Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

overlay_threshold is ignored when using custom overlay
by Maya Yablonski 26 Oct '22

26 Oct '22

External Email - Use Caution Hello, I'm trying to use a custom colormap for an overlay in Freeview and I can't get the threshold option to work. Specifically, I want to display positive values with specific colors, and negative values with different colors, similarly to using the threshold with the default Heat colorscale ('Hot' for positive and 'cold' for negative, values outside the threshold do not appear at all). This is the code I've been using, and it seems to ignore the values provided by overlay_threshold: freeview -f <MYPATH>/sub-01/surf/lh.inflated:overlay=<MYPATH>tmap.curv:overlay_custom=-3,45,0,130,-9,220,210,250,3,255,70,0,9,255,255,0:overlay_threshold=3,9:overlay_color='clearlower','clearhigher' -colorscale This uses the right colors, but creates a continuous colorscale that spans -9 to 9, including the range [-3 3] which I want to threshold out of the map. I tried toggling the overlay_color='clearlower' and 'clearhigher', but couldn't find a combination that thresholded the low values around zero and not the extreme values (<-9 and >9). I also tested different values and seems like overlay_threshold is being completely ignored when overlay_custom is used. I couldn't get the right settings even when using the Freeview GUI. I tested this on Freesurfer versions 7.1.1 and 7.3.2 on MacOS Catalina (10.15.7). I'd appreciate any leads on this! Thanks, Maya

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Re: [Freesurfer] MRI recon-all failed at talairach
by fsbuild 26 Oct '22

26 Oct '22

External Email - Use Caution It looks like your terminal/character settings are messed up in the current terminal session.  That can happen from trying to look at a raw binary or image file in the terminal window or running something that outputs non-standard characters to the terminal (stdout).  I would open a new terminal window, source the freesurfer setup script, and try to identify if something you run corrupts the display of text in the new terminal window. - R. On 10/26/22 10:21, Douglas N. Greve (dgreve(a)mgh.harvard.edu) wrote: What is the error? The funny characters? Can you just send the entire logs (recon-all and avi.log)? On 10/25/2022 11:49 AM, Jonany, Vincent Joe wrote:         External Email - Use Caution         Dear FreeSurfer Developers, I am encountering a weird error in performing recon-all in my dicom directory. I believe the problem is here (snippet copied from talairach_avi.log. I have also attached here the recon-all.log, as well as the talaraich_avi.log. Does anyone know or have seen this problem before? I will appreciate any kind of help, please let me know if I need to provide anything else. FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: MacOS Monterey (apple silicon) $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ /Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 t4_read: talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4pupuÀþN èEÑ�àÔ�àÔ7SÎ0°þN #Öô>ÖxþN °þN �þN SÎðþN þN Ñ@ àþN � Ñ read error t4_read: transform initialized to I4 rotation matrix determinant 1.000000 Thank you in advance! I appreciate any help! Best, Vincent

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MRI recon-all failed at talairach
by Jonany, Vincent Joe 26 Oct '22

26 Oct '22

External Email - Use Caution Dear FreeSurfer Developers, I am encountering a weird error in performing recon-all in my dicom directory. I believe the problem is here (snippet copied from talairach_avi.log. I have also attached here the recon-all.log, as well as the talaraich_avi.log. Does anyone know or have seen this problem before? I will appreciate any kind of help, please let me know if I need to provide anything else. FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: MacOS Monterey (apple silicon) $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ /Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 t4_read: talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4pupuÀþN èEÑ�àÔ�àÔ7SÎ0°þN #Öô>ÖxþN °þN �þN SÎðþN þN Ñ@ àþN � Ñ read error t4_read: transform initialized to I4 rotation matrix determinant 1.000000 Thank you in advance! I appreciate any help! Best, Vincent

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dt_recon eddy correction fail and freeview errors
by Ward Deferm 26 Oct '22

26 Oct '22

External Email - Use Caution Dear Freesurfer Developers, I am trying to perform the dt_recon command for a single participant of my dataset. The original data comes from a philips scanner and was in the PAR/REC format. I converted these files to nifti’s using dcm2niix. This seemed to have worked as I got my nifti files and .bval and .bvec. However, when I run the dt_recon command it does not give me a hard error, but the output is not how it should be. Instead of taking 1-2 hours to complete the command, the command is done in about 3 minutes and I’m doubting if the eddy corrections are actually performed (fsl seems to be installed properly and is recognized when sourcing freesurfer. When trying to view the output with freeview I get 2 outcomes. Sometimes all of the file's work but there is no eddy correction performed and the FA volume is spread all over the brain when looking at this volume using freeview. But other times certain volumes either refuse to load or come up as a blank rectangle. In the freeview command line I then get the error: WARNING: 37103 NaNs found in volume /home/ward/freesurfer/subjects/testdtrecon/dti/ra.nii.gz In the attached files you can find the dt_recon log file. As for version and operating system I am running: 1) freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 2)Ubuntu 22.04.1 LTS Kind regards, Ward Deferm

