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Freeview error
by tsengyuheng1999＠gmail.com 15 Mar '23

15 Mar '23

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Unable to Run Recon-all on T1 Image
by Annie Cooper 15 Mar '23

15 Mar '23

External Email - Use Caution Hi there, I am trying to run recon-all using the Agave Supercomputer at ASU. When I try to run recon-all, these error messages pop up prohibiting me from running recon-all on my T1 image. Here is the error message I received: [asurite@agave2:~/Desktop/T1_IMAGE]$ recon-all -s ATN001v1 -i T1-MPRAGE-8min_Series0301_T1-MPRAGE-8min_20211223085844_301.nii.gz -all mkdir: cannot create directory '/packages/freesurfer-5.0.0/subjects/ATN001v1': Permission denied mkdir: cannot create directory '/packages/freesurfer-5.0.0/subjects/ATN001v1': Permission denied cp: cannot create regular file '/packages/freesurfer-5.0.0/subjects/ATN001v1/scripts/build-stamp.txt': No such file or directory cat: /packages/freesurfer-5.0.0/subjects/ATN001v1/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /packages/freesurfer-5.0.0/subjects Actual FREESURFER_HOME /packages/freesurfer-5.0.0 /packages/freesurfer-5.0.0/subjects/ATN001v1: No such file or directory. I’m curious if the issue is that in order to run recon all and put subject “ATN001v1” into the subjects folder, I have to have the necessary permissions to edit a folder that isn’t under my username in the supercomputer. Please let me know if there are any solutions to this problem. Thanks! Best, Annie

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HELP (I don't have the password to unzip on Winrar/7zip)
by Juan Felipe Gaitan Nocua 14 Mar '23

14 Mar '23

External Email - Use Caution Hello In this email I request help to acquire the password that the freesurfer requests when wanting to unzip the file. I have followed the steps for the installation and this problem does not let me continue. I add that the reason why I will use the program is for research that we are doing at the National University of Colombia for the biomedicine and artificial intelligence research seedbed. Thanks you. *--* *Juan Felipe Gaitan Nocua* *Ingenieria Electronica* *Estudiante de la Universidad Nacional de Colombia* -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web http://secure-web.cisco.com/15qd3FEE_9QR8rTmC4t6iMVtYrajvwHFVh-lK8fSxWhU-Eh… <http://secure-web.cisco.com/14bpKla3JrDHA9RQKrCaHTWEImO7wk8P6tcsn2DyTPxVbPq…>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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Hypothalamus segmentation using hypothalamic subunits vs ScLimbic
by Asmin Alam 13 Mar '23

13 Mar '23

External Email - Use Caution Dear FreeSurfer Experts, I have a question regarding how the hypothalamus volumes are calculated using the hypothalamic subunits function, as opposed to the ScLimbic deep learning tool which is only currently available in the dev version of Freesurfer. My project consists of measuring the volume of the hypothalamus, so I thought of running both algorithms and comparing results to ensure they were consistent. However, they are quite different and I was wondering if there are certain flags/options I should be adding to ensure that the results will relate to each other and why that is the case. What is the key difference in how the hypothalamus is calculated by both these methods? How do I ensure my results are robust/trustworthy? What does noMB mean in the ScLimbic results? I have tried running the ScLimbic function using the original T1 and the --conform flag to make sure that the voxels were isotropic, and then retried by using the nu.mgz as input (as that's what the hypothalamus subunits function uses). Here are the results (also attached): HYPOTHALAMIC SUBUNITS subject 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 test 19.88 25.155 136.715 145.785 131.879 20.078 29.209 134.882 161.009 133.293 459.414 478.471 SC LIMBIC (T1-W and --conform) # Subcortical Limbic Volumetric Stats # Created by mri_sclimbic_seg # NRows 12 # NTableCols 5 # ColHeaders Index SegId NVoxels Volume_mm3 StructName 1 26 469 471.6122 Left-Nucleus-Accumbens 2 58 460 459.8144 Right-Nucleus-Accumbens 3 819 588 571.3680 Left-HypoThal-noMB 4 820 631 586.4990 Right-HypoThal-noMB 5 821 667 707.3562 Left-Fornix 6 822 631 700.7991 Right-Fornix 7 843 58 60.5358 Left-MammillaryBody 8 844 57 64.1979 Right-MammillaryBody 9 865 414 396.2163 Left-Basal-Forebrain 10 866 448 450.1535 Right-Basal-Forebrain 11 869 165 170.6947 Left-SeptalNuc 12 870 151 157.4303 Right-SeptalNuc SC LIMBIC (nu.mgz input) # Subcortical Limbic Volumetric Stats # Created by mri_sclimbic_seg # NRows 12 # NTableCols 5 # ColHeaders Index SegId NVoxels Volume_mm3 StructName 1 26 513 519.7247 Left-Nucleus-Accumbens 2 58 526 537.3985 Right-Nucleus-Accumbens 3 819 575 570.7261 Left-HypoThal-noMB 4 820 613 604.3893 Right-HypoThal-noMB 5 821 657 675.3337 Left-Fornix 6 822 663 691.8721 Right-Fornix 7 843 51 53.4853 Left-MammillaryBody 8 844 58 61.4891 Right-MammillaryBody 9 865 473 483.7591 Left-Basal-Forebrain 10 866 487 496.4204 Right-Basal-Forebrain 11 869 145 153.3073 Left-SeptalNuc 12 870 138 142.8245 Right-SeptalNuc I'm also not sure exactly what the flag "--crop" means for the hypothalamic subunits function. I left it to the default value of 184 but how will changing this affect my final result? Below are also my codes for all three functions: mri_segment_hypothalamic_subunits --s ${subjid} --sd ${sd} --crop 184 mri_sclimbic_seg --i ${sd}/${subjid}/mri//T1.mgz --o ${sd}/${subjid}/mri/sclimbic.mgz --write_volumes --conform mri_sclimbic_seg --i ${sd}/${subjid}/mri//nu.mgz --o ${sd}/${subjid}/mri/sclimbic.mgz --write_volumes Any help is appreciated. Thank you, Asmin UCL Queen Square Institute of Neurology

