Re: [Freesurfer] [External] Re: [External] Re: classes for GLM analysis
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 Get Outlook for iOS <https://secure-web.cisco.com/1qkaPGnEUesscFizw2LPsI4p5jrKjbVVDRinN3KloptB7-u42_llA31m49Ufr_8Clot1-MtBqsFxcEfgWntv3Xxct-AzZoSOiP0ZCcpqxJgJIZshsNB0FNW2KvKglGGKpPSH5xz-sZ_IicnTlZm3kN5YtOsX7TkYCsoY7pREyQYwC5YkV327GXxRAggHHpVOJXY1_xqDa_4ZMygOVqFhEfKqQROsL-mQmUUMj0RbMgk-u8weU3TZ4Q0UlLfAH7Ukpwj7x8ucKzh-QcMS9atfGFlKeRcgg749P_jcVOPKLVJyZk6sEnKn_k2vj6-aHa3iS/https%3A%2F%2Faka.ms%2Fo0ukef> *From:* Zeng,Victor (BIDMC - Keshavan - Psychiatry) *Sent:* Wednesday, March 16, 2022 5:52:54 PM *To:* Freesurfer support list *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-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Wednesday, March 16, 2022 6:09 PM *To:* 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 iOS <https://secure-web.cisco.com/1CmpY6foykm2rgWGgaYrcRzr0P1qxgDx48OEn8PvE6j99IOUxv9ZDpni6l_fwdI0OnVsStgqydtrgGvRxD4iZJCyTKZa8Dw1KUY3OONMPI3cE7Qi1l_KELRl8n24hVPEEhocKMhRUg_1t85ggKzUKEZVAOIz7yPHUVLLZfk39UNS0PrEnMBJfo8A8Np9KAmjpIlyC9joWFe0HLW07DCyeto9M92KBQUpVEzQgHjceUKhsqMkGslqpLpjBUqM27_qtOLXWiFNOjeMJAJGG0Y8htddsdMi5sJj7xe3NOfGAHj9CoVwCN-4CWO9uzpjm0hSj/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F17NelGJ6sesfwsPcUOcH7NLCIl8poWbpnFKSkRs_Tip5fMdIWsq5voGkTtGHzn1xIw9teACerNPVmg1UDC86aygtsYvxBGSc9QJKdZxMm3Y3dOV1lpERz-8vKc-W35SxGCTR7slBrlWoSLntQcxVoI5N_W36lxBKe00LuMnuLFccVkMttfaKkDki2gEKr8rEZfBAP4oLIvzypnlk5I1Xvxx0pH9IvNr3Jhcz2dIr3phyRLDzKH1xF2zITaP2GCEjdSzIMvOq7JGNJG1jnPXQseKuq2b3dOWmyQa-nctRxcywiYYaHXfKoduT5XAwSGGo-wLjxNlMJmdBY1XoH2zdiyw%2Fhttps%2A3A%2A2F%2A2Faka.ms%2A2Fo0ukef__%3BJSUlJQ%21%21CvMGjuU%21vnOXunRQmCxtLIcEPxW_nYbG9yY7BIv3V7k4X1XUzyiTt2WwyEMm6bntnIqPAS9-nTX0Jg%24> *From:* Zeng,Victor (BIDMC - Keshava
Re: [Freesurfer] [External] Re: [External] Re: classes for GLM analysis
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 Get Outlook for iOS<https://secure-web.cisco.com/1qkaPGnEUesscFizw2LPsI4p5jrKjbVVDRinN3KloptB7-u42_llA31m49Ufr_8Clot1-MtBqsFxcEfgWntv3Xxct-AzZoSOiP0ZCcpqxJgJIZshsNB0FNW2KvKglGGKpPSH5xz-sZ_IicnTlZm3kN5YtOsX7TkYCsoY7pREyQYwC5YkV327GXxRAggHHpVOJXY1_xqDa_4ZMygOVqFhEfKqQROsL-mQmUUMj0RbMgk-u8weU3TZ4Q0UlLfAH7Ukpwj7x8ucKzh-QcMS9atfGFlKeRcgg749P_jcVOPKLVJyZk6sEnKn_k2vj6-aHa3iS/https%3A%2F%2Faka.ms%2Fo0ukef> From: Zeng,Victor (BIDMC - Keshavan - Psychiatry) Sent: Wednesday, March 16, 2022 5:52:54 PM To: Freesurfer support list 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-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Wednesday, March 16, 2022 6:09 PM To: 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 iOS<https://secure-web.cisco.com/1osTACKWGhLtiGmV5RsUspNMib35XV0LScomLo2KTEQ5b57Ka5BKp_bZypNK7e4k6HJNUHvnoR4KObVGha_zyK_Qij3Hnq9P4yZr0buqAtQ8keWAs3ldueLYt3H-y-uCsDAk-xVbP3LWXpKp0bBDH3vk6B7ou_B2EcwrQ8IiIybOWc_wdfwU9snnQC-aWU0yI4a_lQv0MteVoK8WJIbVtNGR9IT08bBvsensthGsKpaJJ4xMa3Ibmc99ACnMRsz5x-dYVCuQEuydGpYZ4234Q3H_luJ_GMIUWwBHAyO7f-ccHGBJpus9X13cVbL3iaaaS/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) <mailto:vz...@bidmc.harvard.edu> Sent: Monday, February 21, 2022 5:50:46 PM To: freesurfer@nmr.mgh.harvard.edu<mailto: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
Re: [Freesurfer] [External] Re: [External] Re: classes for GLM analysis
External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Wednesday, March 16, 2022 6:09 PM To: 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 iOS<https://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) <mailto:vz...@bidmc.harvard.edu> Sent: Monday, February 21, 2022 5:50:46 PM To: freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <mailto:dgr...@mgh.harvard.edu> Sent: Sunday, February 13, 2022 12:24 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [External] Re: [Frees
