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mkheadsurf error: mris_smooth and mris_inflate synthesized bizarre output paths
by Yong-Jun Lin 09 Jan '22

09 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, I was attempting to execute the mkheadsurf script to process MRI data and encountered some errors. 1. The first error message is "subjdir: Undefined variable.". After reading through the mkheadsurf script, I realized that is a temporary variable used in a script. Having no idea why this was required in the beginning, I manually entered export subjdir=/Volumes/Lab/SA/MRI/ForMNE/subj01 to circumvent that problem. 2. Indeed the script started running afterwards, but there were two errors at step 1. (Creating a dense scalp tessellation with mkheadsurf) First, mris_smooth -n 10 -b /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/area.seghead -c \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/curv.seghead \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.seghead \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.seghead resulted in error: MRISwriteCurvature: could not open lh./Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.curv.seghead Second, mris_inflate -n 10 -sulc /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/sulc.seghead \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.seghead \ /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.seghead.inflated resulted in error: MRISwriteCurvature: could not open /Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh./Volumes/Lab/SA/MRI/ForMNE/subj01/surf/lh.sulc.seghead Please note that the weird output paths have the output folder repeated twice in different positions. 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, I've attached the mkheadsurf.log in case it's of any use. 1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0 2) Platform: macOSX 10.13.6 3) uname -a: Darwin localhost 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64 4) mkheadsurf.log: see attached Sincerely, -- Yong-Jun Lin Postdoctoral Associate Department of Psychology New York University 6 Washington Place, Room 955 New York, NY 10003 -- Yong-Jun Lin Postdoctoral Associate Department of Psychology New York University 6 Washington Place, Room 955 New York, NY 10003

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The volume of some hypothalamus subunits is 0
by Xiaotong Zhang 09 Jan '22

09 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, When I used the FS.dev version for hypothalamus segmentation, I have segmented it sucessfully. Tensorflow-CPU has been installed to run this module (hypothalamus_seg). The .sh file was: for subj3 in 111 112 114...and 431 do mri_segment_hypothalamic_subunits --i /run/media/guanliyuan/Elements_Learningmaterials/try3_fs/$subj3/mri/orig/001.mgz --o /run/media/guanliyuan/Elements_Learningmaterials/try3_fs/try3fs_seg/$subj3/ --vol /run/media/guanliyuan/Elements_Learningmaterials/try3_fs/try3fs_seg/$subj3/ --threads 1 --cpu done However, in the .csv file of some subjects, there were no the volume of the left and right anterior-inferior. I don't know the reason for this cese. I am looking forward to your reply. Thanks very much in advance. The results were: | Subjects left anterior-inferior left anterior-superior left posterior left tubular inferior left tubular superior right anterior-inferior right anterior-superior right posterior right tubular inferior right tubular superior whole left whole right | | | | | | | 314 | 0 | 4.529 | 67.887 | 25.924 | 56.559 | 0 | 6.571 | 87.712 | 44.5 | 83.406 | 154.899 | 222.189 | | | | | 331 | 14.973 | 23.419 | 128.191 | 152.167 | 140.735 | 0 | 3.832 | 111.306 | 122.421 | 97.331 | 459.485 | 334.89 | | | | 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev 2) Platform: CentOS 7.9 Sincerely, Zhang

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Re: [Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala
by Laura Willers de Souza 09 Jan '22

