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Hello,
I have been struggling to figure out a way to get the significant results of a freesurfer group analysis (just one significant cluster) from either the sig.cluster.summary or sig.mgh file into a binarized ROI in .nii format. I used mri_glmfit to perform the cortical thickness analysis on sMRI data and found the significant cluster only in the left hemisphere. I tried to follow some instructions I found on the FreeSurfer site, however, at the first step/line below (mri_volsynth) the –delta-crsf input was referred to on the site as the vertex number, but on the –help documentation, it was specified that this input should be: col row slice frame : 0-based. Looking at the cluster summary file, for the significant cluster there is a maximum vertex, but I am not sure if this is the vertex number I should be using.
mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness --pdf delta --delta-crsf 5 9 5 1 --o delta.sm00.mgh mris_fwhm --smooth-only --subject fsaverage --hemi lh --i delta.sm00.mgh --niters 10 --o delta.sm10.mgh mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh
When trying the first line above for mri_volsynth, I get this error: Segmentation fault: 11 (so I think my input –deta-crsf is likely wrong). If there is a better way to convert this ROI to a mask, please let me know!
To give additional context, I am hoping to get a binary mask of this ROI that I can use as a mask for an ASL analysis in FSL (to limit the analysis to this ROI). I plan to do this by registering the binary ROI mask to the FSL standard group template (by using the transformation matrix from registering the fsaverage template to FSL’s standard group template first), and then getting the ROI mask from FSL’s group template space into native ASL space. If this plan sounds reasonable to you, it would also be very helpful to know.
I really appreciate your time and help and look forward to hearing back!
Best,
Emily S. Popa, M.S. Staff Research Associate II, Neuroimaging Pacific Brain Health Center | Pacific Neuroscience Institute Foundation | Providence Saint John’s Health Center 1301 20th St. #250 Santa Monica, CA. 90404 (408) 750-7971 (M) [cid3519*image001.jpg@01D7EC78.96AA1AC0]https://secure-web.cisco.com/1hLjiH2EMqrNb1Aj_EN8nMGnwBm1r3goPYCE5vd4lR-hGEOFl7qOUxRDrLjntYJ9EcOJe0QuWgEEzreB6yGdrX5hhszj1ARxOXqtmsyACcl5dNIKxAnZJA3Wcre7CHsUFbeaoxr87bwSH7rfnnc95bSoWzucGojtyayzhyhyY3_W_m_DmsjiXBhFdQhT326RcqmFA0IUnW3R4cvf8Px7Lmk1bOX2KS0KdWg4_9ShQqdMqmjDd4ggqi1dPRfdo1bZC_QbLAuiAXK9S6gCvv2t88dFFBjDeHvGF8mP4TAA_IHtMCl_4VTyFsX7R4ply1FmOODZG7HtALJc7AlDEoqFQgw/https%3A%2F%2Fwww.linkedin.com%2Fin%2Femilypopa%2F [cid3519*image002.jpg@01D7EC78.96AA1AC0] https://secure-web.cisco.com/11wThjE0wBKB7uH7Mdk8M0tt4s97K_cFB0xuOQfaRwID0mtt4sPJjJ16LKbrQComG9Gk2iEaGVcBLQyUwQJEqws-YDod5RsW-utrJRUDmiWPr0EHI52IyCqdkifN0pk8TJNTZql0YniEqi3IdR7vq7eXZLP-DXFVbhRKBlCNFE-mPuiI4Nj4bPMmZweRcU9dKXWyzZwbo-kb72WbjPep2AVXdsCYohwjyfzZVcMb49IHitA4a9DUXaIw3JdWmoWnozn6z-ir0EUWYMVS2VJYs4enN07Z9HseqleVlcWpvPiCplBXhHUeiq7t-W09X5v3L88ODJnLq7Lm2ztt7FZm61w/https%3A%2F%2Fwww.facebook.com%2FPacificNeuroscienceInstitute [cid3519*image003.jpg@01D7EC78.96AA1AC0] https://secure-web.cisco.com/1oGIwvc1noJjNXOvlfvxCGrBAHvKAjS0PHn5htsutbjwTJJOf3nwiwYHqjOceSf3qTy1lVVvnO9AQmh-DooVMEQX6QwF96D1oDlaGdzY4G0LosYbJ3rqGihsEY-N-D6uI86aVxh45NinpG11qGLoDwycdcn0Rtv0sChUSF20vai2yZGOe6Pmt1aBaPEN0LLuLlrl401wbHdP2jT_K_Y-9SBCGELjAmp0eGVuLrjNqrjuyfjS8wMiYFUD7TbTWqBpNqUpyz4voOdB_XpxhBxXtD0S5cm_IycU5O_jpZ86tsgRLtQPVwP6niS2wcu5w34u8xJWb-0NLM1p5lz4qWbzJqQ/https%3A%2F%2Ftwitter.com%2FPacificNeuroPNI [cid3519*image004.jpg@01D7EC78.96AA1AC0] https://secure-web.cisco.com/1cMaCmazMIVCk8v3EhpuiTkZaPsebaExskfX49kF6WWp7PMB6RiRohKVFACOFD_j6NG4DersEoKHYOgw0IdedWsgVHAKjFgXiynmH89xQHoc22GWgm5PIQa4EVkFZ3appBu20Oq1oW7Kv4_6kyU-jnb0cR046VxCuIQezXyNW_MydhZaTb00gR-NrZ-wvS2UvRgg0H2x6tKf43_WHl6qN5IsSbHyDGjRFnBQf_blwuM-5QfW-CClI0-Oas_1r294RZE9sMHDBGM3ooKUsBMN-bqVUOV1ZlC2Zhk8vt2hcuIR78uQDaZwA1VBCj98H8rs8Hl6JBKg2WkV5_d20MlLltw/https%3A%2F%2Fwww.instagram.com%2Fpacificneuro%2F [cid3519*image005.jpg@01D7EC78.96AA1AC0] https://secure-web.cisco.com/17e7d2R-5gmmayIc-Okzb6HMA5_U4NT4cVQtWz_nLOjiv5UtWI9QBQljl4HkIBt4RSF19YIEJknyFVBBCYgctkbvogEpo-h7izNvlbeGqFuDBWlaE6kyM1HwAxFbsYFTQBcARMFo_QjK1fRLn-_NdrwdR1OOwl1hN-hi356J6F1kqxIuUPrzU8pDdbezy_xXt3PhsLQCla4RU0eu2oo-v_UU6Giu0_ipas79Pkx2t2zAXGcqk-6gHLb2dV3C1B3-1krRYHFaZU7JQpb6Df5PY6MlRgPOm3vUh2wJiedA1IFTxsPeTxoMZavvisB3KbSsj/https%3A%2F%2Fwww.pacificneuroscienceinstitute.org%2Fbrain-health%2F
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Hello, I am just following up on my previous question. To put it more shortly (I apologize for making the question so long before), I am just searching for a way to convert a significant cluster from a group analysis into a binary .nii mask so I can use the mask (after some registration steps) to perform ASL analysis in that specific ROI for the same subjects (in FSL).
Best,
Emily S. Popa, M.S. Staff Research Associate II, Neuroimaging Pacific Brain Health Center | Pacific Neuroscience Institute Foundation | Providence Saint John’s Health Center 1301 20th St. #250 Santa Monica, CA. 90404 (408) 750-7971 (M) [cid3519*image001.jpg@01D7EC78.96AA1AC0]https://secure-web.cisco.com/18fNRghnHjYTuH-ptKExvys2maGZwSoN5TQ217KCZX4Ra9md-kQZ_Gf7Mj04HdsyWOzfH5B1OTsT_d33gRwKc0j37upxvt1Xm8JI4DuAG-HFiibQIO8AjXbvIuV2MugHYowVv4-p-7TXPo9bl2nbvNaicXZkECnkVkUm4lnhl_tuIztb9LzLOq2o8AOc39eK-twBUdL1pcKNJ2oGLo2GmbCEyFhS4GkR9__Ntp7iCsVVf12Ih4HPKTkdJCYYOuSVfHawfja_nsNsxGmqpnuaX6iaERxD-lQxrmfgKfdDMOSqlfUKy_ELAmvsvaaOROUG7JqfP7QpDfTjEjhjuD3LTeQ/https%3A%2F%2Fwww.linkedin.com%2Fin%2Femilypopa%2F [cid3519*image002.jpg@01D7EC78.96AA1AC0] https://secure-web.cisco.com/16eictjmErn5lkBfPZ7hjmL8RHWweIpPo2U2PTn2s6q9eKNL8ZyXJPfdS8pArK20PmakFaA-jSfKPzlGbK9HV7PRx0aKnDKiRZuZWnAEgK9vcIltfC4z2IVaQ9-FWLSLlwtBJfcMhkkvtxaGP9hxyg4VsaNIzMvrCQdIBPOPCpEZE_9_egF6-n46ILkkzUTSBcMjWe2D1Dyv9y_o8v1QJhyl0xuSuMvPa_6Q35mMKjQNVLzf4040N4DO34E36HiXv1s2sLFBNXyjANcpWrchQGfF3kZGBwsK_wkWSLcp0s5Zfmj9RUyQ8plt2apXUyRvP_l9VUE-IMxejhdvTt9uhMQ/https%3A%2F%2Fwww.facebook.com%2FPacificNeuroscienceInstitute [cid3519*image003.jpg@01D7EC78.96AA1AC0] https://secure-web.cisco.com/1XLYGF-q48z48tVO2OcP1TXwNDAxgvwLs9gzOR7ZxMyf9h80UE3Z8f1UkPU-ACYtZqtCcRNrKLIYOewgOsNHRWaqmWtuUvhdB_T9Z13-0-WMrFQkQjmqDsOxsBJRojU_F_GJ0LC4OlSAQbrA3Rh-VQwvyXt_V9Z5T0wTHVvSzHiCOSERF6TGsW8DTKdrvBhaRYkbdXesz8dRMNZN9e_ndSem5F-rbk3qS-kczK8pOa5Ey-xzLqEd6T-l0jB8t_ChNgIvK66VSyTjjFVwJO2Lwh67VeW21e0q_Ly75Iwt4Gzcne47A8qJqotJgj1JL18DhN0Msho6_8-hRk75h7TE0Bw/https%3A%2F%2Ftwitter.com%2FPacificNeuroPNI [cid3519*image004.jpg@01D7EC78.96AA1AC0] https://secure-web.cisco.com/1tkspAS4BoabfFNBIunLBb4L0OjHthDW8555L-mqpANb2RTXoF__LMAXdxVTQQissTpWnqEMtYa5aVdfXAp8rWIUbD7_mQv3nZikbG3lLuGFZPP2deNCsDnxtbl7eosCMJtWQLMx0IuzuAqx1X4xiVRVarOH66PsHUuBxbRmQZHAKfcfbzcgnNxyRkZQjxi_v8Ep1oOxKZDYIyFSK4UyYTnNCmdlOUcftxo04tPUfH6CYWLumfAeiIjLo_qhUrNWFmoPTB7XFLFEyOjCue_yzgPP8N-Auuh_OsQ-owd1JlViFev8s9Ix5ILF-YTt3vKbyYVheLmbb-_nIP9zSxLeb5A/https%3A%2F%2Fwww.instagram.com%2Fpacificneuro%2F [cid3519*image005.jpg@01D7EC78.96AA1AC0] https://secure-web.cisco.com/1_8daZCBT3piq9W2bTFmQ3HwGH9rB0rIaoujv1DuighaAWZsODa31FQQdzMuybdGXd8InmhxlJ4Px1yrTdvhK3zMB2t5AaGk41aoGzWbKg5w1vkHe87NKmqGroDqPDcjH77davxtHZRt6G4-MPnk4GnOJ1wEvO0_ALuJowyrNoaOh3DarNe0oqiUsj4WcLVb8r3tb3iSoKDtdNHbrlkPHSruqiscbMxujUCUeCeXzfHkGHqqoOtVMRY7ONXVgkwZE_4JUH-fQtFHpKUY_Yn-_zkn6GAzGLrf30ASirIy6DPY9MxDFrKCFvIpAQdIlTWT3_OJSkTEQ71u0N2S3GLme9w/https%3A%2F%2Fwww.pacificneuroscienceinstitute.org%2Fbrain-health%2F
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Emily Popa epopa@pacificneuro.org Date: Thursday, March 10, 2022 at 2:31 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Turning Significant Cluster (sig.cluster.summary or sig.mgh) into binary .nii ROI
External Email - Use Caution Hello,
I have been struggling to figure out a way to get the significant results of a freesurfer group analysis (just one significant cluster) from either the sig.cluster.summary or sig.mgh file into a binarized ROI in .nii format. I used mri_glmfit to perform the cortical thickness analysis on sMRI data and found the significant cluster only in the left hemisphere. I tried to follow some instructions I found on the FreeSurfer site, however, at the first step/line below (mri_volsynth) the –delta-crsf input was referred to on the site as the vertex number, but on the –help documentation, it was specified that this input should be: col row slice frame : 0-based. Looking at the cluster summary file, for the significant cluster there is a maximum vertex, but I am not sure if this is the vertex number I should be using.
mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness --pdf delta --delta-crsf 5 9 5 1 --o delta.sm00.mgh mris_fwhm --smooth-only --subject fsaverage --hemi lh --i delta.sm00.mgh --niters 10 --o delta.sm10.mgh mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh
When trying the first line above for mri_volsynth, I get this error: Segmentation fault: 11 (so I think my input –deta-crsf is likely wrong). If there is a better way to convert this ROI to a mask, please let me know!
