Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

PhD student opportunity: Caen, France
by briend 25 Mar '20

25 Mar '20

External Email - Use Caution PhD position at the University of Caen (in the Cyceron platform for the MRI part and in the INSERM 1075-COMETE, Caen, France) "Can orthostatic intolerance be predicted by an anatomical indicator?" All the information for the application are here: https://recrutement.cnes.fr/en/annonce/898759-94-can-orthostatic-intoleranc… To apply, we invite you to contact the PhD/research supervisor at COMETE herve.normand(a)unicaen.fr and fill, with him/her, the co-financing part of the online application form by April 15, 2020.

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Re: [Freesurfer] ERROR - build stamps do not match
by Hoopes, Andrew 25 Mar '20

25 Mar '20

Hi Laura, For any study, it is essential that you process all of your subjects on the same operating system. Even though the same FS version is used, there will be underlying system-level differences that may lead to small inconsistencies across your linux and mac results. Also, are your recons dying after printing “build stamps do not match”? That message should just be a warning and not force a recon-all exit unless REQUIRE_FS_MATCH is enabled (it’s not by default). Best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Danielian, Laura (NIH/NINDS) [E]" <danielil(a)ninds.nih.gov> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, March 24, 2020 at 10:05 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] ERROR - build stamps do not match External Email - Use Caution Hi, I have been processing datasets on my Linux on v6.0 but have recently been made to work from home where I only have access to a Mac. I’m getting the following error message when continuing the editing on datasets that were already started on my Linux: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c A few questions: Is it feasible to override this error message for subjects that I have already started processing since they are both using v6.0? I have about half of my data set already fully processed using a Linux – if I start processing the second half from scratch using my Mac, can I eventually combine the 2 parts of the dataset for comparison? If I use a mix of Freesurfer builds on different data sets, can I still process data sets from the same subject using the longitudinal stream? Thanks, Laura Danielian

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recon-all : command not found
by Koustav Chatterjee 25 Mar '20

25 Mar '20

External Email - Use Caution Dear Sir/Madam, Hope this mail finds you well, considering the present pandemic scenario across globe. I have installed FreeSurfer in my PC successfully and I have been following tutorials and freesurfer wiki to learn the basics of it. I have an image with .nii extension saved in usr/local/freesurfer/subjects directory in ubuntu. I wanted to use recon-all command for preprocessing the image.nii. root@ubuntu:/usr/local/freesurfer/subjects# recon-all -s kctest01 -i (the input file.nii) the result shows, recon-all: command not found It would be kind enough if you could please help me out. I am also sharing the screen shot of the terminal window I used for this programming, if it would e of any help. Thank you, Best regards, Koustav

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Error in segmentation of the hippocampal subfields: /tmp/MCR_3634872073/.mcrCache8.4 error
by Pascale Patenaude 24 Mar '20

24 Mar '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to produce an automated segmentation of the hippocampal substructures and the nuclei of the amygdala (see hippocampal module https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) When I try to run the segmentHA_T1.sh SUBJECT_ID [SUBJECTS_DIR] command with the dev version of freesurfer, I keep getting this error: [cid:ced2aa15-ebc9-4e8e-8555-471e7094cf73] I've tried setting the MCR_CACHE_ROOT env variable to somewhere under my user directory. Does anyone have any suggestions on how this can be fixed? Thank you in advance, Pascale

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Re: [Freesurfer] Freeview Error
by fsbuild 24 Mar '20

24 Mar '20

External Email - Use Caution Hello Gian, I suspect the freeview binary is not going to be able to run on Debian linux.  We don’t build or test on Debian linux, but freeview/freesurfer should be fine on CentOS 6, CentOS7 and Ubuntu 18 for linux and also on Mac OS. Maybe someone could help you look at the steps listed here, https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67  for running freeview in a virtual machine.  The instructions there are for setting up the virtual machine to run on Windows and the Mac - but those instructions should also basically work on (Debian) linux.  But you would need to have privileges to install VirtualBox, download some files and uncompress them, etc. - R. On Mar 24, 2020, at 14:20, Gian Marco Duma <gianmarco.duma(a)phd.unipd.it> wrote:        External Email - Use Caution        Dear Freesurfer developers, I'm trying to use freeview but I'm having a lot of problems. I'm not an expert in freesurfer neither in linux programming. I followed all the instructions from the installation page of freesurfer, unfortunately when I try to open freeview I have a simple message, that is 'Abort'.I have Debian operative system.I truly don't know what to do to open freeview. Do you have any suggestion?thanksGian Marco_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview Error
by Gian Marco Duma 24 Mar '20