09 Jan '22

External Email - Use Caution Hii, I'm resending the previous email, because for some reason the other emails didn't go to the mailing list. ----------------------------------------------------- So which file do I put as an argument to --thfile? Or I just don't put the --thfile? And about that tool to convert the table into a map. That's what appeared in that link you sent me. [cid:f2f3a648-ee99-4b43-91f0-2a1059127434] Do I run the second line to get the tool? Thanks again, 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, 4 de janeiro de 2022 19:35 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] Doubts about analysis of hippocampal subfields and nuclei of the amygdala oh, sorry, the --thfile should not be the table file. The sig.mgh has the same info as the table file, so you do not need to pass the table file. On 1/4/2022 4:44 PM, Laura Willers de Souza wrote: External Email - Use Caution Sorry, let me explain better! When mri_glmfit finishes it generates the sig.table.dat file which has the p values of the ROIs (first image below). Then, when mri_fdr finishes, that same sig.table.dat file no longer contains the p-values of the ROIs, but the FDR value (second image). In this way, the p-values of the ROIs are lost. What I would like is to end mri_fdr with a file with the value of fdr + the original sig.table.dat file with the p values of the ROIs. Is there a way to do this? [cid:07085efb-f1e4-4e6c-8604-8d31276ea762][cid:9c5cb8ea-781b-4629-9dc3-8d34536a46a5] On this link you sent there is the following: [cid:7218f44c-2c13-4d62-b054-7f0102164a78] Was it supposed to be like this? 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><mailto:dgreve@mgh.harvard.edu> Enviado: terça-feira, 4 de janeiro de 2022 17:21 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com><mailto:laura.w.desouza@hotmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala On 1/4/2022 2:42 PM, Laura Willers de Souza wrote: External Email - Use Caution The command worked fine! But, in the end, the file that contains the thresholds for each of the ROI (first image below) ends up being replaced by the FDR value (second image below), which is not very good, because this information ends up getting lost. I don't understand what you mean. The value in the file is the threshold that you would use to divide your ROIs into significant vs nonsig groups in a way that meets the FDR criteria; in your case, it looks all but subiculum will pass. Or are you looking for an FDR-corrected p-value for each ROI? Is there any way to save the FDR value in another file and not in the same one where the p-values of the ROI are? And is it possible to visualize the ROIs with the significance scale in freeview? I tried to overlay the sig.mgh file over the inflated surface and also the mri_fdr output.mgh file, but it didn't work. That definitely will not work. What should I do to make this work? You have to convert the table into a map. You can get a tool to do this from here https://secure-web.cisco.com/1zTuJbLvHAGBo6V61VVHiwKCyghSjwmceVznVZ0McksMdz…<https://secure-web.cisco.com/1h610sgx8xUYJT8v3G61D8UsnoyEDEVgkpvN1qNZPm7dXL…> username 'guest' password 'collab' I'm not totally sure it will work as a stand-alone. You might have to download the development version of FS to get it. Specify the subfields segmenation as the --seg option. Thank you so much again, 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><mailto:dgreve@mgh.harvard.edu> Enviado: terça-feira, 4 de janeiro de 2022 15:21 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com><mailto:laura.w.desouza@hotmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala that looks right; I don't think you need a 2nd --thfile (but does not hurt it). On 1/3/2022 3:27 PM, Laura Willers de Souza wrote: External Email - Use Caution Dear Douglas, Once again, thanks so much for the reply! About the mask, I just don't put anything or put "nomask"? With your suggestions, the command looks like this: mri_fdr --fdr .05 --pos --thfile $SUBJECTS_DIR/hipposubfields.lh.T1.v21.CU_CI.glmdir/sig.table.dat --i $SUBJECTS_DIR/hipposubfields.lh.T1.v21.CU_CI.glmdir/group.diff.CU_CI/sig.mgh nomask hipposubfields.lh.T1.v21.CU_CI.mgh --thfile $SUBJECTS_DIR/hipposubfields.rh.T1.v21.CU_CI.glmdir/sig.table.dat --i $SUBJECTS_DIR/hipposubfields.rh.T1.v21.CU_CI.glmdir/group.diff.CU_CI/sig.mgh nomask hipposubfields.rh.T1.v21.CU_CI.mgh Do you think this is correct? As it was before (without the input to --thfile) it was giving the following error: I believe that with these fixes it should work fine, right? Thank you so much 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><mailto:dgreve@mgh.harvard.edu> Enviado: domingo, 02 de dezembro de 2022 Para: Laura Willers de Souza <laura.w.desouza(a)hotmail.com><mailto:laura.w.desouza@hotmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Doubts about analysis of hippocampal subfields and nuclei of the amygdala 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.fsgddods \ --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.mghhipposubfields.lh.T1.v21.CU_CI.mgh --no-log10p --i contrast/rh.sig.mgh rh.mask.mghhipposubfields.rh.T1.v21.CU_CI.mgh --no-log10p For this one, you don't need a mask. Also, don't use --no-log10p (the output of mri_glmfit is in log10p). --thfile needs an argument (eg, threshold.dat) Are these commands correct? Another question, in this type of analysis is image smoothing common? Like was done here https://secure-web.cisco.com/1jlcLGBnd9WfD2ZqLxu7gosP6abdWaUThJ9URWsMygqadR…<https://secure-web.cisco.com/1KedI8-SZfRiRhwkEfi_d25zdjoR6A_msh6cCPc1dap84L…> <https://secure-web.cisco.com/1we0tWxEcmAWpL06CsQ9vqTCkjuPHErSGyrotLh2MGxv3l…> No, it would make no sense here because this is an ROI analysis Thank you so much again! Best regards, *Laura Willers de Souza *

