Freesurfer December 2021

freesurfer@nmr.mgh.harvard.edu

56 participants
87 discussions

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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nu_correct error
by xuan 02 Jan '22

02 Jan '22

External Email - Use Caution 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/1S0VawiNNuSyS8MeobIrxRfE44jhwRaNmudAQj0qf2puij2…

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2x2 ANOVA tp2-tp1 is not an option to be done
by stdp82＠virgilio.it 02 Jan '22

02 Jan '22

External Email - Use Caution Hi list, I have two groups undergoing two different treatments: one's placebo , one's drug. Two timepoints, at baseline (T1, no treatment) and at treatment (T2). 2x2 ANOVA, repeted measures has been applied by following the guidlines and mailing list. IMPORTANTLY, to compute tp2-tp1, as reported in the fsgd example, is not an option to be done because we aiming to assess the interaction between time and treatment. Please chech the design matrix, the command line produces an error. GroupDescriptorFile 1 Title 2x2_repeted_measures Class Subject1 Class Subject2 Class Subject3 Class Subject4 Class Subject5 Class Subject6 Class Subject7 Class Subject8 Class Subject9 Class Subject10 Class Subject11 Class Subject12 Class Subject13 Class Subject14 Class Subject15 Class Subject16 Class Subject17 Class Subject18 Class Subject19 Class Subject20 Class Subject21 Class Subject22 Class Subject23 Class Subject24 Variables tp1-vs-tp2.drug tp1-vs-tp2.plb Input CODE01_tp1 Subject1 1 0 Input CODE02_tp1 Subject2 1 0 Input CODE03_tp1 Subject3 1 0 Input CODE05_tp1 Subject4 1 0 Input CODE06_tp1 Subject5 0 1 Input CODE07_tp1 Subject6 0 1 Input CODE09_tp1 Subject7 0 1 Input CODE10_tp1 Subject8 1 0 Input CODE11_tp1 Subject9 1 0 Input CODE12_tp1 Subject10 0 1 Input CODE13_tp1 Subject11 0 1 Input CODE14_tp1 Subject12 1 0 Input CODE15_tp1 Subject13 1 0 Input CODE16_tp1 Subject14 1 0 Input CODE17_tp1 Subject15 0 1 Input CODE18_tp1 Subject16 1 0 Input CODE19_tp1 Subject17 0 1 Input CODE20_tp1 Subject18 0 1 Input CODE21_tp1 Subject19 0 1 Input CODE22_tp1 Subject20 1 0 Input CODE23_tp1 Subject21 0 1 Input CODE24_tp1 Subject22 0 1 Input CODE25_tp1 Subject23 1 0 Input CODE26_tp1 Subject24 0 1 Input CODE01_tp2 Subject1 -1 0 Input CODE02_tp2 Subject2 -1 0 Input CODE03_tp2 Subject3 -1 0 Input CODE05_tp2 Subject4 -1 0 Input CODE06_tp2 Subject5 0 -1 Input CODE07_tp2 Subject6 0 -1 Input CODE09_tp2 Subject7 0 -1 Input CODE10_tp2 Subject8 -1 0 Input CODE11_tp2 Subject9 -1 0 Input CODE12_tp2 Subject10 0 -1 Input CODE13_tp2 Subject11 0 -1 Input CODE14_tp2 Subject12 -1 0 Input CODE15_tp2 Subject13 -1 0 Input CODE16_tp2 Subject14 -1 0 Input CODE17_tp2 Subject15 0 -1 Input CODE18_tp2 Subject16 -1 0 Input CODE19_tp2 Subject17 0 -1 Input CODE20_tp2 Subject18 0 -1 Input CODE21_tp2 Subject19 0 -1 Input CODE22_tp2 Subject20 -1 0 Input CODE23_tp2 Subject21 0 -1 Input CODE24_tp2 Subject22 0 -1 Input CODE25_tp2 Subject23 -1 0 Input CODE26_tp2 Subject24 0 -1 a) groupxtime.mtx 0 0 1 -1 b) tp1-vs-tp2.Mod.mtx 0 0 1 0 c) tp1-vs-tp2.Plb.mtx 0 0 0 -1 mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir repeted_measures.wls --nii.gz --fsgd Repeted_measure.fsgd --C Tp1-vs-Tp2.Mod.mtx --C Tp1-vs-Tp2.Plb.mtx --C groupxtime.mtx ERROR: dimension mismatch between X and contrast Tp1-vs-Tp2.Mod.mtx X has 72 cols, C has 4 cols

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Re: [Freesurfer] Trac-all -Prep -C Error
by fsbuild 31 Dec '21

31 Dec '21

External Email - Use Caution Hello Elizabeth, To use the latest development build you can set freesurfer home to, /autofs/vast/freesurfer/centos7_x86_64/dev  or /usr/local/freesurfer/dev - R. On Dec 31, 2021, at 16:11, Kaplan, Elizabeth <elizabeth_kaplan(a)brown.edu> wrote:        External Email - Use Caution        Thanks for your prompt response, Anastasia. How do I switch to the dev version? Would I set my FREESURFER_HOME variable to a different pathway? The one I currently use is /autofs/vast/freesurfer/centos7_x86_64/7.2.0Thank you, again! Happy New Year! On Fri, Dec 31, 2021 at 4:01 PM Yendiki, Anastasia <AYENDIKI(a)mgh.harvard.edu> wrote:Hi Elizabeth - If you're using launchpad, just switch to the dev version. It has the latest bug fixes.Happy new year! Anastasia. From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Kaplan, Elizabeth <elizabeth_kaplan@brown.edu>Sent: Friday, December 31, 2021 1:56 PMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Trac-all -Prep -C Error         External Email - Use Caution        Hi All, I am working to process DWI images using Tracula, however I am running into an error when attempting to run the "trac-all -prep -c" command line. The error reads: "Error when attempting to read --index file". I have searched through the archives for guidance and found a similar error resolved here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ltIzM0k-Zs8u6rwdCkwRDCFBNNQGMl7Bl2tUZ… attempted to save the bug fix file to my $FREESURFER_HOME/bin/ directory, however because I am working remotely on Launchpad, I am unable to edit files within this directory. Any suggestions on how to navigate this issue would be greatly appreciated! Best, Liz _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1DRzzjTq57GTrHTYtmc_7CQDJshuZP8JQjS4cK… Kaplan '22She / Her / HersSc.B. Candidate Cognitive Neuroscience B.A. Candidate Contemplative Studies 69 Brown St Mail #4391Providence, RI 02912_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Trac-all -Prep -C Error
by Kaplan, Elizabeth 31 Dec '21

31 Dec '21

External Email - Use Caution Hi All, I am working to process DWI images using Tracula, however I am running into an error when attempting to run the "trac-all -prep -c" command line. The error reads: "Error when attempting to read --index file". I have searched through the archives for guidance and found a similar error resolved here: https://secure-web.cisco.com/1KzdCREiIOVwQ0EaQYziYkN2ydk3Fbs-8eJWpb28ohBnEB… . I attempted to save the bug fix file to my $FREESURFER_HOME/bin/ directory, however because I am working remotely on Launchpad, I am unable to edit files within this directory. Any suggestions on how to navigate this issue would be greatly appreciated! Best, Liz

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Freesurfer December 2021