Freesurfer

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30076 discussions

Anova 2x2 longitudinal
by stdp82＠virgilio.it 30 Nov '21

30 Nov '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. to compute tp2-tp1 is not an option for study design. 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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Which file should be used as the result of automatic freesurfer segmentation?
by 1248742467 30 Nov '21

30 Nov '21

External Email - Use Caution I am going to use Freesurfer to compare the results of automatic segmentation with our proposed method. The label I use is lh.label.DKT31.manual.annot in the mindboggle dataset, so which automatic segmentation result should be used? In addition, are there any references that have relevant segmentation results that I can use directly?

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Information on anova 2x2 longitudinal design
by stdp82＠virgilio.it 30 Nov '21

30 Nov '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

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Re: [Freesurfer] Developer Password
by fsbuild 29 Nov '21

29 Nov '21

External Email - Use Caution Hello Art, Sending the login and update info to your email shortly. - R. On Nov 29, 2021, at 12:18, art.spam(a)web.de wrote:        External Email - Use Caution        Dear freesurfer team, following the instructions on installing the latest freesurfer version on a Windows hosted VirtualBox I'm asked for a developer password on booting.I couldn't find the password anywhere and saw in the archives that people ran into this before as well.Would you please forward me the login data?  Thanks in advance and kind regards, Art Sto _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freeview.app crashing
by fsbuild 29 Nov '21

29 Nov '21

External Email - Use Caution Hello Christian, There is a posting on the freesurfer mail list talking about in general how to deal with freeview crashing on the Mac, but I will send it again to your email. https://secure-web.cisco.com/1e1jc_fAfWM9bqCzlGbCbme4yrpDt-91dbT3jRnUtzP-Lh… I you are working on macOS 11.X BigSur, then I would try getting a new license as older licenses have caused problems.  The link to the license form is, https://secure-web.cisco.com/19eqyrgyBwTeifm0ka9IWTt4P_siVrEJ-U2hnNgRBrwlvV… - R. On Nov 26, 2021, at 12:52, ChristianBauer <christian.bauer(a)ovgu.de> wrote:        External Email - Use Caution        Dear Freesurfer experts,I am having issues with opening Freeview. I am currently using Freesurfer v.7.2.0 and I had no problems setting up Freeusurfer and Freeview on my Desktop computer. However, I have had issues with Freeview crashing on my Mac laptop every now and then and now I cannot open Freeview at all  The error message I am getting is a s follows/Applications/freesurfer/7.2.0/bin/freeview: line 2:  3185 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“I have tried downloading and reinstalling Freesurfer several times as well as trying the stand-alone version. I have also changed the license file as was previously suggested by one of your team. Any advice would be greatly appreciated.Thanks in advance,Christian_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Developer Password
by art.spam＠web.de 29 Nov '21

29 Nov '21

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Fieldmap Echospacing Error
by Kaplan, Elizabeth 29 Nov '21

29 Nov '21

External Email - Use Caution Hi All, I am working on processing diffusion data with Tracula and can't seem to resolve an error I encounter attempting to run the "trac-all -prep -c" command on my data. The error message that I get arises due to the line of code where I specify the echospacing in fieldmap images. It reads that the "flag is not recognized". I am able to run the command smoothly and obtain diffusion metrics when specifying dob0 = 0. I have included my trac-all.log and configuration file for reference. Can anyone offer guidance in navigating this issue? It is greatly appreciated! -- [image: Brown logo] *Liz Kaplan '22* *She / Her / Hers* Sc.B. Candidate Cognitive Neuroscience B.A. Candidate Contemplative Studies 69 Brown St Mail #4391 Providence, RI 02912

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Smoothing and ROI averages from .stats output
by Daniel Westfall 29 Nov '21

29 Nov '21

External Email - Use Caution Good afternoon, It is my understanding that if I am only interested in the already averaged region ROIs that are output in the .stats files that I should not use a smoothing kernel as they are already averaged across all vertices, correct? My specific question has to do with calculating the average cortical thickness and total surface area of the Yeo networks using this command: mri_surf2surf \ --srcsubject fsaverage \ --trgsubject $dir \ --hemi lh \ --sval-annot /$SUBJECTS_DIR/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval /$SUBJECTS_DIR/$dir/label/lh.Yeo2011_7Networks_N1000.annot In this case, if I want to use the output from the lh.Yeo2011_7Networks_N1000.stats then I would NOT want to use the --fwhm 10 flag, as they are already averaged and this could cause bleeding between the different regions, correct? Thank you!

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Visualization error in freeview from recon-all
by achille.teillac＠chu-lyon.fr 29 Nov '21

29 Nov '21

External Email - Use Caution Dear experts, We are working with a large MRI dataset (FLAIR, T1) and we are performing recon-all based on the 3D T1. At the end, no error is detected but the visualization of the pial, white and inflated surfaces in freeview is somehow bad as you can see on the picture attached (lh.pial_freeview, lh.white_freeview, lh.inflated_freeview). Can it be an error that I missed and is there a way to correct it ? Or could it be a 3D rendering issue that can be fixed with visualization options ? Oddly, when I zoom really close for all surfaces, it seems perfectly smoothed... I thought first it could be linked to the topological defect correction (which I didn't do) but when I display the surfaces with paraview it works fine as you can also see on the picture attached (lh.pial_paraview, lh.white_paraview, lh.inflated_paraview). Everything works fine otherwise. Thanks in advance for any help you may provide and I can send you some screenshots highlightening the issue or the recon-all log. Best, Achille Teillac

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Re: [Freesurfer] Help
by Douglas N. Greve 29 Nov '21

29 Nov '21

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 > <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas N. Greve > <dgreve(a)MGH.HARVARD.EDU> > *Sent:* 29 November 2021 04:01 > *To:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)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 >> <https://secure-web.cisco.com/1j67IzVGn-rPDxWTuNJ7rL_6odYOWCRBu23QS17cACnRyi…>. >> >> >> /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/1Kc7a3pEbtZ_tk8Amzoyyo0glZd7MCe1sLIURpc1mdQ8wc…>. >> >> >> _______________________________________________ >> 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-E1yjOjKQ9KDEXvwYBVr3bbOq2bacLh1h8cbFg8HZIRk9…> > > > > /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/1AbbExkRRcd9A1GsUXiwxmB8hzvltggGn77dypaT3DX51u…>. > > > /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/1AwEFqqXcjoj26oT8N6wol9bYPT2t48T1NQwZruliDsSsz…>. >

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