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PostDoc (or qualified PhD) in Cognitive Computational Modeling (fMRI) in Copenhagen
by David Meder 26 Oct '22

26 Oct '22

External Email - Use Caution We are hiring a PostDoc (or qualified PhD student) on cognitive computational neuroimaging. This position is for you if you are interested in how the dopamine system works and like computational modeling. You would be part of a small and dynamic research project on the reward and motor systems in Parkinson’s Disease, embedded in the Movement Disorders research group at the Danish Research Centre for Magnetic Resonance. And all of that in the most liveable city in the world. For any inquiries or questions, write to davidm(a)drcmr.dk <mailto:davidm@drcmr.dk>. Follow this link for all details and for the application: https://secure-web.cisco.com/1P2UVw0p3pRPifdvgHBVRQ_b0Gh8fhcwt4AnFZTaVc0kpC… <https://secure-web.cisco.com/1P2UVw0p3pRPifdvgHBVRQ_b0Gh8fhcwt4AnFZTaVc0kpC…> Deadline is Nov. 13th David Meder Research Fellow Danish Research Centre for Magnetic Resonance DRCMR, Section 714 Copenhagen University Hospital Amager and Hvidovre Kettegaard Alle 30, 2650 Hvidovre, Denmark http://secure-web.cisco.com/15MpSS7cf-43ZjZWVO4wi088tGjgBnwHuBnw3d2e1b5falw…

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LGI and further errors
by FMU 26 Oct '22

26 Oct '22

External Email - Use Caution Hi everyone, I’m running a brain surface ROI analysis using data from the HCP. I need to draw those ROIs to be in annot files format so I can use them for further analysis to calculate sulcal depth (https://secure-web.cisco.com/1BjH9by7q1Ifs37LZrnji4YAMniNy1LLAc_r-1HVnNxAiv… <https://secure-web.cisco.com/1BjH9by7q1Ifs37LZrnji4YAMniNy1LLAc_r-1HVnNxAiv…>). I draw all my sample (n=40), and to proceed to the next step, I need to measure the LGI in each subject. In some samples, I faced a similar error to the one mentioned in this thread: https://secure-web.cisco.com/13Nu69ZC35kQC9epIBWd44yarBEBej9ZnSy-C1Z9Zpg_sr… <https://secure-web.cisco.com/13Nu69ZC35kQC9epIBWd44yarBEBej9ZnSy-C1Z9Zpg_sr…> I tried to run the recon-all lgi again the error remained the same. I did as recommended to run the recon-all -s sub -hemi ?h -autorecon2 & 3 The new surfaces were there, and the recon-all lgi worked fine. However, my annot files were not OK with new surfaces, and I don’t know what is exactly the problem, but I will attach an image showing how the labels looked in the original HCP data brain surface and how they look after the recon-all -s sub -hemi ?h -autorecon2 & 3. I re-downloaded the original surfaces from the HCP database, and it returned to its normal display. I hope someone can help me to solve the problem, and I appreciate it. Mudathir

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Re: [Freesurfer] Fail to install FreeSurfer 7 from the *.deb package
by fsbuild 25 Oct '22

25 Oct '22

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] Thalamic segmentation error
by fsbuild 25 Oct '22

