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Questions about GLM
by Laura Willers de Souza 10 Dec '21

10 Dec '21

External Email - Use Caution Hello FreeSurfer Developers, I would like to assess whether my regression model meets the GLM assumptions, especially if there is no multicollinearity. Is it possible to perform this diagnosis in freesurfer? If not, is there a way to extract the model residues to test in another program? Or, is there any way to perform a regression with correlated variables in freesurfer? 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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Re: [Freesurfer] Help
by Douglas N. Greve 10 Dec '21

10 Dec '21

The data look pretty noisy in those images. My guess is that the WM is not getting segmented properly in that temporal area or there is an incorrectly fixed topology error. Try looking at the wm.mgz (or the filled.mgz instead if you have 7.2). YOu can load surface.defects.mgz to see where the defects are. On 11/29/2021 9:41 AM, Nilab Nasrullah wrote: > > External Email - Use Caution > > Sure. See attached. > > //Nilab > ------------------------------------------------------------------------ > *From:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> > *Sent:* 29 November 2021 15:40 > *To:* Nilab Nasrullah <nilab.nasrullah(a)stud.ki.se>; > freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Help > Can you send them in plain, unzipped format? > > On 11/29/2021 4:07 AM, Nilab Nasrullah wrote: >> >> External Email - Use Caution >> >> I am attaching a few screenshots of the segmented brain as zip-files. >> Hopefully, you can see the results. If not, let me know so I can send >> it to you in a different format. >> >> Thanks, >> Nilab >> ------------------------------------------------------------------------ >> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >> <freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas >> N. Greve <dgreve(a)MGH.HARVARD.EDU> <mailto:dgreve@MGH.HARVARD.EDU> >> *Sent:* 29 November 2021 04:01 >> *To:* freesurfer(a)nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> <freesurfer(a)nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject:* Re: [Freesurfer] Help >> Can you send some pictures? >> >> On 11/23/2021 4:02 AM, Nilab Nasrullah wrote: >>> >>> External Email - Use Caution >>> >>> Hi, >>> >>> I am editing subjects for a research project. After reconstruction, >>> some parts of the brain are not included in the segmentation. Often, >>> some parts of the temporal lobe and the cortex of the occipital lobe >>> are not included. In some cases, the cortex of the frontal lobe is >>> also affected. >>> >>> I have tried using controls points, but the results don't change. I >>> have also reconstructed them again, running autorecon1 and >>> autorecon2&3 separately. I have lowered the watershed parameters, >>> used the gcut command and edited manually after autorecon1 but in >>> the end, the results don't vary significantly compared to running >>> recon-all -all. >>> >>> What can I do to include the missing parts? >>> >>> Thanks, >>> Nilab >>> >>> >>> >>> /När du skickar e-post till Karolinska Institutet (KI) innebär detta >>> att KI kommer att behandla dina personuppgifter. /Här finns >>> information om hur KI behandlar personuppgifter >>> 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>>> >>> >>> /Sending email to Karolinska Institutet (KI) will result in KI >>> processing your personal data./ You can read more about KI’s >>> processing of personal data here >>> 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>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1_T2XmBhpVbXwMIEaFeIYg3-BNsl1o7ClCIZMG5rWzAnUJ…> >> >> >> >> /När du skickar e-post till Karolinska Institutet (KI) innebär detta >> att KI kommer att behandla dina personuppgifter. /Här finns >> information om hur KI behandlar personuppgifter >> <https://secure-web.cisco.com/1UqiNkicTxuFcz1L3T3NkaXbwLeJ62VnJ8kfX7Igvn-ppo…>. >> >> >> /Sending email to Karolinska Institutet (KI) will result in KI >> processing your personal data./ You can read more about KI’s >> processing of personal data here >> <https://secure-web.cisco.com/1lmFcjGGYhT8Lb-8v-jAcUDrxjoMyBBbd5y2oyla2twoET…>. >> > > The information in this e-mail is intended only for the person to whom > it is addressed. If you believe this e-mail was sent to you in error > and the e-mail contains patient information, please contact the Mass > General Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was > sent to you in error but does not contain patient information, please > contact the sender and properly dispose of the e-mail. > > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify > the sender of this message immediately. Continuing to send or respond > to e-mail after receiving this message means you understand and accept > this risk and wish to continue to communicate over unencrypted e-mail. > > > > /När du skickar e-post till Karolinska Institutet (KI) innebär detta > att KI kommer att behandla dina personuppgifter. /Här finns > information om hur KI behandlar personuppgifter > <https://secure-web.cisco.com/1V3Fe_yrtm7ybutBTP5ppHVQtp_Mirnxy38x8LLZoB9fD2…>. > > > /Sending email to Karolinska Institutet (KI) will result in KI > processing your personal data./ You can read more about KI’s > processing of personal data here > <https://secure-web.cisco.com/1qHlChM2jTytSHjWPqLwrPCWHsOVbw3cf6Rd696VC3WQ-n…>. >

