Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Re: [Freesurfer] Passcode Request
by fsbuild 13 May '22

13 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 6, 2022, at 17:12, Eric Mokri <eric.mokri(a)mail.mcgill.ca> wrote:        External Email - Use Caution        Hello,Can I please have the passcode to open the following file for MRI processing: FS_7_2_0_Ubuntu_18_04_06.ova.7zRegards,Eric Mokri_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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VM Passcode
by Viktor Pavliska 13 May '22

13 May '22

External Email - Use Caution hi, I would like to get a passcode for the .7z file for the VM. Thank you in advance Best Regards.

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VM Passcode May 6 Follow up
by Eric Mokri 13 May '22

13 May '22

External Email - Use Caution Hello, Following up on the request posted on May 6th copied below, can I please have the passcode for the FS_7_2_0_Ubuntu_18_04_06.ova.7z file. Regards, Eric ____________________ Hello, Can I please have the passcode to open the following file for MRI processing: FS_7_2_0_Ubuntu_18_04_06.ova.7z Regards, Eric Mokri

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resample_type ignored by mri_convert with --like argument?
by James Hengenius 13 May '22

13 May '22

External Email - Use Caution Hello FS experts, I'm trying to reslice a third-party atlas into the same resolution as my data in MNI space. I am using the following command: mri_convert --like T1w_MNI.nii.gz --resample_type nearest ICBM152_2009c_AtlasWhite.nii.gz WhiteAtlas_resampled.nii.gz Output is: mri_convert --like T1w_MNI.nii.gz --resample_type nearest ICBM152_2009c_AtlasWhite.nii.gz WhiteAtlas_resampled.nii.gz reading from ICBM152_2009c_AtlasWhite.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) INFO: transform src into the like-volume: T1w_MNI.nii.gz writing to WhiteAtlas_resampled.nii.gz... In the resulting resampled atlas, the boundaries of the ROIs appear to use an interpolation and not nearest neighbor (i.e., they take values other than the ROI values in the atlas). Not sure if I can embed images - if so, see the attached for an example: [image: image.png] The output is the same whether I include the --resample_type nearest flag or leave it out, making me think that mri_convert is ignoring the flag and using the default interp option. This can be replicated in the relatively current version "freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b" as well as the older "$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $" (which we keep around for old pipeline compatibility). Any ideas on how to fix this so the ROI interfaces take appropriate (nearest neighbor) values rather than interpolated values? Thanks all! Jim H.

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Cannot Locate Newly Completed Recon-all Data
by Joanna L Eckhardt 13 May '22

13 May '22

External Email - Use Caution Dear FreeSurfer Team, I have exported my SUBJECTS_DIR successfully in the following directory: /home/developer/FreeSurfer/fs-subjects. When I ran my first recon-all command on subject "sub101-ses-FU," it successfully appeared in my fs-subjects directory along with an fsaverage folder. However, I have ran two other subjects with recon-all and neither have appeared in the fs-subjects directory, even though they successfully completed. In the screenshot below it shows I finished recon-all on subject "sub202-sesFU" but it did not populate in my fs-subjects folder. I cannot find sub202-sesFU anywhere and restarting did not help. Do you know where my finished subjects might be? Thank you, Joanna [cid:882a1098-c364-44f5-bee4-8c41b5421a63] -- Joanna Eckhardt Neurosciences Graduate Program University of California, San Diego

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mri_surf2surf error: could not read surface
by Margot Wagner 12 May '22

12 May '22

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to run the HCPPipeline <https://secure-web.cisco.com/1PrAyMCdNwWvmMb6-wd3cHZJPug7g4q9HEG-M9vN9SZYsj…> using their provided example data according to their Installation and Usage Intructions <https://secure-web.cisco.com/1Y9my6pk8D5YRbrVEZ1pMFY43_her0g021-eYiIxAcX3X1…> . Currently, I am trying to run FreeSurferPipelineBatch.sh and got an error message in FreeSurferPipeline.sh when it tries to run mri_surf2surf: Reading source surface reg /nadata/cnl/home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w/100307/surf/lh.white.preaparc No such file or directory mri_surf2surf: could not read surface /nadata/cnl/home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w/100307/surf/lh.white.preaparc No such file or directory ERROR: This occurs immediately after attempting to run mri_surf2surf --s 100307 --hemi lh --sval-xyz white.preaparc --surfreg white.preaparc --reg transforms/rawavg2conf.dat rawavg.cmdc.mgz --tval-xyz rawavg.cmdc.mgz --tval white.preaparc.rawavg It appears no file lh.white.preaparc is made, nor any file matching "white" or "preaparc". I have been unable to find similar errors. Attached is the output from the FreeSurferPipeline run as well as recon-all.log. 1) FreeSurfer version: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 2) Platform: Debian GNU/Linux 10 (buster) 3) uname -a: Linux porter 4.19.0-20-amd64 #1 SMP Debian 4.19.235-1 (2022-03-17) x86_64 GNU/Linux 4) recon-all.log: see attached Thank you for your assistance. -- Best Regards, Margot Wagner Graduate Student Researcher UCSD Bioengineering

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Reversing mri_convert
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 12 May '22

12 May '22

External Email - Use Caution Hi, I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii I now have something registered to the T1.nii and would like to move it back to Freesurfer space. How would you go about doing that? I am assuming I would do the inverse of the mri_convert, but I can't seem to find the option to write the matrix. Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Recon-all
by krystaly 12 May '22

12 May '22

External Email - Use Caution Dear Freesurfer experts, I am new to FS 7.2.0 (Window 10), and trying to run the Recon-all command as demonstrated on the website (https://secure-web.cisco.com/1UHVC1FSZYmyuNB9-Imz9busENdngVDz-sSAkkWD-mKGV9…) Before running the command, I have converted DICOM files into NIFTI files. I, then, moved the nii files to Desktop at FS. They are in the folder named “Sub-132”. However, I got the following errors: developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s Sub-132 -i Sub-132_SAG_T1_MPRAGE_(INC_UPPER_CX_AS_MUCH)__2.nii -all bash: syntax error near unexpected token `(' To make another attempt, I tried to process with another T1 image, and I got the following error: developer@developer-VirtualBox:~/Desktop/Sub-132$ recon-all -s Sub-132 -i Sub-132_T1_COR_5_0.5__250_i00002.nii -all mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/7.2.0/subjects/Sub-132': Permission denied cp: cannot create regular file '/usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b /usr/local/freesurfer/7.2.0/subjects/Sub-132/scripts/patchdir.txt: No such file or directory. I reckoned that the T1 images could not be processed with only 1 plane. Would you please kindly advise on merging 3-plane T1 images into one comprehensive T1-weighter image for further processing? Or would you please let me know what went wrong in this case? Thanks. Best regards, Krystal

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error estimates in FS total brain volumes
by Alexopoulos, Dimitrios 12 May '22

12 May '22

External Email - Use Caution Hi all, What is a reasonable estimate of the error margin in the total brain volume estimates of Freesurfer? Is there a reference that discusses this? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Request VM passcode
by Santiago Fernández 12 May '22

12 May '22

External Email - Use Caution Hi, I would like to use the VM with FreeSurfer. Could you send me the passcode? Thanks! Regards, Santi.

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