Freesurfer November 2022

freesurfer@nmr.mgh.harvard.edu

80 participants
119 discussions

aparcstats2table segmentation fault error
by Eric Yin 15 Nov '22

15 Nov '22

External Email - Use Caution Hello! I’m trying to run the aparcstats2table function on a single participant and I cannot seem to get rid of the following segmentation fault error. I checked the forums and did not find anyone with the same problem. [cid:image002.png@01D8F92C.C6B09C50] I have tried a few different options. First, I read that aparcstats2table requires PATH to lead to python2, but this call would throw the error that freesurfer has not been sourced properly even though I sourced it manually. Please find my Freesurfer version in the screenshot as well. I’m running on CentOS Linux v7 (Core). [cid:image006.png@01D8F92C.C6B09C50] Then I thought that it might be because freesurfer/7.2.0 requires a newer version of python, but it also did not work for python3 or python3.6. [cid:image009.png@01D8F92C.C6B09C50] Please let me know if I’m doing something wrong, or if anyone has run into a similar issue. Thank you for your time.

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freeview -v file stuck loading at 99% in 7.2 but not 6.0.1
by Drucker, Daniel 15 Nov '22

15 Nov '22

Hi, If I do: $ freeview -v myfile.nii.gz If I'm pointed at my 6.0.1 freesurfer, this works fine. In 7.2, the freeview window pops up, the loading bar gets to 99%, then then nothing else happens. I'm not sure what to do to debug this further. -- Daniel M. Drucker, Ph.D. Director of IT McLean Hospital Imaging Center Harvard Medical School

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Pial surfaces include cerebellum - unable to fix with manual edits
by Raij, Tommi A. 15 Nov '22

15 Nov '22

Dear Surfers, I have a case where recon-all labels cerebellum as cerebral white matter (aparc+aseg.mgz) and the pial surfaces therefore include the cerebellum. The error has been resistant to attempts to fix the situation with manual edits to $SUBJECT/mri/brain.finalsurfs.mgz and re-running autorecon3 (with or without autorecon2). Specifically: Without manual edits, recon-all hangs at the stage: ... CORRECTING DEFECT 0 (vertices=34440, convex hull=821, v0=4192) XL defect detected... ... After exiting with Ctrl-C, brain.finalsurfs.mgz include cerebellum, and the pial surfaces include cerebellum. I guess the "defect" FS is trying to correct is the cerebellum that was mislabeled. My manual edits to brain.finalsurfs.mgz consisted of removing cerebellum by painting with brush value = 1 (freeview voxel edit tool). Thereafter, I recomputed autorecon 3: recon-all -autorecon3 -s $SUBJECT -no-isrunning With this, recon-all finishes "without error" but the recomputed aparc+aseg.mgz still thinks cerebellum is cerebral white matter and the pial surfaces again include cerebellum. This is with Martinos Center stable version 6. Any suggestions would be greatly appreciated! Also happy to send a link to the original T1 and recon-all results if you would like. Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th st Charlestown, MA 02129

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Freesurfer Passcode
by Nadeem Schwen 15 Nov '22

15 Nov '22

External Email - Use Caution Hi! I am trying to 3D print my child's recent brain MRI. Can I please have the passcode to unzip the Virtualbox image for Freesurfer? Thanks in advance!

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aseg.mgz not created
by O'Dor, Sarah,PhD 15 Nov '22

15 Nov '22

Good morning, Recon-all finished without error, but no aseg.mgz file was created. I cannot find any errors in the recon-all.log (attached) to indicate what may have happened. Any suggestions on how to troublshoot this? Thank you, Sarah

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password request for file FS_7_2_0_Ubuntu_18_04_06.ova.7z
by ISABELLA ARIZA CUBEROS 14 Nov '22

14 Nov '22

External Email - Use Caution Hello, I hope finds you well. I would like to request for the password to FS_7_2_0_Ubuntu_18_04_06.ova.7z file to be able to expand it. Thank you for your time. -- *Isabella Ariza Cuberos* Bioingeniera Énfasis en Neuroimagen Pasante Grupo Neuropsicología y Conducta - GRUNECO Universidad de Antioquia -- "La información aquí contenida es para uso exclusivo de la persona o entidad de destino. Está estrictamente prohibida su utilización, copia, descarga, distribución, modificación y/o reproducción total o parcial, sin el permiso expreso de Universidad de Antioquia, pues su contenido puede ser de carácter confidencial y/o contener material privilegiado. Si usted recibió esta información por error, por favor contacte en forma inmediata a quien la envió y borre este material de su computador. Universidad de Antioquia no es responsable por la información contenida en esta comunicación, el directo responsable es quien la firma o el autor de la misma." -- UdeA

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Pass code request for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Eduardo Europa 12 Nov '22

12 Nov '22

External Email - Use Caution Hello, This is a request to receive the pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z Thank you, *Eduardo Europa, PhD, CCC-SLP (he/him)* Assistant Professor, Communicative Disorders & Sciences San José State University eduardo.europa(a)sjsu.edu Visit my website: https://secure-web.cisco.com/1bg97TFGS27e-eo0fDqTrd0vj7supBHYYlcL4qEd1DTPLS…

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Virtual Machine zip Password
by Cesare Jenkins 12 Nov '22

12 Nov '22

External Email - Use Caution Could I please obtain the password to unzip the virtual machine zip file (the most recent one, 7.2 I believe)? Thanks, Cesare

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Only extract stats information question
by 蔡嘉鑫 12 Nov '22

12 Nov '22

External Email - Use Caution Dear freesurfer, Greeting! We met a problem need your kind help. What if I only need extract the stats information in freesurfer? You know it will take a long time to run all step. Can I only get the 'stats' information and shorten the running time? Best wishes! Jiaxin Cai

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How to set original orientation for converted images
by Haiyun Chen 11 Nov '22

11 Nov '22

External Email - Use Caution Hello FreeSurfer Experts, I converted the aseg.mgz file to aseg.nii using mri_convert command, the aseg.mgz file is located in the directory below based on your tutorial: tutorial_data_20190918_1558/practice_with_data/Subj001/mri When I open the file aseg.nii in a different application, the original orientation is not sagittal. In the MRI protocol, the original orientation is sagittal. Could you please help to tell how to set the original orientation of output images to be sagittal? Thank you in advance! Best regards Haiyun

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Freesurfer November 2022