohWIbe9tDyDc8fVZUJ_v1KTsJLUnQP04g79MxnlFuKNxknOo-IqbpEzNKBQao0B2ALpLzqZON9xwp1VX53Bc4yDM--1gAyd6ocwWVK7WpTGxyHY3x7zXw_Vd5o2M5RHxlrL-8Q5CcJLyFT9V2-J6GASLNz0kNV16joDe-ehG7a5_cnxuKyq5RIgWDIUsENquGg2IrEYV6H0ZFo2qnNVk9drS/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21CvMGjuU%21oWSHsHxjED1I9do4R5UyRdbrrRZ0JwASmA6lT5nMBEMbU4m_jfTGWrhBU-2K4sn01nxIwg%24
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Just to double check the numbers - I seem to have been getting into an error in how many columns in the FSGD it is expecting.
I have 9 different sites, 4 different patient groups, and M/F -> 72 classes. I also am covarying for four different factors, so the contrast matrix I am making is 72*(4+1) long. Since I want to regress out the four factors completely, only the first 72 numbers in 360 contrast matters. My FSGD file has 4 columns e.g like
Input GP0001 NCBostonM 60 12000 -0.01 -0.02
It says ERROR: gdfReadV1: Input line 1, subjid = GP0001 Found 4 variables, expected. 10
Where is this 10 coming from?
Get Outlook for iOShttps://secure-web.cisco.com/17NelGJ6sesfwsPcUOcH7NLCIl8poWbpnFKSkRs_Tip5fMdIWsq5voGkTtGHzn1xIw9teACerNPVmg1UDC86aygtsYvxBGSc9QJKdZxMm3Y3dOV1lpERz-8vKc-W35SxGCTR7slBrlWoSLntQcxVoI5N_W36lxBKe00LuMnuLFccVkMttfaKkDki2gEKr8rEZfBAP4oLIvzypnlk5I1Xvxx0pH9IvNr3Jhcz2dIr3phyRLDzKH1xF2zITaP2GCEjdSzIMvOq7JGNJG1jnPXQseKuq2b3dOWmyQa-nctRxcywiYYaHXfKoduT5XAwSGGo-wLjxNlMJmdBY1XoH2zdiyw/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: Zeng,Victor (BIDMC - Keshavan - Psychiatry) vzeng@bidmc.harvard.edu Sent: Monday, February 21, 2022 5:50:46 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [External] Re: [Freesurfer] classes for GLM analysis
Do you have a Freesurfer page I can read up on those hybrid ways just to see whether that could be an option?
Also, although its a binary, you would recommend against have sex be a continuous measurement like age, due to the design of how the contrasts are determined? I.e continuous measurements aren't treated like integers
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Sunday, February 13, 2022 12:24 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] classes for GLM analysis
It is probably not going to work very well if you have some classes that only have one member. You can eliminate members of classes that only have a few members. If you really need to have those cases, there are hybrid ways to analyze the data (but you can't use an FSGD at that point)
On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi all,
I am doing an analysis and generating the FSGD. I understand sex and race are classes in this context, but something I was also hoping to regress out is the effects of scanner/sequences. We have a large participant size, so we have around 10+ scanner/sequences, which makes for a large amount of classes combinations, with some having just 1 (if not zero) fitting into a class.
Would you proceed with this nonetheless? If not, should scanner/sequence be something that we consider? Should we find some other way to adjust site (I don't think we can z-score...). Or can we consider site/scanner as a continuous variable
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1jeXnxopqSKQus5HtrXGBSnMnebRQctQZP6y6IyW3i1EDeN...https://secure-web.cisco.com/1wpDGvsfnmwi95mRxzFR_Ov4P-_AFL5ltPf5Tm8n7V0q6tYIsavWDqG6IOxJ1u9JYUJbK2lra4GSZIU6Hr3_jOvK2VSrmSB708iP6vPzJTIgV7BP7flaNLqC2BAhbbMX6xghHBZ8QQMvZVX4BJ5ch3FJb4fQJAYRrzw9DH9ch4Ljhdgp6iCxkhDn6Tf2XJWkcmUV5D67z8JXbusRHOcP4zZ6wxT0A6S5dMBLfCK5keFmcnavwUS5FCco609oa4qh95iStdk6IEc9OKrsM1eQSyCfv5qeyXJhMd4AbviGsHLuqVfAx5NuA1oIOAbhAvvt96iw80NNfRotA2y-GRA1urQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!CvMGjuU!oWSHsHxjED1I9do4R5UyRdbrrRZ0JwASmA6lT5nMBEMbU4m_jfTGWrhBU-2K4sn01nxIwg$
Can't tell without the fsgd file
On 3/7/2022 8:30 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Just to double check the numbers - I seem to have been getting into an error in how many columns in the FSGD it is expecting.