To give additional context, I am hoping to get a binary mask of this ROI that I can use as a mask for an ASL analysis in FSL (to limit the analysis to this ROI). I plan to do this by registering the binary ROI mask to the FSL standard group template (by using the transformation matrix from registering the fsaverage template to FSL’s standard group template first), and then getting the ROI mask from FSL’s group template space into native ASL space. If this plan sounds reasonable to you, it would also be very helpful to know.
I really appreciate your time and help and look forward to hearing back!
Best,
Emily S. Popa, M.S. Staff Research Associate II, Neuroimaging Pacific Brain Health Center | Pacific Neuroscience Institute Foundation | Providence Saint John’s Health Center 1301 20th St. #250 Santa Monica, CA. 90404 (408) 750-7971 (M) [cid3519*image001.jpg@01D7EC78.96AA1AC0]https://secure-web.cisco.com/1hLjiH2EMqrNb1Aj_EN8nMGnwBm1r3goPYCE5vd4lR-hGEOFl7qOUxRDrLjntYJ9EcOJe0QuWgEEzreB6yGdrX5hhszj1ARxOXqtmsyACcl5dNIKxAnZJA3Wcre7CHsUFbeaoxr87bwSH7rfnnc95bSoWzucGojtyayzhyhyY3_W_m_DmsjiXBhFdQhT326RcqmFA0IUnW3R4cvf8Px7Lmk1bOX2KS0KdWg4_9ShQqdMqmjDd4ggqi1dPRfdo1bZC_QbLAuiAXK9S6gCvv2t88dFFBjDeHvGF8mP4TAA_IHtMCl_4VTyFsX7R4ply1FmOODZG7HtALJc7AlDEoqFQgw/https%3A%2F%2Fwww.linkedin.com%2Fin%2Femilypopa%2F [cid3519*image002.jpg@01D7EC78.96AA1AC0] https://secure-web.cisco.com/11wThjE0wBKB7uH7Mdk8M0tt4s97K_cFB0xuOQfaRwID0mtt4sPJjJ16LKbrQComG9Gk2iEaGVcBLQyUwQJEqws-YDod5RsW-utrJRUDmiWPr0EHI52IyCqdkifN0pk8TJNTZql0YniEqi3IdR7vq7eXZLP-DXFVbhRKBlCNFE-mPuiI4Nj4bPMmZweRcU9dKXWyzZwbo-kb72WbjPep2AVXdsCYohwjyfzZVcMb49IHitA4a9DUXaIw3JdWmoWnozn6z-ir0EUWYMVS2VJYs4enN07Z9HseqleVlcWpvPiCplBXhHUeiq7t-W09X5v3L88ODJnLq7Lm2ztt7FZm61w/https%3A%2F%2Fwww.facebook.com%2FPacificNeuroscienceInstitute [cid3519*image003.jpg@01D7EC78.96AA1AC0] https://secure-web.cisco.com/1oGIwvc1noJjNXOvlfvxCGrBAHvKAjS0PHn5htsutbjwTJJOf3nwiwYHqjOceSf3qTy1lVVvnO9AQmh-DooVMEQX6QwF96D1oDlaGdzY4G0LosYbJ3rqGihsEY-N-D6uI86aVxh45NinpG11qGLoDwycdcn0Rtv0sChUSF20vai2yZGOe6Pmt1aBaPEN0LLuLlrl401wbHdP2jT_K_Y-9SBCGELjAmp0eGVuLrjNqrjuyfjS8wMiYFUD7TbTWqBpNqUpyz4voOdB_XpxhBxXtD0S5cm_IycU5O_jpZ86tsgRLtQPVwP6niS2wcu5w34u8xJWb-0NLM1p5lz4qWbzJqQ/https%3A%2F%2Ftwitter.com%2FPacificNeuroPNI [cid3519*image004.jpg@01D7EC78.96AA1AC0] https://secure-web.cisco.com/1cMaCmazMIVCk8v3EhpuiTkZaPsebaExskfX49kF6WWp7PMB6RiRohKVFACOFD_j6NG4DersEoKHYOgw0IdedWsgVHAKjFgXiynmH89xQHoc22GWgm5PIQa4EVkFZ3appBu20Oq1oW7Kv4_6kyU-jnb0cR046VxCuIQezXyNW_MydhZaTb00gR-NrZ-wvS2UvRgg0H2x6tKf43_WHl6qN5IsSbHyDGjRFnBQf_blwuM-5QfW-CClI0-Oas_1r294RZE9sMHDBGM3ooKUsBMN-bqVUOV1ZlC2Zhk8vt2hcuIR78uQDaZwA1VBCj98H8rs8Hl6JBKg2WkV5_d20MlLltw/https%3A%2F%2Fwww.instagram.com%2Fpacificneuro%2F [cid3519*image005.jpg@01D7EC78.96AA1AC0] https://secure-web.cisco.com/17e7d2R-5gmmayIc-Okzb6HMA5_U4NT4cVQtWz_nLOjiv5UtWI9QBQljl4HkIBt4RSF19YIEJknyFVBBCYgctkbvogEpo-h7izNvlbeGqFuDBWlaE6kyM1HwAxFbsYFTQBcARMFo_QjK1fRLn-_NdrwdR1OOwl1hN-hi356J6F1kqxIuUPrzU8pDdbezy_xXt3PhsLQCla4RU0eu2oo-v_UU6Giu0_ipas79Pkx2t2zAXGcqk-6gHLb2dV3C1B3-1krRYHFaZU7JQpb6Df5PY6MlRgPOm3vUh2wJiedA1IFTxsPeTxoMZavvisB3KbSsj/https%3A%2F%2Fwww.pacificneuroscienceinstitute.org%2Fbrain-health%2F
Are you trying to create a volume-based binary mask or a surface-based mask? From the commands below, it looks like surface (but why would you need it to be in nii?). In the surface case, you can just mri_binarize --i ocn.mgh --match clusterno --o clusterno.mask.nii where "ocn" is the ocn file created by mri_glmfit-sim and clusterno is the number of the cluster
