Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Passcode request for Freesurfer virtual machine
by Gillian Grennan 28 Nov '22

28 Nov '22

External Email - Use Caution Hi, I am a graduate student at the University of Washington. I am trying to download the FS_7_2_0_Ubuntu_18_04_06.ova.7z but was prompted for a password. Could I get access to this password? Best, Gillian

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Pass code request for Freesurfer virtual machine
by Eduardo Europa 28 Nov '22

28 Nov '22

External Email - Use Caution Hello, I would like to follow up on my request to receive the pass code for the Freesurfer virtual machine: FS_7_2_0_Ubuntu_18_04_06.ova.7z Thank you, *Eduardo Europa, PhD, CCC-SLP (he/him)* Assistant Professor, Communicative Disorders & Sciences San José State University eduardo.europa(a)sjsu.edu

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Re: [Freesurfer] VM password
by fsbuild 28 Nov '22

28 Nov '22

External Email - Use Caution Hello Eyesha, The password was (re)sent to your email about ~30 minutes ago - please check your spam filters. The password is for the VM itself and not tied to the machine hosting the VM. - R. On Nov 28, 2022, at 20:04, Eyesha Younus <eyeshayounas(a)gmail.com> wrote:        External Email - Use Caution        Hello,I need a password to install the VM. Is this password tied to an email address or to a machine?The reason I ask this is because I need to install the VM on two computers; one personal and one work. Thanks_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Permission denied error
by fsbuild 28 Nov '22

28 Nov '22

External Email - Use Caution Hello Adam, I hope you saw the previous email I sent you about changing SUBJECTS_DIR to be different from the default.   Just wondering if you did that for SUBJECTS_DIR before running the recon-all. - R. On Nov 23, 2022, at 23:13, Adam Tartaglia <aetartaglia(a)gmail.com> wrote:        External Email - Use Caution        Hello,Immediately after running recon-all, I get an error that says cannot create directory, permission denied. I am not sure as to why this is happening. My license is in the correct location.Thank you for your time,- Adam_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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VM password
by Eyesha Younus 28 Nov '22

28 Nov '22

External Email - Use Caution Hello, I need a password to install the VM. Is this password tied to an email address or to a machine? The reason I ask this is because I need to install the VM on two computers; one personal and one work. Thanks

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New subscriber
by Eyesha Younas 28 Nov '22

28 Nov '22

External Email - Use Caution Sending my email to become able to post to the forum. Thanks Sent from my iPhone

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Calculating Distortion in mris_flatten()
by Sarah Lavelle 28 Nov '22

