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Tracula trac-all -prep error
by Powell, Jake Robert 30 Jan '22

30 Jan '22

External Email - Use Caution Hello, I am trying to run the command trac-all -prep -c dmrircmultiscan.example -jobs prep.txt using a config file made for a cross-sectional study with multiple scans. Each subjects has 2 scans. When I run the command I get this error message. length of pathway list (/proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/pathlist.txt) and endpoint label ID list ERROR: () do not match Under the hood I noticed a gmids variable could be set. I this something I need to do for this data structure? I have previously not had issues using one scan. Below is the config file text. Thank you in advance! # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 or 2 # Default: 1 (yes) # set dorotbvecs = 1 # Intra-subject (diffusion-to-T1) registration method # 1: Affine with a correlation ratio cost # 2: Affine with a mutual information cost # 3: Affine with a boundary-based cost (default) # set intrareg = 3 # Degrees of freedom for intra-subject registration # Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine) # Default: 6 for infants, 9 otherwise # set intradof = 9 # Maximum rotation angle (degrees) for intra-subject registration # Default: 3 for infants, 90 otherwise # set intrarot = 90 # Inter-subject registration method # 1: Affine T1-to-T1 with a correlation ratio cost # 2: Affine T1-to-T1 with a mutual information cost # 3: Affine T1-to-T1 with a robust cost (default for infants) # 4: Nonlinear T1-to-T1 with CVS # 5: Nonlinear FA-to-FA with SyN (default) # set interreg = 5 # Target brain for inter-subject registration # Default for affine T1-to-T1: # $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # Default for nonlinear T1-to-T1: # $FREESURFER_HOME/subjects/cvs_avg35/ # Default for nonlinear FA-to-FA: # $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz # # I think this fixed my issue with syntax # set intertrg = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/MGH35_HCP_FA_template.nii.gz # Whole-brain segmentation used to extract the anatomical neighborhood priors # of the pathways of interest # Must exist in each subject's FreeSurfer recon directory, under: # $SUBJECTS_DIR/$subjid/mri/$segname.mgz # Default: aparc+aseg # set segname = aparc+aseg # Use the thalamic nuclei segmentation? # This is highly recommended to use for any pathways that terminate in # or neighbor the thalamus # When used, it is merged with the whole-brain segmentation above # Must exist in each subject's FreeSurfer recon directory, under: # $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz # Default: 1 (yes) # set usethalnuc = 0 # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # #set thrbet = 0.5 # Paths to reconstruct # Default: All paths in $FREESURFER_HOME/trctrain/hcp/pathlist.txt # set pathlist = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/pathlist.txt # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist (recommended, with more points for longer paths) # Default: As in $FREESURFER_HOME/trctrain/hcp/pathlist.txt # set ncpts = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/pathlist.txt # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # set trainfile = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/trainlist.txt # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 200 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 7500 # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # set reinit = 0 Jake R. Powell, MS, LAT, ATC Doctoral Student - Human Movement Science Matthew Gfeller Sport-Related Traumatic Brain Injury Research Center 2207 Stallings Evans Sports Medicine Center The University of North Carolina at Chapel Hill P 919-962-0409 E jrpowell(a)unc.edu<mailto:jrpowell@unc.edu>

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mri_cor2label --surf "dim mismatch between surface"
by Zeng, Qi 29 Jan '22

