Freesurfer January 2022

freesurfer@nmr.mgh.harvard.edu

69 participants
112 discussions

Re: [Freesurfer] Questions about contrasts
by Laura Willers de Souza 03 Jan '22

03 Jan '22

External Email - Use Caution Dear Douglas, Thank you so much for all the help! Now I think I finally get it. Best regards, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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Possible to Specify Default Version of MATLAB for selxavg3-sess?
by Yadav, Shrikanth Muralidhar 02 Jan '22

02 Jan '22

Hello Freesurfer Developers, I am having trouble with my first level analysis using selxavg3-sess. I passed the -debug flag in my command and noticed that MATLAB 2021a was being used. However, the command worked as expected before MATLAB was updated from 2020b. Is there a way I can specify freesurfer (v6.0.0) to use a specific version of MATLAB? I tried passing the -octave flag but got the following error ERROR: cannot find /usr/local/freesurfer/stable5_1_0/matlab/ The full command: selxavg3-sess -s 002_S_0413_V1_fMRI -overwrite -a lh-FastADNI12state1 -no-preproc -force -debug Thank you Shrikanth

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Cohen´s D effect size
by Steve Petersen 02 Jan '22

02 Jan '22

External Email - Use Caution Dear Freesurfer experts, I am attempting to estimate the Cohen's D effect size of significant clusters using the suggested command <https://secure-web.cisco.com/1jHNDOrJJ6TcImjSXLGzeh59SUh27A8_HOdinuqzuimVg7…>: fscalc gamma.mgh div rstd.mgh -o cohensd.mgh Now, I get the cohensd.mgh file but I am not able to open this file. How can I see the particular effect size of each significant cluster included in the sig.cluster.summary file?. Thank you very much for your help! Best regards,

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Re: [Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala
by Laura Willers de Souza 02 Jan '22

02 Jan '22

External Email - Use Caution Dear Douglas, Thanks so much for your answer. Could you check if the following commands to perform ROI analysis with GLM are correct? 1. Create the table with the volumes of the hippocampal segmentation (1 command for each hemisphere - only replace lh with rh): asegstats2table --statsfile hipposubfields.lh.T1.v21.stats --fsgd CU_CI.fsgd \ --meas volume \ --all-segs \ --tablefile hipposubfields.lh.T1.v21.CU_CI.dat 2. GLM Analysis – DODS (1 command for each hemisphere - only replace lh with rh): mri_glmfit \ --table hipposubfields.lh.T1.v21.CU_CI.dat \ --fsgd CU_CI.fsgd dods \ --C group.diff.CU_CI.mtx \ --glmdir hipposubfields.lh.T1.v21.CU_CI.glmdir 3. Correction for multiple comparisons – FDR: mri_fdr --fdr .05 --pos --thfile --i contrast/lh.sig.mgh lh.mask.mgh hipposubfields.lh.T1.v21.CU_CI.mgh --no-log10p --i contrast/rh.sig.mgh rh.mask.mgh hipposubfields.rh.T1.v21.CU_CI.mgh --no-log10p Are these commands correct? Another question, in this type of analysis is image smoothing common? Like was done here https://secure-web.cisco.com/1ZjmO80yeIcvew54e44mv0-Yzru83V18CRkiga2XGIlA0l… Thank you so much again! Best regards, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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cp: cannot stat 'rh.white.preaparc.K': No such file or directory
by Atsushi Yamaguchi 02 Jan '22

02 Jan '22

External Email - Use Caution * { font-size: 13px; font-family: 'MS Pゴシック', sans-serif;}p, ul, ol, blockquote { margin: 0;}a { color: #0064c8; text-decoration: none;}a:hover { color: #0057af; text-decoration: underline;}a:active { color: #004c98;} Hello FreeSurfer Developers, I'm attempting to run recon-all on structural MRI data of Human Connectome Project (ex. T1w.nii.gz from folder"102109_3T_Structural_preproc"), but I get the following error : ERROR: From recon-all.log. cp rh.white.preaparc.K rh.white.K cp: cannot stat 'rh.white.preaparc.K': No such file or directory I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a 2) Platform: Linux-generic-Ubuntu SMP 3) uname -a: Linux l4n 5.4.0-91-generic #102-Ubuntu SMP Fri Nov 5 16:31:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached ----- total integrated curvature = 10.482*4pi (131.726) --> -9 handles ICI = 191.0, FI = 2265.8, variation=34649.724 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H cp rh.white.preaparc.H rh.white.H cp: cannot stat 'rh.white.preaparc.H': No such file or directory rm -f rh.white.K cp rh.white.preaparc.K rh.white.K cp: cannot stat 'rh.white.preaparc.K': No such file or directory mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 245 vertices thresholded to be in k1 ~ [-0.20 0.44], k2 ~ [-0.08 0.05] total integrated curvature = 0.489*4pi (6.143) --> 1 handles ICI = 1.6, FI = 11.7, variation=193.559 152 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 189 vertices thresholded to be in [-0.11 0.21] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.014, std = 0.023 done. PIDs (30184 30187 30190 30193 30196 30199 30202 30205 30208 30211 30214 30217) completed and logs appended. Linux l4n 5.4.0-91-generic #102-Ubuntu SMP Fri Nov 5 16:31:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 102019 exited with ERRORS at Sun Dec 19 09:54:10 JST 2021 To report a problem, see http://secure-web.cisco.com/15KASrM8j7vzxN_8pxIkjHwLBEnLcXT3hlwaVHxLiXkrf2R…