24 Mar '20

External Email - Use Caution Dear Freesurfer developers, I'm trying to use freeview but I'm having a lot of problems. I'm not an expert in freesurfer neither in linux programming. I followed all the instructions from the installation page of freesurfer, unfortunately when I try to open freeview I have a simple message, that is 'Abort'. I have Debian operative system. I truly don't know what to do to open freeview. Do you have any suggestion? thanks Gian Marco

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ERROR - build stamps do not match
by Danielian, Laura (NIH/NINDS) [E] 24 Mar '20

24 Mar '20

External Email - Use Caution Hi, I have been processing datasets on my Linux on v6.0 but have recently been made to work from home where I only have access to a Mac. I’m getting the following error message when continuing the editing on datasets that were already started on my Linux: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c A few questions: Is it feasible to override this error message for subjects that I have already started processing since they are both using v6.0? I have about half of my data set already fully processed using a Linux – if I start processing the second half from scratch using my Mac, can I eventually combine the 2 parts of the dataset for comparison? If I use a mix of Freesurfer builds on different data sets, can I still process data sets from the same subject using the longitudinal stream? Thanks, Laura Danielian

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Segmentation Issues
by Harriet Cornwell 24 Mar '20

24 Mar '20

External Email - Use Caution Hello, We are using FreeSurfer v5.3. and are sometimes finding that a brain can seem okay when it is first run through the recon-all process and is edited, but then when it is re-run the segmentation seems to deteriorate hugely. I have screenshotted an example below. Are you able to advise us on why this might be happening and what we could do about this? One of the options I had thought about was to re-run the recon-all from scratch but it doesn’t seem very time efficient to do this for multiple brains. Any suggestions would be gratefully received! Thank you.

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SurfaceRAS and RAS coordinates are different on reconstructed surface of monkey
by wangzhiwei3233 23 Mar '20

23 Mar '20

External Email - Use Caution Hello FreeSurfer Developers, I am trying to reconstructing surface of monkey brain. I have got surface files, such as ?h.white, ?h.pial, ?h.area and so on. However, I found the surface light was abnormally dark(as shown in following picture), it seems like that the light source was inside the brain. And I found the RAS and SurfaceRAS coordiantes were different. I got the surface files as following steps: (1) I got the wm.mgz file manually; (2) I filled the wm.mgz and changed the values in left and right hemispheres to 255 and 127, respectively; (3) I generated ?h.orig via command "mri_tessellate filled.mgz 255 lh.orig -n" Then I found RAS and SurfaceRAS coordiantes in ?h.orig were different. Which steps did I made a mistake? The voxel size of raw image was 0.5*0.5*0.5 mm, was the image resolution the cause? Thank you very much! zhiwei here is the information of raw image: Volume information for T1.mgz type: MGH dimensions: 137 x 175 x 107 voxel sizes: 0.500000, 0.500000, 0.500000 type: FLOAT (3) fov: 87.500 dof: 0 xstart: -34.2, xend: 34.2 ystart: -43.8, yend: 43.8 zstart: -26.8, zend: 26.8 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -6.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 3.7500 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.5000 0.0000 0.0000 -33.7500 0.0000 0.5000 0.0000 -49.7500 0.0000 0.0000 0.5000 -23.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0.125 ras to voxel transform: 2.0000 0.0000 0.0000 67.5000 0.0000 2.0000 0.0000 99.5000 0.0000 0.0000 2.0000 46.0000 0.0000 0.0000 0.0000 1.0000

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R-version of read_annotation.m
by Athanasia Monika Mowinckel 23 Mar '20

23 Mar '20

External Email - Use Caution Hi. I’m closing in on a version of read_annotation.m that runs entirely in R. I know I am not the only one wanting something not needing Matlab, and my initial idea was to contribute this version (acknowledging Bruce in the documentation as the author of the original function of course), to the Freesurfer R package (https://github.com/muschellij2/freesurfer) I wanted to check in with you first on how and if this was ok, or if you have other suggestions to how this can be shared. All the best, Athanasia Monika Mowinckel Staff scientist Phone: +47 22845022 e-mail: a.m.mowinckel(a)psykologi.uio.no<mailto:a.m.mowinckel@psykologi.uio.no> Center for Lifespan Changes in Brain and Cognition (LCBC) Department of Psychology University of Oslo POB 1094 Blindern 0317 Oslo Norway [LCBC] <https://www.oslobrains.no/> [Lifebrain] <https://www.lifebrain.uio.no//>

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