29 Jan '22

External Email - Use Caution Hi, I saw the same question has been asked and no answer was provided: I run ---- "mri_cor2label --c fsaverage/mri/aseg.mgz --id 4 --l fsaverage/label/Left-Lateral-Ventricle.label --surf fsaverage lh" ----- to hopefully extract lateral ventricles volume into a overlay of surface base. however, gave me error: "dim mismatch between surface (100515) and input (16777216)". What should I change? BTW, Also have questions for the following steps and hope you can answer that too: 1. convert surface-based label to volume, "mri_label2vol --label fsaverage/label/Left-Lateral-Ventricle.label --subject fsaverage --hemi lh --identify --temp fsaverage/mri/T1.mgz --o fsaverage/mri/lh.Left-Lateral-Ventricle.nii --proj frac 0 1 0.01 2. Better ROI with mri_binarize "mri_binarize" --dilate 1 -erode 1 --i fsaverage/mri/h.Left-Lateral-Ventricle.nii --o fsaverage/mri/h.Left-Lateral-Ventricle.nii --min 1 3. constrain the thick ROI "mris_calc -o fsaverage/mri/h.Left-Lateral-Ventricle.nii fsaverage/mri/h.Left-Lateral-Ventricle.nii mul fsaverage/mri/h.Left-Lateral-Ventricle.ribbon.mgz 4. Questions: Are the aforementioned steps correct? In the end, if I have a couple of ROIs, what should I use to combine them. or just load them separately with lh.white and lh.pial. Best, Qi

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Password ubuntu
by Dan Emanuel Antonesa 29 Jan '22

29 Jan '22

External Email - Use Caution Hello, I'm trying to setup freesurfer in VirtualBox and it asked me to email you for the password. Best Regards, -- *Dr. Dănuț Emanuel Antonesă* Medic rezident Radiologie-Imagistică Medicală emanuelantonesa(a)gmail.com

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Transform a surface (e.g., lh.white) with a register.dat (12 dof)
by Yixin Ma 28 Jan '22

28 Jan '22

External Email - Use Caution Hi FreeSurfer developer, I want to transform surfaces files (lh.white, lh.pial, rh.white, and rh.pial) with a registration matrix that has 12 degrees of freedom. Is there a function in FreeSurfer that can do so? Very best, Yixin Ma

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Freesurfer Ubuntu VM documentation updated
by fsbuild 28 Jan '22

28 Jan '22

External Email - Use Caution The Freesurfer Ubuntu VM documentation has been updated to describe how to mount an external drive plugged into the Windows machine in the VM.  See towards the bottom of the page under "Share a directory ...", https://secure-web.cisco.com/12kQxE07BvTEpf6PBZdobfuBYlzrxz4JsMUZ649qdrKnj4… - R.

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display specific ROIs in surface brain
by Zeng, Qi 28 Jan '22

28 Jan '22

External Email - Use Caution Hi, I followed mri_annotation2label and mris_label2annot to create my ROIs annotation for lh.white view. No errors were made, however, 2 problems occurs (attached the freeview output): 1) the nearby regions (middletemporal & superiortemporal) are of similar color (orange vs. red), can I change the color using commands so that I can separate the nearby area more. 2) I also incorporate the entorhinal into the annotation, however, it doesn't show in 2D. However, when I also load orig.mgz, I can see it from a 3d in green (also attached). So it is possible that I make it visible in 2D for all my ROIs or an alternative for loading orig.mgz? 3) I went through some papers and graphs, their surface display for ROIs seems to be more soft on edges thanmine. I am sure it is not lh.white, lh.inflated or lh.pial. what do you think they load (attached lh.white_alternative1, 2,3) Thank you so much! Best, Qi

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I cannot edit white matter mask
by Rosalia Dacosta Aguayo 28 Jan '22

28 Jan '22

External Email - Use Caution Dear Freesurfer team, I am quality-checking the segmentation work from FreeSurfer version 7.1 and I have a subject whose white matter mask I cannot edit. I wonder why is this happening? The white matter mask has a lot of holes and the brush does not work over them. I know the brush is working because I have been editing other white matter masks but this subject is different. Any help would be appreciated My best regards, Rosie

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Re: [Freesurfer] Using SPM segmentations in FreeSurfer
by falk.luesebrink＠med.ovgu.de 28 Jan '22

