Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Passcode for FreeSurfer VM
by Aleksandra Petrovskaia 16 May '22

16 May '22

External Email - Use Caution Dear all, I hope you are doing well. I am an intern at the University of Gothenburg, Sweden, could you please provide me with a passcode for FreeSurfer VM image? I would like to use this version: https://secure-web.cisco.com/1yZkS0R8VnbO1QWzTX29VVIIW4VCNsXbflY7tg4lYbLNqc… Best wishes, Alexandra <https://secure-web.cisco.com/1EaXcElE2e36pVP4hKX6lRltCa5zEeDsgA6QGW0ugUdxgQ…> Без вирусов. http://secure-web.cisco.com/1Qc214ZMYtI0RLObvR0XBJdDSK2mgbyIuNC7SSyx5EDNCrn… <https://secure-web.cisco.com/1EaXcElE2e36pVP4hKX6lRltCa5zEeDsgA6QGW0ugUdxgQ…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Fwd: Passcode for FreeSurfer VM
by Aleksandra Petrovskaia 15 May '22

15 May '22

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

13 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 13, 2022, at 12:01, Viktor Pavliska <Viktor.Pavliska(a)osu.cz> wrote:       External Email - Use Caution        hi,I would like to get a passcode for the .7z file for the VM.Thank you in advanceBest Regards._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

13 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 12, 2022, at 12:59, Santiago Fernández <santiagofdezglez(a)gmail.com> wrote:        External Email - Use Caution        Hi,I would like to use the VM with FreeSurfer. Could you send me the passcode?Thanks!Regards,Santi._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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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