I have 9 different sites, 4 different patient groups, and M/F -> 72 classes. I also am covarying for four different factors, so the contrast matrix I am making is 72*(4+1) long. Since I want to regress out the four factors completely, only the first 72 numbers in 360 contrast matters. My FSGD file has 4 columns e.g like
Input GP0001 NCBostonM 60 12000 -0.01 -0.02
It says ERROR: gdfReadV1: Input line 1, subjid = GP0001 Found 4 variables, expected. 10
Where is this 10 coming from?
Get Outlook for iOS
https://secure-web.cisco.com/17NelGJ6sesfwsPcUOcH7NLCIl8poWbpnFKSkRs_Tip5fMdIWsq5voGkTtGHzn1xIw9teACerNPVmg1UDC86aygtsYvxBGSc9QJKdZxMm3Y3dOV1lpERz-8vKc-W35SxGCTR7slBrlWoSLntQcxVoI5N_W36lxBKe00LuMnuLFccVkMttfaKkDki2gEKr8rEZfBAP4oLIvzypnlk5I1Xvxx0pH9IvNr3Jhcz2dIr3phyRLDzKH1xF2zITaP2GCEjdSzIMvOq7JGNJG1jnPXQseKuq2b3dOWmyQa-nctRxcywiYYaHXfKoduT5XAwSGGo-wLjxNlMJmdBY1XoH2zdiyw/https%3A%2F%2Faka.ms%2Fo0ukef
*From:* Zeng,Victor (BIDMC - Keshavan - Psychiatry) vzeng@bidmc.harvard.edu *Sent:* Monday, February 21, 2022 5:50:46 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [External] Re: [Freesurfer] classes for GLM analysis Do you have a Freesurfer page I can read up on those hybrid ways just to see whether that could be an option?
Also, although its a binary, you would recommend against have sex be a continuous measurement like age, due to the design of how the contrasts are determined? I.e continuous measurements aren't treated like integers
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab
--
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Sunday, February 13, 2022 12:24 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] classes for GLM analysis It is probably not going to work very well if you have some classes that only have one member. You can eliminate members of classes that only have a few members. If you really need to have those cases, there are hybrid ways to analyze the data (but you can't use an FSGD at that point)
On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi all,
I am doing an analysis and generating the FSGD. I understand sex and race are classes in this context, but something I was also hoping to regress out is the effects of scanner/sequences. We have a large participant size, so we have around 10+ scanner/sequences, which makes for a large amount of classes combinations, with some having just 1 (if not zero) fitting into a class.
Would you proceed with this nonetheless? If not, should scanner/sequence be something that we consider? Should we find some other way to adjust site (I don't think we can z-score...). Or can we consider site/scanner as a continuous variable
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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/17qN5bDkuaeK781Lqatoj7wq00PaGKTEtcEQvhi_FMPstmuXqCbw1qu_o6m09Gx4i6uzhknWy3SdQKE8Kb42oK-aio4Z9BzzYUaW_YPZQxDITHj-XRutpm12FBHGiBhhjS4fGEam49ZyUl-0RuilU7txRjrKBOCCcsMxELYwLBlBvM23K9AWEX11Fji5iPijRXtSy4HuznIM_2nykUGok-ydbPxoYKFMVlxMuIWIzRXLiFzltn0SRH5tVQCCenBq1ij3h-gtSrMR9kxsTnFh47IjilDG3VyDbP-ABFnjzWd-65nT6_0-J2yvS26iWhf2IVujw-_cA2300rli3E8W6jg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21CvMGjuU%21oWSHsHxjED1I9do4R5UyRdbrrRZ0JwASmA6lT5nMBEMbU4m_jfTGWrhBU-2K4sn01nxIwg%24
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Sorry for the different approach - but I just propensity matched people for now so I don't have to deal with so many confounding variables. Now I am trying to do multiple correction, with mriglmfit-sim not working because of high FWHM (you can ignore my other email about that...). So therefore, I am trying palm, and come up with this error:
Running PALM alpha119 using MATLAB 8.3.0.532 (R2014a) with the following options: -i /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisMGH/Replication/rh.pial_lgi.NCBT1_.10.mgh -m /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisGLM/Replication/rh.pial_lgi.NCBT1_.10.glmdir/mask.mgh -d design.mat -t design.con -logp -n 1000 -C 1.958920 -o fsp -twotail -s /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white.avg.area.mgh Found FSL in /usr/share/fsl/5.0 Found FreeSurfer in /usr/local/freesurfer/dev7 Found SPM in /home/gamma/spm8 Loading surface 1/1: /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white Reading input 1/1: /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisMGH/Replication/rh.pial_lgi.NCBT1_.10.mgh Reading design matrix and contrasts. Elapsed time parsing inputs: ~ 7.22525 seconds. Number of possible permutations is 9.7768e+204. Generating 1000 shufflings (permutations only). Building null distribution. 0.1% [Design 1/1, Contrast 1/1, Shuffling 1/1000, Modality 1/1] /bin/sh: line 1: 14553 Illegal instruction matlab -display iconic < run_palm.m error: cannot find expected palm output "fsp_clustere_tstat_fwep.mgz"
This is with Freesurfer dev 20211206. Thanks and sorry for so many questions lately Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Wednesday, March 16, 2022 6:09 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] [External] Re: classes for GLM analysis
Can't tell without the fsgd file
On 3/7/2022 8:30 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Just to double check the numbers - I seem to have been getting into an error in how many columns in the FSGD it is expecting.
I have 9 different sites, 4 different patient groups, and M/F -> 72 classes. I also am covarying for four different factors, so the contrast matrix I am making is 72*(4+1) long. Since I want to regress out the four factors completely, only the first 72 numbers in 360 contrast matters. My FSGD file has 4 columns e.g like
Input GP0001 NCBostonM 60 12000 -0.01 -0.02
It says ERROR: gdfReadV1: Input line 1, subjid = GP0001 Found 4 variables, expected. 10
Where is this 10 coming from?
Get Outlook for iOShttps://secure-web.cisco.com/1jPI_PycH5-Ur53XMtyifxrU5YNFNj1DKLFRmFEuOeKBfQxuzEBx35FZZfRUvopO7uNsQlRIYx0nApIMXSf_mhadhvPL_sZzEquEFyV2Mc_ZlFpbsC6JNZ6KbHRnyjnuLCYEB_IEnSnUyRWZpD-Mpm0mDFLnlWp9Vww0I2ESucoygMpRx1xRLt-fahrYPMgHva83siLqQ-OSBfzdV3N4DzBFMlikDvMPa0hjJVVfIZ807rlO3EbS6NVO-yQPkIWBJoUrcSrjyHoTRt2f0Z0e6qir5NFwcfIqAnlwdr1ZCkiwPN9hsfmYvkrGlF-Rh-N_E/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F17NelGJ6sesfwsPcUOcH7NLCIl8poWbpnFKSkRs_Tip5fMdIWsq5voGkTtGHzn1xIw9teACerNPVmg1UDC86aygtsYvxBGSc9QJKdZxMm3Y3dOV1lpERz-8vKc-W35SxGCTR7slBrlWoSLntQcxVoI5N_W36lxBKe00LuMnuLFccVkMttfaKkDki2gEKr8rEZfBAP4oLIvzypnlk5I1Xvxx0pH9IvNr3Jhcz2dIr3phyRLDzKH1xF2zITaP2GCEjdSzIMvOq7JGNJG1jnPXQseKuq2b3dOWmyQa-nctRxcywiYYaHXfKoduT5XAwSGGo-wLjxNlMJmdBY1XoH2zdiyw%2Fhttps*3A*2F*2Faka.ms*2Fo0ukef__;JSUlJQ!!CvMGjuU!vnOXunRQmCxtLIcEPxW_nYbG9yY7BIv3V7k4X1XUzyiTt2WwyEMm6bntnIqPAS9-nTX0Jg$ ________________________________ From: Zeng,Victor (BIDMC - Keshavan - Psychiatry) vzeng@bidmc.harvard.edumailto:vzeng@bidmc.harvard.edu Sent: Monday, February 21, 2022 5:50:46 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [External] Re: [Freesurfer] classes for GLM analysis
Do you have a Freesurfer page I can read up on those hybrid ways just to see whether that could be an option?