28 Jan '22

External Email - Use Caution Oh, sorry... Following the steps from the previous mail you should run this command: mri_mask brain.mgz new_segmentation.mgz wm.seg.mgz Best, Falk ________________________________ Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von falk.luesebrink(a)med.ovgu.de <falk.luesebrink(a)med.ovgu.de> Gesendet: Montag, 24. Januar 2022 08:41:15 An: Freesurfer support list Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer External Email - Use Caution Hi Nathan, well, once again, I can't be much of help with regards to your error message. Have you had a look at the data and does it looks reasonable up to that point? Which FreeSurfer version are you running? FreeSurfer needs to have the data in a very specific form. In case of the white matter segmentation the resulting volume should have a value of 110 where white matter is located. The SPM segmentation has values of 0 to 1. Therefore, if you would simply try to use that, it wouldn't work. The given command should do that while using the SPM segmentation to mask the brain.mgz. Afterwards, the ventricles and subcortical structures will be filled based on the aseg.presurf.mgz and set to values of 250. The other commands changes the WM segmentation so that the neighbors of all voxels labeled as WM have a face in common - no edges or corners allowed. Best, Falk <http://secure-web.cisco.com/1mIUaa7F-i8b4cYwNnbztpMSGC1LS0vhF8ATfmhtgiZxT6l…> ________________________________ Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von Nathan Kindred (PGR) <N.Kindred1(a)newcastle.ac.uk> Gesendet: Freitag, 21. Januar 2022 18:18:14 An: Freesurfer support list Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer External Email - Use Caution Hi Falk, Thank you, I appreciate your help. By using the convert and mask steps you used I can get through to the -pial stage of autorecon3 before hitting an error (command terminated by signal 11). I was wondering about the mri_edit_wm_with_aseg and mri_pretess steps you take though as won’t these essentially overwrite the wm.mgz file so that the SPM segmentation is no longer incorporated? Apologies if I am miss understanding, that is just what appears to happen when I try to replicate those steps (with those included I hit no errors but the outputs are unchanged from before I incorporated the SPM file). Best, Nathan From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of falk.luesebrink(a)med.ovgu.de <falk.luesebrink(a)med.ovgu.de> Date: Thursday, 20 January 2022 at 07:57 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using SPM segmentations in FreeSurfer External Email - Use Caution Hi Nathan, well, I never encountered that error. Therefore, I probably can't be of much help. Anyways, if you provide more details, e.g. which FreeSurfer version you are using, the recon-all.log, and what commands you are running exactly to incorporate the SPM segmentation someone else probably can help. When I was using different WM segmentations in v6, I did the following: * Convert the segmentation (e.g. mri_convert -rl wm.mgz new_segmentation.nii new_segmentation.mgz) * Mask