28 Nov '22

External Email - Use Caution Hi Bruce, Thank you very much for your response. I would like to calculate this distance error for specific regions on the flatmap after the transformation, so I can formulate cuts to minimize it for the region I am interested in. Do you have any suggestions on how I can do it? From reading your paper : *Fischl B, Sereno MI, Dale AM. Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. Neuroimage. 1999 Feb;9(2):195-207. doi: 10.1006/nimg.1998.0396. PMID: 9931269, *I understand that distances are calculated using the corrected *Dijkstra **algorithm* as an estimator of geodesic distances. In your response, you said that the distance error is calculated with: *100 * (mean(abs(distance error)) / mean(original_distances))* Are the *original_distances = the geodesic distances (gd) calculated (using the Dijkstra algorithm) for each vertex on the inflated surface*? Is the *distance error = (gd on the flatmap) - (gd on the inflated surface)?* Do you know how I can do this in matlab for just *one region using the DKTaltas*? for example, the superior frontal? Any help would be greatly appreciated! Kind regards, Sarah On Wed, 9 Nov 2022 at 17:02, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/139TUXRjgPFOTa0MZdiWthcoqzpoQBP-aVztjPSGSautEU… > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Calculating Distortion in mris_flatten() (Sarah Lavelle) > 2. Fwd: average lobar cortical thickness (James Brown) > 3. Re: Calculating Distortion in mris_flatten() > (Fischl, Bruce R.,PHD) > 4. Re: volumes/surfaces FS6.0 vs FS7.2/3.2 (Nolan, Jackson) > 5. Re: [External] Re: Mapping the labels onto the aparc atlas > (Zeng, Victor (BIDMC - Keshavan - Psychiatry)) > 6. Question about a skullstripping error (dimitra kokkinou) > 7. Re: Fwd: Longitudinal FS pipeline consistently interrupts at > -Sphere for all participants (Huang, Yujing) > 8. cortical thickness in frontal lobe (James Brown) > 9. Re: [External] Re: Mapping the labels onto the aparc atlas > (Huang, Yujing) > 10. Re: Option -contrasurfreg in FreeSurfer 7.X (Douglas N. Greve) > 11. Re: FreeSurfer Hippocampus Segmentation Question > (Douglas N. Greve) > 12. Re: Question about freesurfer default settings. (Douglas N. Greve) > 13. Re: Help: Vertex Properties (Douglas N. Greve) > 14. Re: acompcor in fsfast (Douglas N. Greve) > 15. Re: Fwd: average lobar cortical thickness (Douglas N. Greve) > 16. Re: Question about a skullstripping error (Douglas N. Greve) > 17. Re: cortical thickness in frontal lobe (Douglas N. Greve) > 18. Re: Fwd: average lobar cortical thickness > (Fernanda Hansen P. de Moraes) > 19. Cerebellum segmentation pipeline (AJ) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 8 Nov 2022 17:20:22 +0000 > From: Sarah Lavelle <lavells1(a)tcd.ie> > Subject: [Freesurfer] Calculating Distortion in mris_flatten() > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > < > CABRNrkfJFpcKP0jhBX4Fmv6OKr1KamrNr5Tap_5bM3H5v--eyQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi freesurfers, > > Does anyone know how to measure the distortion of your inflated surface -> > flatmap transformation (using mris_flatten)? > > When being run, the function outputs "final distance error ...%" in the > terminal. What exactly does this mean? and how is this calculated? > > I would like to research optimal cuts for flatmaps, depending on the region > of interest (ROI), so we can minimize the distortion of the ROI itself > on the 2D map. If anyone has any ideas on how this can be done or is > interested in working with me on this, please contact me via < > lavells1(a)tcd.ie> > > Kind regards, > Sarah >

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recon-all failing to generate wm surface
by Christopher Mcnorgan 28 Nov '22

28 Nov '22

External Email - Use Caution A student and I have independently been trying to reconstruct a dataset. We've tried it a couple different ways using either an additional FLAIR or a T2 image and always hit a point where the process halts because of a missing surface file: Loading lh.white surf error: No such file or directory error: MRISread(/home/cpmcnorg/VMP/FS_002/surf/lh.white): could not open file This has happened when running just the autorecon1 step or both autorecon1 and autorecon2. I'm using freesurfer 7.2.0 on a linux computer, and my student is running 7.3.2 on a Mac. In my most recent test, I ran recon-all -autorecon1 -autorecon2 -i <path to T1 file> -T2 <path to T2 file> -subjid <ID> and I have several surface files (e.g., ?h.orig and even ?h.white.preaparc) but not the ?h.white surface. I'm unclear what's causing the recon-all script to look for the wm surface before it's been created.

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TRACULA: domainname: Command not found.
by Ward Deferm 28 Nov '22

28 Nov '22

External Email - Use Caution DearFreesurfer developers, when trying to run trac-all -prep I am running into this error gbw-d-m0128:DIFFUSION r0755008$ trac-all -prep -c /Users/r0755008/Desktop/mri_data/TRACULA/TRACULA_CONFIGURATION_FILE.txt domainname: Command not found. Too many ('s. ERROR: Syntax error in configuration file /Users/r0755008/Desktop/mri_data/TRACULA/TRACULA_CONFIGURATION_FILE.txt I checked the file but there seem to be no errors in the ('s. This error has previously been encountered https://secure-web.cisco.com/1sKX4EXSdl-lzzKBfb369ful1KJMpWkExgYjXUfdMyAgEi… but there is no solution proposed for the facts that the domainname command is missing from my mac in the /usr/bin folder. What can i do to solve this error. In the attachments you can find the tracula config file if this would be helpful. Thank you for the help. Kind regards, Ward Deferm

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Editing the coregistration
by Asa Borzabadi Farahani 27 Nov '22

27 Nov '22

External Email - Use Caution Hi, I hope this email finds you well. I am doing slab imaging and when I run preproc-sess command to do the functional preprocessing, the results of co-registration are not optimal, hence I need to do manual editing and save a new transformation file. After that, should I run the preproc-sess with option -regfile again? if not, what is the solution. Regards, Asa Farahani

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