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mri_gcut gives "error: Could not set locale"
by Vishal Mohanty 10 Dec '21

10 Dec '21

External Email - Use Caution Hi This is Vishal Mohanty, a Research Assistant at the CNS Lab<https://secure-web.cisco.com/15W4gGDirofYO8-hxBJZzt-0Z-M9nlsafkwxgoE1yBXcR-…> at Stanford which is headed by Prof. Kilian Pohl<http://secure-web.cisco.com/1SZ4eEoYf_E7omrj4INdi5GjmRCw5BV-qQfn2PUzBkhAmhz…>. We are running Freesurfer commands for processing of our MRI data on Sherlock<https://secure-web.cisco.com/1ELFOu5r8C0zuhwJthCGAIpaL-g9geTHv3j06pTTPK06DK…> which is the HPC cluster at Stanford. We are seeing some errors in running mri_gcut of the type: CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/gcut_t1b_brain.nii.gz ======================================================================== error: No such file or directory error: Could not set locale^@ I'm attaching the full log file. Could you please help me understand what's the issue and how to fix it. Do let me know what other information would be needed from my end. Thanks and Regards Vishal Mohanty MS CS Candidate (2023) Stanford University

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howto create a .label files with dilated content
by Krieger, Donald N. 10 Dec '21

10 Dec '21

External Email - Use Caution I wish to use the "-dilate n" capability of mri_extract_label or other tool to create label files for ctx regions. mri_extract_label appears to only be capable of writing output to .mgz files and I do not find a tool for extracting labels from a .mgz into an ascii .label file. Your direction would be welcome. Thanks - Don [cid:image001.jpg@01D7E53E.59F4AFA0] Don Krieger, Ph.D. Research Scientist Department of Neurological Surgery University of Pittsburgh

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Qdec error
by Arian Klows 10 Dec '21

10 Dec '21

External Email - Use Caution Dear FS experts, I have freesurfer-linux-centos7_x86_64-7.1.1 on my computer and when I run qdec, I get the following error: Tk_Init error: invalid command name "tcl_findLibrary" Error initializing Tcl. Could anyone please tell me what this means?

2 1

FSGD file
by Laura Willers de Souza 10 Dec '21

10 Dec '21

External Email - Use Caution Hello FreeSurfer Developers, I would like to know what I put in the FSGD file for patients who don't have data for a variable. In my case, I want to analyze CU (cognitively unimpaired) patients versus CI (cognitively impaired) patients, controlling for CSF and plasma cortisol values. And some patients have only the CSF value and others only the plasma value. Would the analysis be correct if I put the mean of the non-missing values of this variable in those cells that don't have data? Would you be so kind to help me with that? Thanks in advance! Laura.