brain.mgz using the segmentation (e.g. mri_mask brain.mgz new_segmentation.mgz wm.mgz) * Then continuing with the remaining steps of the segmentation stage accoring to the recon-all table (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1RWkD9q9eCja6mIMMwKBpTWWFQ5PbuMZrYDBZdgbIW7Yok…<https://secure-web.cisco.com/1reDdF1_RCvW1SGMg5MMY-wNwDhAcqYlMuRhT7puZZazh6… -eiEfuVnxEsFGJ_BDbWV5Vvhp8DXYvq0pbAMZpoReB6ERBzfAEp6u_T9joWGQX5b3F0vTAEGUh6bY3vcO8F70NmZCAhvzqxSzA6oJmHKlXuqoe4p1MDlDt20A8EyV3oESStmEgvCMc8O2DPvuiRBqjOM9d5JZSZ2ZakNr6H_llRM8aJh8XDUJmv1aFfE3T0a2UMJ2bz43xy_jEZSLjJo8a6MwlIgeVGD0UsPQhYLCsK4ff9qaZ6Q%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252FReconAllTableStableV6.0%26amp%3Bdata%3D04%257C01%257CN.Kindred1%2540newcastle.ac.uk%257C162fbeaa1c654f80909008d9dbea65b5%257C9c5012c9b61644c2a91766814fbe3e87%257C1%257C0%257C637782622499068823%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C2000%26amp%3Bsdata%3DdzLH8xPfzoOZHO5Gmlew9NBRmGfH3nDb6AfWcqoKS70%253D%26amp%3Breserved%3D0>) by running * mri_edit_wm_with_aseg wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz * mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz * Then continuing with the remaining stages of autorecon2 of recon-all by running * recon-all -s <your_ID> -fill -tessellate -smooth1 -inflate1 -qsphere -fix -white -smooth2 -inflate2 -curvHK -curvstats -autorecon3 This will work for FreeSurfer v6. For v7 the stages of recon-all have changed and you might miss something. However, there is no such table like for v6 and I haven't been using v7 much, so I can't provide a guide like above for v7. Best, Falk ________________________________ Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von Nathan Kindred (PGR) <N.Kindred1(a)newcastle.ac.uk> Gesendet: Mittwoch, 19. Januar 2022 14:00:23 An: Freesurfer support list Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer External Email - Use Caution Hi Falk, Thank you for the response! I have given your suggestion a try and I am still getting the following error: free(): double free detected in tcache 2 Command terminated by signal 6 Best, Nathan From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of falk.luesebrink(a)med.ovgu.de <falk.luesebrink(a)med.ovgu.de> Date: Wednesday, 19 January 2022 at 12:52 To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using SPM segmentations in FreeSurfer ⚠ External sender. Take care when opening links or attachments. Do not provide your login details. External Email - Use Caution Hi Nathan, are you sure that the SPM segmentation and the wm.mgz share the same space? You could try e.g. mri_convert -rl wm.mgz your_spm_segmentation.nii spm_wm.mgz Best, Falk ________________________________ Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von Nathan Kindred (PGR) <N.Kindred1(a)newcastle.ac.uk> Gesendet: Mittwoch, 19. Januar 2022 13:29:46 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: [Freesurfer] Using SPM segmentations in FreeSurfer External Email - Use Caution Hi, I have been trying to incorporate segmentation files from SPM into FreeSurfer to improve the surfaces, but I am not sure if I