Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

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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MRI skewness
by Peled, Noam,PhD 24 Oct '22

24 Oct '22

Dear group, I have a T1 dicoms that looks like that: [cid:image001.png@01D8E7D5.31FD8C20] But the T1.mgz recon-all produces looks like that: [cid:image002.png@01D8E7D5.31FD8C20] How can I fix this skewness? Here is the dicoms info: type: MGH dimensions: 640 x 640 x 243 voxel sizes: 0.390625, 0.390625, 1.000000 type: SHORT (4) fov: 250.000 dof: 1 xstart: -125.0, xend: 125.0 ystart: -125.0, yend: 125.0 zstart: -121.5, zend: 121.5 TR: 700.00 msec, TE: 15.00 msec, TI: -1.00 msec, flip angle: 120.00 degrees nframes: 1 PhEncDir: ROW FieldStrength: 3.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.4231, c_r = -55.4712 : x_a = -0.0000, y_a = 0.0377, z_a = 0.9059, c_a = 29.9016 : x_s = 0.0000, y_s = -0.9993, z_s = 0.0165, c_s = -19.3352 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -0.3906 -0.0000 -0.4231 120.9404 -0.0000 0.0147 0.9059 -84.8789 0.0000 -0.3903 0.0165 103.5695 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -0.138228 ras to voxel transform: -2.5600 -1.1949 -0.0451 212.8522 -0.0000 0.0467 -2.5601 269.1053 0.0000 1.1031 0.0416 89.3201 -0.0000 -0.0000 -0.0000 1.0000 Thanks! Noam The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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mri_segment
by James Brown 24 Oct '22

24 Oct '22

External Email - Use Caution Dear Freesurfer experts, I would like to inquire about the flags "-whi" and "-ghi" in the command "mri_segement". According to FS wiki, the command "mri_normalize" sets white matter voxels around ~110 and gray matter around ~70. - The default white matter high limit in the command mri_segemnt is 125, what is the highest value to consider white matter voxels in an image? Is it 125? - What are the situations where we need to set the gray and white matter voxels at a high limit of 100 and 125 respectively in the command mri_segment? Does the brightness of the image or motion play a role in the decision of choosing high limits values? Thank you, James

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Question about sclimbic
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 24 Oct '22

24 Oct '22

External Email - Use Caution I receive an error when I try to run the sclimbic module, do you have any suggestions on why this might be happening? : Loaded input image from /mnt/V/Datasets/BSNIP2/Processing/Finished_q2/GP1462~1/mri/nu.mgz Traceback (most recent call last): File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 1048, in <module> main() File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 232, in main segmenter.process_files(**params) File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 577, in process_files post, seg, vox_counts, volumes, mean_probs = self.segment(image) File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 497, in segment conformed = self.preprocess(image) File "/usr/local/freesurfer/7.3.2/python/scripts/mri_sclimbic_seg", line 489, in preprocess processed = image.conform(shape=(*self.inshape, self.nchannels), voxsize=1.0, orientation='RAS', dtype='float32', copy=False) File "/usr/local/freesurfer/7.3.2/python/lib/python3.8/site-packages/surfa/image/framed.py", line 574, in conform conformed = conformed.reshape(shape, copy=False) File "/usr/local/freesurfer/7.3.2/python/lib/python3.8/site-packages/surfa/image/framed.py", line 515, in reshape delta = (np.array(shape) - np.array(self.baseshape)) / 2 ValueError: operands could not be broadcast together with shapes (4,) (3,) Segmentation fault Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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B0 distortion correction (a clearer question)
by Addison, Reuben 24 Oct '22

24 Oct '22

I sent a question earlier on but I do don’t think I was clearer the first time. I am trying to do a distortion correction using (epidewarp.fsl) epidewarp.fsl \ --mag mag.nii.gz \ --dph dphase.nii.gz \ --tediff YOUR_TE_DIFF --esp YOUR_ESP \ --vsm bold/b0dcmap.nii.gz The issue we collected two field maps one in the AP direction and one in the PA direction (hence I have two different mag and phase volumes). I am not quite sure how if I should create two different maps and keep them in my bold folder for my FSFAST pipeline

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White Matter Hypointensities Not Calculating for Left and Right
by Atwater, Emanuel R 24 Oct '22

24 Oct '22

External Email - Use Caution Hello Freesurfer Team, My issue is within the aseg.stats information. There is WM-hypointensities volumetric data present, however, there are "0's" for Left and Right WM-hypointensities. Why are the hypointensities not being calculated/separated for the left and right hemisphere? FS version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b Aseg.stats: see attached for sample V/r, Emanuel Atwater

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