Freesurfer November 2022

freesurfer@nmr.mgh.harvard.edu

80 participants
119 discussions

T1w/T2w ratio maps: acquisition parameters T1w and T2w
by Steve Petersen 03 Nov '22

03 Nov '22

External Email - Use Caution Dear FreeSurfer experts, I would like to calculate myelin maps using the ratio between T1w and T2w scans. However, the acquisition parameters of the T2w images are slightly different (e.g.* voxel size T1w* = 1mm3* vs* *voxel size T2w* = 0.35 mm3 ;* T1w matrix:* 240 x 240 *vs* *T2w matrix:* 640 x 640). The first step of the protocol would involve a robust registration between the two MRI images (e.g. bbregister method) which would lead to a downsampling of the T2w images. My question is, could I conduct a reliable analysis of T1w/T2w ratio maps despite these differences in the acquisition parameters between both MRI sequences?. Thank you very much in advance. Best regards, Steve.

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Freeview on WSL in Windows 10
by Monica Crotti 03 Nov '22

03 Nov '22

External Email - Use Caution Dear Freesurfer developers, I am writing to you with regard to two issue I would like to address: 1. I subscribe to the email list but when I am trying to access the page https://secure-web.cisco.com/1qLrYVPbmja0VA1ig3yYFVqbYmPXWNvZMOj2UgG9-EL7bo… I got the following error [cid:6ec71e48-7fd8-453b-9462-5f6760179b73] 2. I installed Freesurfer on a WSL2 environment on my computer Windows 10. Neverthless, I am unable to run the freeview command. I looked into web for solutions related to the error I got which is the following freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory Following what I found on the web, I run the following commands $sudo add-apt-repository ppa:ubuntuhandbook1/ppasudo apt-get install qt4-dev-tools libqt4-dev libqtcore4 libqtgui4? and I get the following errors base) root@GBW-L-W3359:/usr/local/KUL_apps/freesurfer# cd bin/ (base) root@GBW-L-W3359:/usr/local/KUL_apps/freesurfer/bin# ldd 'freeview.bin' | grep not libvtkverdict.so.5.6 => not found libvtkGraphics.so.5.6 => not found libvtkmetaio.so.5.6 => not found libvtkpng.so.5.6 => not found libvtkzlib.so.5.6 => not found libvtksqlite.so.5.6 => not found libvtkImaging.so.5.6 => not found libvtkFiltering.so.5.6 => not found libvtkCommon.so.5.6 => not found libvtksys.so.5.6 => not found libvtkGenericFiltering.so.5.6 => not found libvtkexoIIc.so.5.6 => not found libvtkNetCDF.so.5.6 => not found libvtkVolumeRendering.so.5.6 => not found libvtkRendering.so.5.6 => not found libvtkftgl.so.5.6 => not found libvtkWidgets.so.5.6 => not found libvtkHybrid.so.5.6 => not found libvtkIO.so.5.6 => not found libvtkDICOMParser.so.5.6 => not found I was wondering if you could help me in solving this issue. Thank you in advance, Best regards Monica Monica Crotti, M.Sc. | PhD Student Locomotor and Neurological Disorders Group Department of Development and Regeneration KU Leuven, Belgium

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Password request for the FS_7_2_0_Ubuntu_18_04_06.ova VirtualBox image
by Siemerkus Jakob 03 Nov '22

03 Nov '22

External Email - Use Caution Dear FreeSurfer community, I just downloaded the Virtualbox S_7_2_0_Ubuntu_18_04_06.ova - image and would kindly like to ask if you could send me the password for unzipping the archive. Thank you very much in advance, J

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Re: [Freesurfer] Longitudinal FS pipeline consistently interrupts at -Sphere for all participants
by fsbuild 02 Nov '22

02 Nov '22

External Email - Use Caution One way we’ve seen recon-all eventually fail running on Linux hosted on Windows is whatever is virtualizing Linux to run on top of the Windows OS - simply runs out of memory at some point in the processing pipeline.  That can result in a message in the recon-all.log like a file was not found, i.e., a computation fails and the results are not saved in a file that later on is expected to be found, opened and read.  I don’t see messages like that in your log. It might be helpful to know more about how you are running Linux on windows, e.g., if you are using the built-in Windows Subsystem for Linux (WSL) or using a VM running on something like VirtualBox. You could also send along the output in the linux terminal from:$ cat /etc/os-release$ cat $FREESURFER_HOME/build-stamp.txt - R. On Nov 2, 2022, at 15:03, Julie Ottoy <julie.jj.ottoy(a)gmail.com> wrote:<recon-all.log>

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Longitudinal FS pipeline consistently interrupts at -Sphere for all participants
by Julie Ottoy 02 Nov '22

02 Nov '22

External Email - Use Caution Hello Freesurfer Developers We are looking to run the longitudinal pipeline as described by this tutorial (https://secure-web.cisco.com/1O8OKVmECT3n0PpssaY4YzbcyidYXVp_1CQ3Kv3XSoGyso… <https://secure-web.cisco.com/1XnIvBg4ECBcV2V6_v5B_1X0Tsq_7ShBYJRYFn7EdCPdr9…>. We are currently trying to run recon-all on a few participants, but each run seems to get stuck at the -Sphere step in part 3 x.long.x for each participant. I’ve looked through the mailing list and couldn’t find anyone with a similar issue. Would you have any ideas on how to fix this? I’ve attached the status.log and error reports as screenshots in this email, as well as our recon-all.log files as well. Our freesurfer version is freesurfer-linux-centos7_x86_64-7.2.0 and my platform is Windows 11 version 21H2 (I read that Freesurfer can be run, but is not officially supported on Windows so I’m not sure if my OS is the issue here). I've tried to run it on different Windows platforms to make sure it's not related to one in particular. But it still got stuck at that same step for each participant. I've tried both v7.2.0 and 7.1.1. Thank you in advance for your time.