am going about it in the right way. I have been replacing the wm.mgz file with a file from SPM and then running ‘recon-all -s ${subject} -autorecon2-wm -autorecon3’, but I keep getting errors. I have tried using both conform and conform_min as part of mri_convert when replacing the wm.mgz file with an SPM file but in both cases I still get errors. Are there other steps I should be taking or a different line of code I should run to get this to work? Thanks, Nathan _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1_Qii5dzGydqhjVxT6Jr6Mmj7pjHELmS6AHzEcuhsGBwkb… erved%3D0<https://secure-web.cisco.com/1hIRlFHzyIerqJlNin-8Em5XvbgE6tJBPxotWajmp70ATH…><https://secure-web.cisco.com/1MrKneav6PXmfdQRDU4Jvcls21C4f6JTZZ-Tgq3S19B7h4… J-kty-qy8-UnuhgFpz3PkBTwk9vT-i6joFgVschSr8Ab11NwMErEwvVXgzPvc1sWucTKIIRZWMlIgfWdU-z5p6N1SB0PYqh5rGgT0O0EPzMN1M/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1sf6L0NHJmhkr10Cj74JcEIEEcoND2pR2q0X9Pm9lMkMR5LyldwoXLMPs1mD3hBeEqQ3hcHfXesZFKgFzz5Enia-82_2rxoJMrsi6NeZxJSOsfbVnI2wxtB8IHFALA6nKvi4tL98vRHEEghhEJJA4_DdcLEvH9Ix_Zfv0czIF9TJualfnQ0kgRhpdtO26eeI3mStgLO35_hhmO5AV9U_2vIt9P1jSaByTKh1d85ojjCtv-Y_9Fx9werVTVjKwm0zT_8IT22pB8-HoYVRVbhbiNYCziFpw8NLXBOlEvoN8U2hBp_g2oo1gl9TvoJH1oWKzJFtYOga9PdRes7w9xdMWlA%252Fhttps%25253A%25252F%25252Feur03.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fmail.nmr.mgh.harvard.edu%2525252Fmailman%2525252Flistinfo%2525252Ffreesurfer%252526data%25253D04%2525257C01%2525257Cn.kindred1%25252540newcastle.ac.uk%2525257Cf53b338b194a4f634fa408d9db4a8342%2525257C9c5012c9b61644c2a91766814fbe3e87%2525257C1%2525257C0%2525257C637781935340044379%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C2000%252526sdata%25253DQoKAAdwJTjthPD0gPZPmt0owIasgazNfdz6hI9CYRK0%2525253D%252526reserved%25253D0%26amp%3Bdata%3D04%257C01%257CN.Kindred1%2540newcastle.ac.uk%257C162fbeaa1c654f80909008d9dbea65b5%257C9c5012c9b61644c2a91766814fbe3e87%257C1%257C0%257C637782622499068823%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C2000%26amp%3Bsdata%3D3nZeE%252BmlGSmo2G6dIta5y6i3qezq24YVrPYxf%252Fo%252Bb3Y%253D%26amp%3Breserved%3D0%253chttps%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1qP4Jy-ZkJCg8fJaNq7BoJiZKPJyBcdrMGJqMXQVE40fMwCpTZchKdAfKRVcRq8abnakPJRCfynb4Qri0idb3vh95cJmWtCLdOaspS484l-NlX4clzX8ZbkoCrYwZhwzxVeZp74-Pau1NThLJvWlewUzgIt8VZE2qSzLCYhPLR6yqNjsD0CH6HM5bCAJXkJvxnGW-upt16I_PCoGOzOtm_zx1emJ233uUV06chy6Ap6_PUJGuunpx6XrNxtmtq5PbkC5GOcayi8KgumqIjzTf0_f57ixOdCg9T1-_kgqh3EjJJj1E0Z6ObiYxXDFP7lQ1ACn_c5IvcMvbxl7glZI1ig%252Fhttps%25253A%25252F%25252Feur0 3.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fmail.nmr.mgh.harvard.edu%2525252Fmailman%2525252Flistinfo%2525252Ffreesurfer%252526amp%25253Bdata%25253D04%2525257C01%2525257Cn.kindred1%25252540newcastle.ac.uk%2525257Cf53b338b194a4f634fa408d9db4a8342%2525257C9c5012c9b61644c2a91766814fbe3e87%2525257C1%2525257C> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1RuGPocKtZY2K8YbNQJLTPEapQBTi6urGjhTEePQsR1xi6…<https://secure-web.cisco.com/1Q8HjxX0L-3jb5TnPYDh3lmWfdEplgputrVSdkPnRTlyzD…> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1lUdqOMMUWeBV8aIT0Asi1eOemYmgN6_-kmM9SlRsfjP6r…