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Freeview Transform Volume tool - output nifti keeps rotations but loses translations
by Christopher Panks 02 Jan '22

02 Jan '22

External Email - Use Caution I'm trying to get images of post-mortem brains, some from cadavers, some excised, into standard space. I'm new to Freeview, so I'm not sure if I'm doing something wrong, or my expectations are wrong. I find the Transform Volume tool easy to use to get an image that is correctly rotated, and shifted so that the image is centered in the frame. The image looks great in the Freeview panes. Upon saving and then opening the output nifti, I find the rotational changes have stuck, but the image is as off-center as the original, with the coronal and axial off towards one side, and the sagittal not at the midbrain. When saving the image, I click on 'Save Volume as...', leave the boxes unchecked ('do not resample'', and 'crop to' ), I modify the file name, then click OK. I don't click on 'Move Center...', I don't check 'Apply to all...'. My expectation is that the image would not only be correctly rotated, but that it would also be centered. Is that the expected behavior here? I've tried the 'Move Center to Current Cursor Location', and the Apply to all visible volumes, and see no difference. The off-centeredness is visible in multiple viewers, FSLEyes, MRIcroGL, and ROIEditor. The directions seem so simple and clear, I'm just baffled. Thank you!

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Interpreting Covariate Paired Analysis Results
by PDMD SRALab 02 Jan '22

02 Jan '22

External Email - Use Caution We are using a paired analysis approach to study cortical thickness in a dataset with 2 timepoints (called pre-protocol and post-protocol). Regarding the mean cluster summary (contrast: [1 0]), we understand positive values to mean pre > post (thinning) and negative values to mean post > pre (thickening). The covariate results are more difficult to interpret. For instance, we’re interested in looking at the effects of age (contrast: [0 1]) on the cortical thickness results. In the age cluster summary, is it fair to interpret positive results as positive correlation (older subjects show more thickening) and negative results as inverse correlation (older subjects show more thinning) or is the interpretation more complex than this? We’re getting mainly negative cluster results for age so this interpretation may make sense, but we’d like more clarity. Thank you for your help.

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Overlaying gfreat results to surface
by 刘宇琦 02 Jan '22

02 Jan '22

External Email - Use Caution Hi Freesurfer experts: I have a question on displaying results from FSL FEAT on surface reconstructed by freesurfer, especially results from higher-level analysis from gfeat directories. So I have successfully done recon-all on the participant's T1. I've also performed both first-level and higher-level analyses in FEAT. In overlaying first-level results from .feat directories, I did the following: reg-feat2anat --feat sub1_run1.feat --subject sub1 feat2surf --feat featdir Then, I overlaid the zstat1.mgh generated by the second command to surface, applying the anat2exf.register.dat file generated by the first command. It all worked fine. However, I'm not sure how to overlay zstat1.nii.gz from higher-level analyses (.gfeat/cope1.feat/stats/) to surface. According to online tutorials I found below, I could overay the zstat1.nii.gz file to surface, applying the anat2std.register.dat file from the first command above. But it didn't work. The figure on the left below shows results on 3D volume space and the figure on the right shows z values on surface using the method above. However, nothing showed up on surface and the values shown in the Config window are weird. My guess is that I have to first convert zstat1.nii.gz to zstat1.mgh and then apply registration, but I'm not exactly sure. Can anyone give any instructions? My other question is that the oneline tutorials on this issue use tkmedit and tkregister2 tools to inspect registration from feat to surface. However, none of these commands opens gui windows on my end. I'm using Ubuntu 18.04 on a Win10 and FreeSurfer 7. I guess these tools are replaced by Freeview but I don't know how to check feat2surf registration in Freeview. Can anyone provide some guidance? Thank you, Yuqi

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Fw:nu_correct error
by xuan 02 Jan '22

02 Jan '22

External Email - Use Caution Oops, forget about the log file.  Here it is ------------------ Original ------------------ From: "xuan" <pearl940311(a)foxmail.com>; Date: Wed, Dec 15, 2021 08:28 PM To: "freesurfer"<freesurfer(a)nmr.mgh.harvard.edu>; Subject: nu_correct error Dear FreeSurfer Experts, I am attempting to recon-all for my one subject for testing on my lab server. However, I get following error: ncopen: filename "./tmp.mri_nu_correct.mni.13492/nu1.mnc": Not a netCDF file miopen: MINC package entry point Error opening ./tmp.mri_nu_correct.mni.13492/nu1.mnc mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.13492/nu1.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.13492/nu1.mnc... And here is the relevant information: (1)FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c (2)Platform: Linux node-1-3 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux (3)log file: please see attached file. Thanks for the help! Best, Xuan Xuan Bu, Ph.D. State Key Laboratory of Cognitive Neuroscience & Learning Beijing Normal University Email: pearl904311(a)foxmail.com Webpage: http://secure-web.cisco.com/1sAYTPWqEOYnQckeJw_qP7iUC93VX2nG1YJZE_-U3zUgEna…