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Freesurfer labels vertices and not faces?
by Daniel Schwartz 01 Nov '22

01 Nov '22

External Email - Use Caution Hi, I've more of a general question. It seems to me that, if I use mris_convert (to convert to ascii) to take a closer look at, for example, rh.pial.asc, and an annot2label, there are exactly enough rows to label each vertex of each triangle, but not enough label rows to color each face (defined by 3 vertex indices). I don't really understand how one can "color" a vertex. As an aside, when defining a patch in, say, MATLAB, one defines the color of each row in 'Faces'. Could someone help me understand what exactly is going on here? As one can imagine it's bizarrely and frustratingly difficult to search for this question/answer on Google or the Freesurfer listserv. Thanks! Daniel

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Re: [Freesurfer] help
by Sarah Lavelle 01 Nov '22

01 Nov '22

External Email - Use Caution Hi Bruce, Thank you for your response, I really appreciate it. I am trying to understand the *mris_flatten* code so I can *quantify distortions* from inflated surface to flatmap for *parcelated regions*. There is a value printed of "total metric distortion ..%". I'm wondering how this is calculated because I can't find it anywhere on github. I would like to get this distortion value for a region of interest. Do you have any advice on how this could be done? Also, has there been any work on *automating the cuts*? Thanks, Sarah Hi Sarah Sorry, I?m not sure we have much to add. We don?t flatten much any longer, and the cuts are kind of ad hoc ? the one around the medial wall to get rid of non-cortical stuff, then the radial ones from there to remove particularly the curvature from the 3 poles. Mostly we just follow what Anders and Marty started doing way back when Bruce On Tue, 25 Oct 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/1kKhwjU99c5iofRTZoE0kIx6UgoX3fbPqapKpqVjol5sRm… > 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. Re: Fail to install FreeSurfer 7 from the *.deb package (fsbuild) > 2. Re: FreeSurfer Mac crash (fsbuild) > 3. help (Sarah Lavelle) > 4. Re: help (Fischl, Bruce R.,PHD) > 5. MRI recon-all failed at talairach (Jonany, Vincent Joe) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 25 Oct 2022 06:14:54 +0200 > From: fsbuild <fsbuild(a)contbay.com> > Subject: Re: [Freesurfer] Fail to install FreeSurfer 7 from the *.deb > package > To: freesurfer(a)nmr.mgh.harvard.edu > Cc: liangqunjun(a)foxmail.com > Message-ID: <9e9ccbd9762dc3fe12a584cc5905b258(a)trashmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > This error in the log reports the file is likely corrupted and so could > not be unpacked and installed, > > > > dpkg-deb (subprocess): decompressing archive member: lzma error: > compressed data > >  is corrupt > > The md5 checksum of the file > downloaded to your machine needs to match the MD5 sum column > for the file as listed on the download page.  Check you see the > output listed below before trying to install the .pkg file (and re-download > if necessary). > > - R. > > > $ md5sum  freesurfer_ubuntu20-7.3.2_amd64.deb > b2d0f8e6285f4a8da72d008a6390a7fe  freesurfer_ubuntu20-7.3.2_amd64.deb > > > >

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Re: [Freesurfer] Issues Loading files from a Network Drive
by fsbuild 31 Oct '22

31 Oct '22

External Email - Use Caution Hello M, If you scroll down on this pagehttps://surfer.nmr.mgh.harvard.edu/fswiki/VM_67to the link for,Vbox_Windows_mount_external_drive - you will see an example of mounting an external SSD that has been formatted in the old exFAT file system.  I think that just works as is in the current VM w/o installing anything extra. If your NAS is formatted using Windows NTFS, then I think you will need to install some additional software in the VM in order to try mounting it.   I would first check about how your NAS is setup.   If it is NTFS formatted, you can try following this post to install the fuse software in the Linux VM and then try adding read only or read/write mount points to it inside the VM.   You might first try mounting things read only. https://secure-web.cisco.com/1sX6e0mzHWcMONw_UNzeH9a8TmqsfHaKzi8_FTDxExAK9I… - R. On Oct 31, 2022, at 19:40, Marielena Mendoza <marie.mendoza017(a)gmail.com> wrote:        External Email - Use Caution        Hello,I am having issues accessing files using "load volume."  The files I am trying to load are from a Network Attached Storage server. I can access the files fine through files explorer, but the entire directory does not appear when trying to select volume files. I installed Free Surfer on my Windows 11 laptop using Ubuntu 18. I also tried changing my directory for Subjects and received the following error WARNING: /mnt/network-drive/file path/... does not exist. Has anyone encountered this issue and have suggestions on how to fix this?Best,M_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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About recon-all -i option
by Ryosuke Hayashi 31 Oct '22

31 Oct '22

External Email - Use Caution Dear All, Hi. I have a question about the -i option for "recon-all". According to the explanation on the following page, the -i option specifies DICOM and NIfTI files, but is it OK to specify a mgz file with the -i option? https://secure-web.cisco.com/1UYHLpktzY4BG51M3Fy6Hmuwp2mf6dniSilXbYvOmS82Wj… I want to create a generic script file that calls NIfTI and mgz files as follows. recon-all -subject $SUBJECTS_ID -i $IMAGE_FILE -all Thank you, ryo

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Freesurfer November 2022