Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

"Smooth display" in FreeView using command line
by Arman Avesta 04 Nov '22

04 Nov '22

External Email - Use Caution Hi Gang, Happy Friday! I'm using this little command to overlay two volumes (brainbox.mgz and target.nii.gz) in FreeView: freeview -v brainbox.mgz:opacity=0.75 target.nii.gz:colormap=heat:opacity=0.5 I want to show target.nii.gz contours as "Smooth display", which is a checkbox in FreeView as shown here: Is there a property in the "freeview" command (like :colormap or :opacity) that can do it (instead of checking that box in FreeView every time)? I randomly tried :display=smooth, but it didn't work :D Thank you for your help, Arman

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Fw: TRACULA error- segmentation fault
by Shanika Jayakody 03 Nov '22

03 Nov '22

External Email - Use Caution Dear TRACULA team I got an error in pre processing that "Writing output files to /gs/gsfs0/users/helena_blumen_lab/TRACULA/30285/dlabel/syn/lh.cst_avg16_syn_bbr_* Writing spline volume to /gs/gsfs0/users/helena_blumen_lab/TRACULA/30285/dlabel/syn/lh.cst_avg16_syn_bbr_cpts_7.nii.gz Segmentation fault (core dumped) Linux cpu-769.cluster.local 4.18.0-305.19.1.el8_4.x86_64 #1 SMP Tue Sep 7 07:07:31 EDT 2021 x86_64 x86_64 x86_64 GNU/Linux" I checked Freesurfer mail and found it could happen when older version are used but I use 7.2 I have attached the configuration file. Thank you for any suggestions. This happened for another ID as well but for a different tract. I have been using similar configuration files and trac-prep finished without error for my other subjects Regards Oshadi

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Longitudinal stream bug ?
by Lauri Tuominen 03 Nov '22

03 Nov '22

External Email - Use Caution Hi FreeSurfer Developers, I am trying to run a longitudinal analysis on Ubuntu 20.04.1 LTS, freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551, and Python 3.8.5. I use the following command: long_mris_slopes --qdec ../tables/long.all.table.dat \ --meas thickness \ --hemi lh \ --sd $SUBJECTS_DIR \ --do-spc --do-label \ --generic-time \ --fwhm 15 \ --qcache fsaverage \ --stack-spc ../group/lh.generictime.thickness-spc.stack.mgh \ --isec-labels lh.generictime.fsaverage.cortex.label Error message I get is this: mris_calc -o ./tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh ./tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh add ./tmp-template_P08_lh_thickness_mfuld5s6/beta0.mgh Saving result to './tmp-template_P08_lh_thickness_mfuld5s6/betam.mgh' (type = MGH ) [ ok ] Traceback (most recent call last): File "/mnt/scratch/software/freesurfer//python/scripts/long_mris_slopes", line 1005, in <module> if fwhm > 0: TypeError: '>' not supported between instances of 'str' and 'int' I tried to search for this error but did not see anything. Would anyone have any thoughts on how to fix this? Thanks in advance Lauri Tuominen?

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Requesting Pass Code for FS_7_2_0_ubuntu_18_04_06.ova VirtualBox Image
by Preston Bowman 03 Nov '22

03 Nov '22

External Email - Use Caution Good morning, I would like to kindly request the pass code for the FS_7_2_0_ubuntu_18_04_06.ova VirtualBox Image. Thanks, Preston

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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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