25 Oct '22

External Email - Use Caution You shouldn’t be getting errors about libcuda (which we do not support). If you have not already done so, please try the script we provide to install the Matlab runtime environment, $ cd $FREESURFER_HOME/bin$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr  R2014b - R. On Oct 19, 2022, at 16:41, Alan Francis <alandarkenergy(a)gmail.com> wrote:        External Email - Use Caution        Hi Eugenio -Thanks for your reply. We have a Linux Tech. He installed it for me. Should I reinstall the runtime ?Thanks,AlanOn Tue, Oct 18, 2022 at 2:59 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote:Dear Alan,How did you install the runtime? Did you follow the instructions in the wiki?Cheers,/EugenioJuan Eugenio IglesiasMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1CU2rXmtEeXSOj0JKFwB3VuWcd145hFeSGV-cS6… Oct 18, 2022, at 2:37 PM, Alan Francis <alandarkenergy(a)gmail.com> wrote:        External Email - Use Caution        Hi Eugenio -Hope all is well. I am running FS 7.2. I have installed the MATLAB Runtime 2014b. However when I run the thalamic segmentation routine I get this error. Please help.Thanks,Alancopernicus:~/IMAGING> segmentThalamicNuclei.sh 973770Setting ITK threads to 1#--------------------------------------------#@# Thalamic Nuclei processing Tue Oct 18 12:25:06 PM CDT 2022------------------------------------------Setting up environment variables---LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/freesurfer/bin/SegmentThalamicNuclei: error while loading shared libraries: libicudata.so.52: cannot open shared object file: No such file or directoryCommand exited with non-zero status 127@#@FSTIME  2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 e 0.01 S 0.00 U 0.00 P 33% M 2256 F 11 R 621 W 0 c 1 w 25 I 1776 O 0 L 0.69 0.22 0.07@#@FSLOADPOST 2022:10:18:12:25:06 run_SegmentThalamicNuclei.sh N 14 0.69 0.22 0.07127Linux copernicus 5.15.0-50-generic #56-Ubuntu SMP Tue Sep 20 13:23:26 UTC 2022 x86_64 x86_64 x86_64 GNU/LinuxThalamic nuclei exited with ERRORS at Tue Oct 18 12:25:06 PM CDT 2022For more details, see the log file /home/alanfrancis/IMAGING/FREESURFER_SUBJECTS//973770/scripts/thalamic-nuclei-mainFreeSurferT1.log-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of NeuroscienceUniversity of Texas, School of MedicineRio Grande ValleyTexas.                                                                                                           _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1elpe2JjxvZ4Lo-xTfcLTjcLXPpUXKRXvDvCfL… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/114BijDJeA9ze3ZzU7Hd1_nRFQWrlOUbZle3uB… information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-7MN4BIp5M3Ef13cSzQVtEGvwS4yeQfhmdc4y… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tJqHFXPSZkdeGg5_8J1m5U2932-B3u1BJvXvY…; .-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of NeuroscienceUniversity of Texas, School of MedicineRio Grande ValleyTexas.                                                                                                           _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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help
by Sarah Lavelle 25 Oct '22

25 Oct '22

External Email - Use Caution Dear freesurfer, Are there any additional resources on how to make cuts? I have found this https://secure-web.cisco.com/18_liDyv7h8S0t-GuSrqbS0mexl0ornQBxqLR6v5JlLJUx… but it isn't enough for the project I am doing. I want to flatten the whole surface but I may need to change where I am cutting from patient to patient. How do you know how big the hole should be? and how many relaxation cuts should you make? How long should they be? If you have any more guidance on how to cut to minimise distortion, please let me know! Also when I perform the mris_flatten function using my patch, my terminal gives me a % near the end saying "41% total metric distortion". Can you confirm that this value is the total metric distortion from an inflated surface to a flatmap surface using my chosen patch? Many thanks, Sarah Lavelle Trinity College Dublin

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Re: [Freesurfer] FreeSurfer Mac crash
by fsbuild 25 Oct '22

25 Oct '22

External Email - Use Caution Try running the commands below in a new terminal window.  You can run the bash shell and set the environment variable FS_LICENSE to point to the license.txt file you downloaded after filling out the form, https://secure-web.cisco.com/1IL6-bXyqY3LwkwCeLHW8BrasqmSMK-CMfK…;  I used an Intel Mac below, but it should work if you are on a newer Mac with the M1 or M2 chip. - R. - - - - - - - iMac:~ myuserid$ bashThe default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1q1PYonuAvBGkY2sdlfWfdq5vkeftncQHnhJhoCzvdI_yr… sw_versProductName: macOSProductVersion: 12.6  <-- RUNNING MAC OS 12.6  (ON AN INTEL MAC)BuildVersion: 21G115iMac:~$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 iMac:~$ source /Applications/freesurfer/7.3.2/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.3.2-20220804-6354275 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.3.2 FSFAST_HOME       /Applications/freesurfer/7.3.2/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.3.2/subjects MNI_DIR           /Applications/freesurfer/7.3.2/mni iMac:~$ pwd /Users/myuserid iMac:~$ echo $HOME /Users/myuserid iMac:~$ ls license.txt license.txt iMac:~$ export FS_LICENSE=$HOME/license.txt iMac:~$ which freeview /Applications/freesurfer/7.3.2/bin/freeview iMac:~$ freeview   <-- SHOULD OPEN AN EMPTY FREEVIEW WINDOW iMac:~$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz   <-- SHOULD DISPLAY KNOWN TO BE GOOD VOLUME FILE On Oct 23, 2022, at 12:29, Parya Rahimi <paryara7(a)gmail.com> wrote:       External Email - Use Caution        Hello, I recently downloaded freesurfer and when I try to load a volume, the application just crashes and shows me the error I copied below. Please let me know how to fix this. Thank youRegards,Parya Rahimi

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