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Re: [Freesurfer] Reading files from a hard drive (on Windows in the Fressurfer Ubuntu VM)
by krystaly 27 Jan '22

27 Jan '22

External Email - Use Caution I’m not sure if this is the correct way (please see the attached) to solve my problem. Please kindly advise. Thank you for your attention. Best regards, Krystal From: fsbuild<mailto:fsbuild@contbay.com> Sent: Tuesday, January 25, 2022 9:57 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: ts+ml(a)rcmd.org<mailto:ts+ml@rcmd.org> Subject: Re: [Freesurfer] Reading files from a hard drive (on Windows in the Fressurfer Ubuntu VM)

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Re: [Freesurfer] Reading files from a hard drive (on Windows in the Fressurfer Ubuntu VM)
by fsbuild 27 Jan '22

27 Jan '22

External Email - Use Caution You can try mounting a directory different drive and directory instead of  of C:\shared, e.g., your external drive might show up under letter T: and maybe you want to mount a directory there like T:\files    I would try navigating to the external drive in the VirtualBox popup menu.  If the external drive is not listed in Windows Explorer then I don’t think VirtualBox will see it. - R. On Jan 24, 2022, at 20:40, krystaly <krystaly(a)hku.hk> wrote:        External Email - Use Caution        Dear R., Thank you for your advice! As my files are huge, my C drive has no enough space to save them. I was wondering if there is any way to read directly from the hard drive. Thanks. Best regards,Krystal From: fsbuildSent: Monday, January 24, 2022 6:50 PMTo: freesurfer@nmr.mgh.harvard.eduCc: krystaly; ts+ml@rcmd.orgSubject: Re: [Freesurfer] Reading files from a hard drive (on Windows in the Fressurfer Ubuntu VM) You can setup a shared folder in Windows to contain files the VM can see.  if your external hard drive shows up in Windows Explorer, then you can copy files from there into the shared folder.This posting shows an example,MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1l7wS4dpanB7trP1Eh5eKdfPXUVC0FuLjPJef… this example you,- create a shared folder on your C drive using Explorer, i.e., C:\shared- with the VM running, go to the pull down menu for “Devices” in the VirtualBox application and select “shared folder”- click on shared folders- click on the folder icon with a + sign- in the popup menu click on the arrow next to the field for “Folder Path” a navigate to the shared folder on Windows to set the path, i.e., C:\shared- click OK (don’t fill in anything else) to get out of the popup menu- click OK to get out of the shared folders menu… back in the VM in your terminal window do …$ cd$ mkdir guest_shared$ mount -t vboxsf shared ~/guest_shared…an icon for the mounted folder named guest_shared should appear on the Ubuntu desktop … double click on it and/or use the terminal to go there ...$ cd guest_sharedThen it should work to copy files into C:\shared on the Windows side and see them in the Ubuntu VM.- R.On Jan 24, 2022, at 04:19, Tim Schäfer <ts+ml(a)rcmd.org> wrote:       External Email - Use Caution        Dear Krystal,FreeSurfer does not know about hard disks, the operating system is responsible for that. In this case the problem most likely is with the Virtual Machine (VM), which needs to get access to the hard disk. You should be able to make a folder on your host system (the physical machine) available to the VM system somehow in the VM software. It should not matter which harddisk that folder is on. This is sometimes called 'mounting' the folder. Once you can see the folder inside the VM, FreeSurfer will also be able to see it. Good luck!TimOn 01/24/2022 1:50 AM krystaly <krystaly(a)hku.hk> wrote:External Email - Use Caution        Hi FreeSurfer experts,I’m trying to open nifty/ DICOM files, which are stored in a hard drive (SEAGATE - Backup Plus Hub; Model: SRD0PV1). However, the files cannot be found in any of the folders on Freesurfer 7.1.0 of which operates on Visual Machine on Window 10.May I know whether I should: 1.  Import those folders to Freesurfer for viewing at Freeview; or 2.  Set anything for opening the files directly from the hard drive?Please kindly advise. Thanks a lot.Best regards,Krystal_______________________________________________Freesurfer mailing listFreesurfer@nmr..mgh.harvard.eduhttps://secure-web.cisco.com/1JG2wguzlymmvbwtzbW0WPy_QcmP7r_KfWhZrRkmOo_9ZelrtECWjbzOVlbro1PvNx1SYxdQ4FGzgF_W-dtI4C1hLXMvEjAy-W3B2RkK-OKt9OwkXa8PQVTTwFI8TLimbJIM7CxxCi6SdfvcPsZDUR1cDemEKirf_qlHbI6XRTzzyRi6ighdVFD1piAnTrgTnP2ywRwPF4ib0UQU0nAuBu4dBsykhlRBOFs3JeCYwPUJqwcTTVNDmjToJ2duYB5DraoFLZSv7J7NhYboH9JC4HUxl7Fh6sejZ0z76ijfG5aThBuRzsFcS7JCEw7SjlavxKsD1zEPX0vfpbqtPw3gCjQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, Germany_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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