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(无主题)
by 李晓舒 09 Jan '22

09 Jan '22

External Email - Use Caution I need the license for freesurfer，thanks a lot！ Best wishes！

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Re: [Freesurfer] Ubuntu VM Password reques
by fsbuild 08 Jan '22

08 Jan '22

External Email - Use Caution Hello Jihye, Sending the info to your email shortly. - R.. On Jan 6, 2022, at 23:01, Jihye Noh <jihyennn(a)gmail.com> wrote:        External Email - Use Caution        Hello,I am attempting to start Ubuntu, but Ubuntu requests a login password for the Developer account.Can I ask for the password?Thank you_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Ubuntu VM Password reques
by Jihye Noh 06 Jan '22

06 Jan '22

External Email - Use Caution Hello, I am attempting to start Ubuntu, but Ubuntu requests a login password for the Developer account. Can I ask for the password? Thank you

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7T fmri analysis in native space
by Nasiriavanaki, Zahra,M.D. 06 Jan '22

06 Jan '22

Hello freesurfers, I have one quick question and appreciate it very much if you could please respond. I have been running some resting state fmri analysis acquired on 7T scanner. In order to do the analysis on the surface, I’ve been using "-surface self lh” for left hemisphere analysis in mkanalysis-sess. My question is if there is an equivalent command to use for subcortical analysis. I have been using -mni305 1 for subcortical analysis. but I’m not sure if this the right flag to use when doing the analysis on the subject’s own space and not on fsaverage? here are the commnds I’ve been using. running the analysis with mni305 1, gives me maps like the one attached. I can’t see any blob, but I see dots of activation, which makes me think there’s something wrong. mkanalysis-sess -a stat_native.lh -runlistfile goodruns -fsd bold3 -surface self lh -fwhm 0 -event-related -TR 3 -nc 24 -polyfit 2 -nuisreg mcprextreg 6 -tpef TPEF.txt -spmhrf 0 -refeventdur 3 -per-run -nskip 0 -p stat.par -force mkanalysis-sess -a stat_native.mni -runlistfile goodruns -fsd bold3 -mni305 1 -fwhm 0 -event-related -TR 3 -nc 24 -polyfit 2 -nuisreg mcprextreg 6 -tpef TPEF.txt -spmhrf 0 -refeventdur 3 -per-run -nskip 0 -p stat.par -force Thanks, Mona

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slicesdir for FreeSurfer
by Boa Sorte Silva, Narlon 05 Jan '22

05 Jan '22

External Email - Use Caution Hi there, Hope all is well Is there a tool in FreeSurfer similar to FSL's slicesdir? That could output a web report or something similar? Thanks for your help! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon

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Tracula Processing: MRI_binarize error
by Kaplan, Elizabeth 04 Jan '22

04 Jan '22

External Email - Use Caution Hello, I am working to process DWI images using Tracula, however my processing stops during the mri_binarize command. In my Trac-all.log, it reads "mri_binarize done" Furthermore, when I run the command independently it runs smoothly, without error. My configuration file and trac-all.log are included below. Thank you in advance for any suggestions on how to navigate this issue Elizabeth

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Ventricle segmentation issue - ventricle mislabeled as white matter
by Kang, Jee Won 04 Jan '22

04 Jan '22

External Email - Use Caution Hello all, I found a very common error in our data while I was correcting recons. The lateral ventricles (usually the horns) are being misclassified as white matter in aseg.mgz. This happened in around 1/3 of our 108 subjects. We were able to fix this issue by manually filling in the ventricles in aseg.presurf.mgz and re-running Freesurfer with the command autorecon2-noaseg -autorecon3, but this is obviously quite a labor-intensive fix for a substantial portion of our data. This was also the only way to fix the segmentation - filling in the mislabeled areas as 255 in the wm.mgz did not fix the problem. I'm not sure why Freesurfer is having issues here, as the areas it is mislabeling have very distinct intensity boundaries - the T1 intensity is usually between 20 and 45 in the areas that are being mislabeled. I've attached a screenshot of a subject's aseg.presurf.mgz who had this ventricle segmentation issue, and you can see that a large portion of the right ventricle has just not been segmented properly; the intensity of the area in the aseg.presurf.mgz and wm.mgz volumes is just 0, and it was 41 (R cerebral white matter) in aseg.mgz. Would you be able to provide some insight into why this might have been happening, and what we could do in the future to prevent such extensive manual editing in the future? I can also say that this data was processed with a T2 image as well, and supplying that flag didn't help with the segmentation issue. Thank you, Jee Won

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