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REtrieve perimeter from generated surfaces
by Fernanda Hansen P. de Moraes 10 Dec '21

10 Dec '21

External Email - Use Caution Dear FreeSurfer experts, Is there a way to estimate the perimeter from a surface (e.g. ?h.pial) for each slice in an automated manner at any orientation? Thank you very much, Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino e metaBIO (IF-UFRJ)

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Information on anova 2x2 longitudinal design
by stdp82＠virgilio.it 10 Dec '21

10 Dec '21

External Email - Use Caution Hi list, I have two groups undergoing two different treatments: one's placebo (n=12), one's drug (n=12). 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. 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

2 1

Errors with mkanalysis-sess: missing file fmcpr.brainmask.fsaverage.lh
by Hiersche, Kelly J. 10 Dec '21

10 Dec '21

External Email - Use Caution Hello FreeSurfer Developers, First, I am new to using Freesurfer, so I apologize if any information is unclear. I am attempting to use the following tutorial https://secure-web.cisco.com/1i0LcvXc_pWxYrG0y8LzlZO7IfvmC_UpV6cd9EBpLiYz69… to do a surface based GLM in an individual subject (using my own data, not the tutorial data), but I am getting the following error: Error using MRIread (line 76) ERROR: cannot determine format of /subnum/bold/runnum/masks/fmcpr.brainmask.fsaverage.lh (MRIread) I am getting that error because the fmcpr.brainmask.fsaverage.lh does not exist. To fix this error, I re-ran preprocessing using the following tutorial: https://secure-web.cisco.com/1Sor7-h_gxGA_NBXCIF2cnCakBuzWn-uVbkP71hrF-15-u… After preprocessing, I still got the same error. Here are the files that do exist in that path: subnum/bold/run-num/masks brain.e3.nii.gz brain.fsaverage.lh.pr.nii.gz brain.fsaverage.rh.pr.nii.gz brain.mni305.2mm.pr.nii.gz brain.nii.gz.mkbrainmask.log brain.fsaverage.lh.nii.gz brain.fsaverage.rh.nii.gz brain.mni305.2mm.nii.gz brain.nii.gz There are some fmcpr files in this folder: subnum/bold/run-num fmcpr.brainmask.norm.2x2x2.nii.gz fmcpr.mcdat fmcpr.norm.nii.gz fmcpr.sm5.fsaverage.rh.nii.gz fmcpr.brainmask.normtmp.2x2x2.nii.gz fmcpr.nii.gz fmcpr.sm0.norm.nii.gz fmcpr.sm5.mni305.2mm.nii.gz fmcpr.mat.aff12.1D fmcpr.nii.gz.mclog fmcpr.sm5.fsaverage.lh.nii.gz fmcpr.sm5.norm.nii.gz Here are the commands I am running: mkanalysis-sess -fsd bold -rlf $analysis_stem-$run_set.rlf -surface fsaverage $hemi -event-related -paradigm $PARA_NAME -refeventdur 18 -nconditions $nconditions -mask $func_stem.brainmask -gammafit 2.25 1.25 -nuisreg mcprextreg 6 -TR 1.0000 -polyfit 1 -analysis $analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -tpexclude $tpe$TPE_STEM -funcstem $func_stem.sm$kernel$REG_STEM -per-run mkcontrast-sess -analysis $analysis_stem-$run_set-$func_stem-$tpe.sm5.$hemi.$REG_STEM -contrast Con1-Con2 -a 1 -c 2 preproc-sess -fsd bold -rlf $analysis_stem-$run_set.rlf -surface fsaverage lhrh -mni305 -fwhm 5 -per-run 1. I am running freesurfer through matlab on the Ohio Supercomputer; freesurfer/6.0.0 Thank you for all your troubleshooting help! Kelly

2 3

editing the aseg.mag using another tool and then rerunning
by Alexopoulos, Dimitrios 10 Dec '21

10 Dec '21

External Email - Use Caution A quick question. Is it feasible or even possible to edit the aseg.mgz using another program (i.e. ITK-snap after converting to nifti), and rerunning the pipeline using the revised aseg as input To regenerate volumes and surfaces? Do WM edits need to need to be completed on the WM.mgz and/or using Control Points? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 1

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