Also, although its a binary, you would recommend against have sex be a continuous measurement like age, due to the design of how the contrasts are determined? I.e continuous measurements aren't treated like integers
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu 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 Sent: Sunday, February 13, 2022 12:24 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] classes for GLM analysis
It is probably not going to work very well if you have some classes that only have one member. You can eliminate members of classes that only have a few members. If you really need to have those cases, there are hybrid ways to analyze the data (but you can't use an FSGD at that point)
On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi all,
I am doing an analysis and generating the FSGD. I understand sex and race are classes in this context, but something I was also hoping to regress out is the effects of scanner/sequences. We have a large participant size, so we have around 10+ scanner/sequences, which makes for a large amount of classes combinations, with some having just 1 (if not zero) fitting into a class.
Would you proceed with this nonetheless? If not, should scanner/sequence be something that we consider? Should we find some other way to adjust site (I don't think we can z-score...). Or can we consider site/scanner as a continuous variable
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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It is seemingly working in matlab R2021b rather than matlab R2014a. Can you confirm this? Otherwise that should be noted in the wiki
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Sorry for the different approach - but I just propensity matched people for now so I don't have to deal with so many confounding variables. Now I am trying to do multiple correction, with mriglmfit-sim not working because of high FWHM (you can ignore my other email about that...). So therefore, I am trying palm, and come up with this error:
Running PALM alpha119 using MATLAB 8.3.0.532 (R2014a) with the following options: -i /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisMGH/Replication/rh.pial_lgi.NCBT1_.10.mgh -m /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisGLM/Replication/rh.pial_lgi.NCBT1_.10.glmdir/mask.mgh -d design.mat -t design.con -logp -n 1000 -C 1.958920 -o fsp -twotail -s /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white.avg.area.mgh Found FSL in /usr/share/fsl/5.0 Found FreeSurfer in /usr/local/freesurfer/dev7 Found SPM in /home/gamma/spm8 Loading surface 1/1: /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white Reading input 1/1: /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisMGH/Replication/rh.pial_lgi.NCBT1_.10.mgh Reading design matrix and contrasts. Elapsed time parsing inputs: ~ 7.22525 seconds. Number of possible permutations is 9.7768e+204. Generating 1000 shufflings (permutations only). Building null distribution. 0.1% [Design 1/1, Contrast 1/1, Shuffling 1/1000, Modality 1/1] /bin/sh: line 1: 14553 Illegal instruction matlab -display iconic < run_palm.m error: cannot find expected palm output "fsp_clustere_tstat_fwep.mgz"
This is with Freesurfer dev 20211206. Thanks and sorry for so many questions lately Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Wednesday, March 16, 2022 6:09 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] [External] Re: classes for GLM analysis
Can't tell without the fsgd file
On 3/7/2022 8:30 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Just to double check the numbers - I seem to have been getting into an error in how many columns in the FSGD it is expecting.
I have 9 different sites, 4 different patient groups, and M/F -> 72 classes. I also am covarying for four different factors, so the contrast matrix I am making is 72*(4+1) long. Since I want to regress out the four factors completely, only the first 72 numbers in 360 contrast matters. My FSGD file has 4 columns e.g like
Input GP0001 NCBostonM 60 12000 -0.01 -0.02
It says ERROR: gdfReadV1: Input line 1, subjid = GP0001 Found 4 variables, expected. 10
Where is this 10 coming from?
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Do you have a Freesurfer page I can read up on those hybrid ways just to see whether that could be an option?
Also, although its a binary, you would recommend against have sex be a continuous measurement like age, due to the design of how the contrasts are determined? I.e continuous measurements aren't treated like integers
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu 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 Sent: Sunday, February 13, 2022 12:24 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] classes for GLM analysis
It is probably not going to work very well if you have some classes that only have one member. You can eliminate members of classes that only have a few members. If you really need to have those cases, there are hybrid ways to analyze the data (but you can't use an FSGD at that point)
On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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Hi all,
I am doing an analysis and generating the FSGD. I understand sex and race are classes in this context, but something I was also hoping to regress out is the effects of scanner/sequences. We have a large participant size, so we have around 10+ scanner/sequences, which makes for a large amount of classes combinations, with some having just 1 (if not zero) fitting into a class.
Would you proceed with this nonetheless? If not, should scanner/sequence be something that we consider? Should we find some other way to adjust site (I don't think we can z-score...). Or can we consider site/scanner as a continuous variable
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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it does not suprise me that 2014 is not working as that is pretty old. I've been using 2018 and that seems to work.