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Re: [Freesurfer] Questions about contrasts
by Laura Willers de Souza 02 Jan '22

02 Jan '22

External Email - Use Caution Dear Douglas, Again, thanks for the reply. Please check if I understand correctly: * First I do the contrast [0 0 -1 1] to test if there is an interaction between diagnosis and cortisol; if there is, I do DOSS [1 -1 0], if there isnt’t, I continue with DODS. * Having no interaction, I do the contrast [1 -1 0 0] to check if only the diagnosis changes cortical thickness regardless of cortisol. Did I interpret correctly? And how do I check if cortisol changes cortical thickness regardless of diagnosis (assuming there is no interaction)? Thanks again! Best, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil --------------------------------------------------------------------------------------------------- De: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Enviado: terça-feira, 14 de dezembro de 2021 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Questions about contrasts This contrast will do it: [1 -1 0 0] But I would first test [0 0 -1 1] to see if the slopes are different. If not, then use [1 -1 0] with DOSS instead of DODS --------------------------------------------------------------------------------------------------- De: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Enviado: terça-feira, 14 de dezembro de 2021 17:30 Para: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Re: Questions about contrasts Dear Douglas, Thank you so much for your answer! Sorry, but I don't think I explained myself correctly in the previous email. I want to analyze the difference in cortical thickness between two groups (CU and CI), adjusting for a covariate (cortisol CSF) and the interaction between them. So my model would be: cortical thickness ~ diagnosis + CSF cortisol + diagnosis*CSF cortisol Using the GLM DODS, the contrasts, according to the wiki example (https://secure-web.cisco.com/1TXDxaJK3TqwFMC6pi74Rk7x9g2fbD-V3AF6Mb-mJgTcED…<https://secure-web.cisco.com/1qbucUNWhNS-2uW6Lox1w2bMK8EUHU0lm2XC7ywMcgAz1o…>), would be: * To verify if only the diagnosis regression coefficient is significant (diagnosis changes cortical thickness regardless of cortisol): 1 -1 0 0 * To verify if the regression coefficient of the interaction between diagnosis and cortisol is significant (the two change cortical thickness dependently): 0 0 1 -1 * To verify if only the cortisol regression coefficient is significant (cortisol changes cortical thickness regardless of diagnosis): 0 0 0.5 0.5 Are these contrasts corret to represent the model we designed? Thank you so much again! Best regards, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil --------------------------------------------------------------------------------------------------- De: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Enviado: terça-feira, 12 de dezembro de 2021 18:23 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Questions about contrasts The model is actually, two independent linear models: thicknessCU = CUOffset + CUcortisol*CUslope thicknessCI = CIOffset + CIcortisol*CIslope There will be four regression parameters: [CUOffset CUslope CIOffset CIslope] --------------------------------------------------------------------------------------------------- De: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Enviado: terça-feira, 12 de dezembro de 2021 10:48 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Questions about contrasts Hello FreeSurfer Developers, I want to perform an analysis of the difference between two groups in cortical thickness, having cortisol levels as covariate. This is my model: cortical thickness ~ pathology (CU/CI) + CSF cortisol + pathology*CSF cortisol From the GLM DODS analysis I want to know if: * the regression coefficient is significant only for the difference between groups, this could possibly mean two things: the difference in offset [1 -1 0 0] or the difference in slopes ([0 0 1 -1] * or only for cortisol, [0 0 0.5 0.5] will test whether the cortisol slope is different than 0 * or for both, both what? * or if the coefficient of the intercept between group and cortisol is significant. this does not make sense to me Is my FSGD file (attached) correct? What would the contrasts look like? --------------------------------------------------------------------------------------------------- De: Laura Willers de Souza <laura.w.desouza(a)hotmail.com> Enviado: terça-feira, 09 de dezembro de 2021 19:50 Para: Douglas N. Greve <dgreve(a)mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Assunto: Questions about contrasts Hello FreeSurfer Developers, I want to perform an analysis of the difference between two groups in cortical thickness, having cortisol levels as covariate. This is my model: cortical thickness ~ pathology (CU/CI) + CSF cortisol + pathology*CSF cortisol From the GLM DODS analysis I want to know if: * the regression coefficient is significant only for the difference between groups, * or only for cortisol, * or for both, * or if the coefficient of the intercept between group and cortisol is significant. Is my FSGD file (attached) correct? What would the contrasts look like? Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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Freesurfer January 2022