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Password for Zip file
by Technology Kishoge 13 Mar '23

13 Mar '23

External Email - Use Caution Hello, I am trying to set up the software using Virtual Box but require the password for the zip file? Thanks

1 0

Along- tract multiple comparison result visualisation and summary interpretation
by miracle ozzoude 13 Mar '23

13 Mar '23

External Email - Use Caution Hello, Please, can someone answer my questions regarding the along-tract stats using mri_glmfit and mri_glmfit-sim with permutation for version 7.2. 1) I ran it and I found a significant negative association between FA and clinical score (see attached summary file). how do I know the entire length of the tract and how much was affected based on the summary file; should I be interpreting the results from the summary file differently? 2) Also when performing clusterwise correction for multiple comparison for along-tract analyses, should the bonferroni flag (--2spaces) be included? This is because it wasn't mentioned/included in the tracula statistics tutorial nor the publication "Using diffusion MRI data acquired with ultra-high gradient strength to improve tractography in routine-quality data". 3) Lastly, is it appropriate to embed the perm.th13.neg.sig.cluster.mgh from mri_glmfit-sim in dmri_trk2trk? Many thanks, Paul

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how the variance calculated for t-value in the first level GLM in fsfast
by haoran.x＠gmail.com 13 Mar '23

13 Mar '23

External Email - Use Caution Hi, I have a naïve question. When I use GLM for a single subject timeseries data, how the variance is evaluated to get the t value? I know the beta values and contrast matrix make the numerator for the t value. How is the denominator made? Is it through the fitting residual ie std(residual), or is it from session by session or run by run variance? Can I find the formula somewhere? I was not able to find the answer in tutorial or the existing mailing list. Thanks a lot! Best, Haoran

2 1

mri_glmfit with age-squared
by Triebswetter, Curtis 13 Mar '23

13 Mar '23

External Email - Use Caution Hello Freesurfer experts, I am attempting to run the command mri_glmfit --y lh.RBS_ADRC_N0_control.10.mgh --fsgd RBS_ADRC_APOE_age22.fsgd dods --C APOE_ageINT.mtx --surf fsaverage lh --cortex --glmdir lh.RBS_ADRC_N0.glmdir On this .fsgd file: “RBS_ADRC_APOE_age22.txt” Using the following design matrix: “lh.RBS_ADRC_N0.txt” I am receiving the error message: -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. I would appreciate your insights into what may be the likely cause of this error and apologize that the files are in text format. If need be, I can convert these to their proper formats. misc information: Freesurfer 6.00 CentOS v7 Best, Curtis

2 1

How to find topological defects
by KennethSPrice 13 Mar '23

13 Mar '23

External Email - Use Caution Hello Freesurfers, I've found the tutorial for editing wm.mgz (https://secure-web.cisco.com/1_VE6Du8jnccjig75E4hpWkJh1_YR3uP_xPzMfYusO6K01…) I'm curious if there is a way to find the topological defects easily? Is there a text file in the stats folder, for example, which locates the coordinates of topological defects? Thanks, Ken Sent with [Proton Mail](https://secure-web.cisco.com/1KF2a2rKWu_5CevMXrlKZAUb4EzG3VQGOQnGyxhP… secure email.

2 3

mri_segstats
by John Anderson 13 Mar '23

13 Mar '23

External Email - Use Caution Dear Freesurfer community, Please forgive me for the basic nature of my question. I was wondering whether there is an argument that can be included in mri_segstats to display the results in cubic centimeters (cm^3) instead of cubic millimeters (mm^3). thanks for any suggestions. Thank you, John

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