On 3/24/2022 9:31 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
It is seemingly working in matlab R2021b rather than matlab R2014a. Can you confirm this? Otherwise that should be noted in the wiki
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*From:* Zeng,Victor (BIDMC - Keshavan - Psychiatry) vzeng@bidmc.harvard.edu *Sent:* Wednesday, March 16, 2022 5:52:54 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [External] Re: [Freesurfer] [External] Re: classes for GLM analysis Sorry for the different approach - but I just propensity matched people for now so I don't have to deal with so many confounding variables. Now I am trying to do multiple correction, with mriglmfit-sim not working because of high FWHM (you can ignore my other email about that...). So therefore, I am trying palm, and come up with this error:
Running PALM alpha119 using MATLAB 8.3.0.532 (R2014a) with the following options: -i /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisMGH/Replication/rh.pial_lgi.NCBT1_.10.mgh -m /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisGLM/Replication/rh.pial_lgi.NCBT1_.10.glmdir/mask.mgh -d design.mat -t design.con -logp -n 1000 -C 1.958920 -o fsp -twotail -s /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white.avg.area.mgh Found FSL in /usr/share/fsl/5.0 Found FreeSurfer in /usr/local/freesurfer/dev7 Found SPM in /home/gamma/spm8 Loading surface 1/1: /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/fsaverage/surf/rh.white Reading input 1/1: /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/0analysisMGH/Replication/rh.pial_lgi.NCBT1_.10.mgh Reading design matrix and contrasts. Elapsed time parsing inputs: ~ 7.22525 seconds. Number of possible permutations is 9.7768e+204. Generating 1000 shufflings (permutations only). Building null distribution. 0.1% [Design 1/1, Contrast 1/1, Shuffling 1/1000, Modality 1/1] /bin/sh: line 1: 14553 Illegal instruction matlab -display iconic < run_palm.m error: cannot find expected palm output "fsp_clustere_tstat_fwep.mgz"
This is with Freesurfer dev 20211206. Thanks and sorry for so many questions lately Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab
--
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Wednesday, March 16, 2022 6:09 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] [External] Re: classes for GLM analysis Can't tell without the fsgd file
On 3/7/2022 8:30 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Just to double check the numbers - I seem to have been getting into an error in how many columns in the FSGD it is expecting.
I have 9 different sites, 4 different patient groups, and M/F -> 72 classes. I also am covarying for four different factors, so the contrast matrix I am making is 72*(4+1) long. Since I want to regress out the four factors completely, only the first 72 numbers in 360 contrast matters. My FSGD file has 4 columns e.g like
Input GP0001 NCBostonM 60 12000 -0.01 -0.02
It says ERROR: gdfReadV1: Input line 1, subjid = GP0001 Found 4 variables, expected. 10
Where is this 10 coming from?
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*From:* Zeng,Victor (BIDMC - Keshavan - Psychiatry) vzeng@bidmc.harvard.edu mailto:vzeng@bidmc.harvard.edu *Sent:* Monday, February 21, 2022 5:50:46 PM *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: [External] Re: [Freesurfer] classes for GLM analysis Do you have a Freesurfer page I can read up on those hybrid ways just to see whether that could be an option?
Also, although its a binary, you would recommend against have sex be a continuous measurement like age, due to the design of how the contrasts are determined? I.e continuous measurements aren't treated like integers
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab
--
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu 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 *Sent:* Sunday, February 13, 2022 12:24 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* [External] Re: [Freesurfer] classes for GLM analysis It is probably not going to work very well if you have some classes that only have one member. You can eliminate members of classes that only have a few members. If you really need to have those cases, there are hybrid ways to analyze the data (but you can't use an FSGD at that point)
On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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Hi all,
I am doing an analysis and generating the FSGD. I understand sex and race are classes in this context, but something I was also hoping to regress out is the effects of scanner/sequences. We have a large participant size, so we have around 10+ scanner/sequences, which makes for a large amount of classes combinations, with some having just 1 (if not zero) fitting into a class.
Would you proceed with this nonetheless? If not, should scanner/sequence be something that we consider? Should we find some other way to adjust site (I don't think we can z-score...). Or can we consider site/scanner as a continuous variable
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
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Douglas N. Greve -
Zeng, Victor (BIDMC - Keshavan - Psychiatry)