Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

Re: [Freesurfer] VirtualBox pass code
by fsbuild 28 Apr '22

28 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 27, 2022, at 21:54, JESS WOOLF <jwoolf(a)deakin.edu.au> wrote:       External Email - Use Caution        Hello,Will you please send me the pass code for the Virtual Box  ova.7z file?Thank you,Jess_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] help - unzip Ubuntu ova password
by fsbuild 28 Apr '22

28 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 27, 2022, at 15:31, Dan Lerner <dan(a)findsurgicalsciences.com> wrote:        External Email - Use Caution        Hi,Setting up the Ubuntu vm provided by FreeSurfer. I'm emailing for the password as per the instructions.Thanks,Dan_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Request for 7Zip Archive passcode
by fsbuild 28 Apr '22

28 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 26, 2022, at 14:01, Logan Tate <lwtate21(a)gmail.com> wrote:        External Email - Use Caution        Hi, I made a prior request but believe the passcode was sent to someone who posted under my request, and not myself. I just need a passcode to archive the zip folder for file FS_7_2_0_Ubuntu_18_04_06.ova.7zSorry for the spam! Thank you._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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VirtualBox pass code
by JESS WOOLF 27 Apr '22

27 Apr '22

External Email - Use Caution Hello, Will you please send me the pass code for the Virtual Box ova.7z file? Thank you, Jess

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Re: [Freesurfer] recon-all error
by Huang, Yujing 27 Apr '22

27 Apr '22

Hi Rebecca, I’m trying to get more information to determine how it core dumped. 1. Can you confirm that you are running Freesurfer 6.0? 2. From which directory, did you run recon-all and dcmunpack? 3. Can you try dcmunpack by passing it full path to dicom directory? Thanks. Yujing -------- Forwarded Message -------- Subject: [Freesurfer] recon-all error Date: Sun, 10 Apr 2022 07:01:30 +1000 From: cooperr1(a)student.unimelb.edu.au<mailto:cooperr1@student.unimelb.edu.au> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> External Email - Use Caution Dear FreeSurfer developers, I’m attempting to run recon-all on a set of T1-weighted images acquired in the 1980s-1990s and am having trouble with the recon-all pipeline. I have used the original dicom files in the recon-all using the command below. Command: recon-all -s 1003156_dicom -i 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256/002/I.001 -all Error message: /Applications/freesurfer_v6/bin/mri_convert: line 3: 8196 Segmentation fault: 11 mri_convert.bin "$@" The recon-all.log is also attached. I’ve also explored using dcmunpack and obtain the following result: Command: dcmunpack -src 2008-11-13_GE_001910/13.39_-_PACE/Ax_3D_512x256 Message: cat: /tmp/dcmdir-all.89439: No such file or directory Found 0 unique series: Patient: Undefined variable. Do you have any idea what might be the problem? Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: Mac OS X 10.13.3 Recon-all.log: attached. With warm regards, Rebecca Cooper

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Does PETSurfer calculate ROI-wise values by averaging?
by Zhener Zhang 27 Apr '22

27 Apr '22

External Email - Use Caution Hello, I have a question regarding the way ROI-wise values are calculated using PETSurfer. We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively small ROI like Putamen has one of the highest values of regional distribution of a PET tracer. Is it the case that the PETSurfer ROI-wise value outputs were averaged, or normalized by each ROI’s volume? And what measure was divided, GM volume, number of voxels, or something else? Thank you in advance! Best regards, Zhener

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Paracingulate
by Roxanna Korologou-Linden 27 Apr '22

27 Apr '22

External Email - Use Caution Hi, I have been reading papers referring to the paracingulate cortex. What does this correspond to in the Desikan-Killiany atlas used in FreeSurfer? I am trying to compare my results to previous studies. I would appreciate your insight. Thanks, Roxanna

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help - unzip Ubuntu ova password
by Dan Lerner 27 Apr '22

27 Apr '22

External Email - Use Caution Hi, Setting up the Ubuntu vm provided by FreeSurfer. I'm emailing for the password as per the instructions. Thanks, Dan

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Resampling of surface-based bivariate data
by Burke Rosen 27 Apr '22

27 Apr '22

External Email - Use Caution Is there a way to resample a vertex-by-vertex matrix of data from one subject to another or to ico? For example, I have calculated the Euclidean distance matrix for all the vertices of lh.white for my subjects and wish to find the average distance matrix. Another example might be functional connectivity values. If the data were univariate (i.e. vectors not matrices), I could save my measure as a .w file for each subject and use mri_surf2surf to morph each vector to ico and then average across the resulting ico vectors. One idea is to use make_average_subject to morph each subject’s surface to ico and then calculate bivariate measures on these surfaces. This might be ok for the functional connectivity case. However, this morphing distorts the absolute size of the surface, so the Euclidean distance matrix would be untenably distorted. In other words, is there an extension of mri_surf2surf (or maybe mris_convert) that operates on v(i,j) measures rather than v(i) measures? Thank you, -Burke

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Re: [Freesurfer] pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by fsbuild 27 Apr '22

27 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R.On Apr 23, 2022, at 20:56, Peng, Shichun <speng(a)northwell.edu> wrote:        External Email - Use Caution        Could you please send me the pass code to unzip the file?Thanks,ShichunThe information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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