On 3/16/2022 3:00 PM, Emily Popa wrote:
External Email - Use Caution
Hello, I am just following up on my previous question. To put it more shortly (I apologize for making the question so long before), I am just searching for a way to convert a significant cluster from a group analysis into a binary .nii mask so I can use the mask (after some registration steps) to perform ASL analysis in that specific ROI for the same subjects (in FSL).
Best,
Emily S. Popa, M.S.
Staff Research Associate II, Neuroimaging
Pacific Brain Health Center | Pacific Neuroscience Institute Foundation | Providence Saint John’s Health Center
1301 20^th St. #250 Santa Monica, CA. 90404
(408) 750-7971 (M)
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*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Emily Popa epopa@pacificneuro.org *Date: *Thursday, March 10, 2022 at 2:31 PM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Turning Significant Cluster (sig.cluster.summary or sig.mgh) into binary .nii ROI
* External Email - Use Caution *
Hello,
I have been struggling to figure out a way to get the significant results of a freesurfer group analysis (just one significant cluster) from either the sig.cluster.summary or sig.mgh file into a binarized ROI in .nii format. I used mri_glmfit to perform the cortical thickness analysis on sMRI data and found the significant cluster only in the left hemisphere. I tried to follow some instructions I found on the FreeSurfer site, however, at the first step/line below (mri_volsynth) the –delta-crsf input was referred to on the site as the vertex number, but on the –help documentation, it was specified that this input should be: col row slice frame : 0-based. Looking at the cluster summary file, for the significant cluster there is a maximum vertex, but I am not sure if this is the vertex number I should be using.
mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness --pdf delta --delta-crsf 5 9 5 1 --o delta.sm00.mgh
mris_fwhm --smooth-only --subject fsaverage --hemi lh --i delta.sm00.mgh --niters 10 --o delta.sm10.mgh
mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh
When trying the first line above for mri_volsynth, I get this error: Segmentation fault: 11 (so I think my input –deta-crsf is likely wrong). If there is a better way to convert this ROI to a mask, please let me know!
To give additional context, I am hoping to get a binary mask of this ROI that I can use as a mask for an ASL analysis in FSL (to limit the analysis to this ROI). I plan to do this by registering the binary ROI mask to the FSL standard group template (by using the transformation matrix from registering the fsaverage template to FSL’s standard group template first), and then getting the ROI mask from FSL’s group template space into native ASL space. If this plan sounds reasonable to you, it would also be very helpful to know.
I really appreciate your time and help and look forward to hearing back!
Best,
Emily S. Popa, M.S.
Staff Research Associate II, Neuroimaging
Pacific Brain Health Center | Pacific Neuroscience Institute Foundation | Providence Saint John’s Health Center
1301 20^th St. #250 Santa Monica, CA. 90404
(408) 750-7971 (M)
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Emily Popa