Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Tech Support removal
by penamarquezl95 16 Nov '22

16 Nov '22

External Email - Use Caution Hi, Can you please remove my email from FreeSurfer's email support. I don't want to keep receiving emails. Thank you, Sincerely, Luis Pena Marquez President of Graduate Students Association (GSA) [cid:638a6427-c72e-4c44-aebc-2e664d5d262f]

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Unsupported Datatype
by Rachel Wagner 16 Nov '22

16 Nov '22

External Email - Use Caution Hello, I’m getting the following error, not sure how to resolve! developer@developer-VirtualBox:~$ mri_convert dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii dicom-series-005-t2_swi_tra_p2_3mm_Mag.mgz mri_convert dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii dicom-series-005-t2_swi_tra_p2_3mm_Mag.mgz reading from dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii... niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm error: No such file or directory error: niiRead(): unsupported datatype 128 (with scl_slope = 0) in /home/developer/dicom-series-005-t2_swi_tra_p2_3mm_Mag.nii Thanks! Rachel Wagner

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Re: [Freesurfer] Issue with rotation during longitudinal base creation
by Andrew Beaudin 16 Nov '22

16 Nov '22

External Email - Use Caution Hi Nathan, I am reaching out because it looks like we are coming up against a similar issue with Freesurfer's 'mri_robust_template' and I was wondering if you have been able to figure out this error for your images. I am receiving the similar error message calling 'mri_robust_template' directly from the terminal (i.e., outside of Freesurfer's longitudinal pipeline) on our GE T1w images. I also posted my question to the Freesurfer mailing list a while ago (https://secure-web.cisco.com/1RpTwN8ji-OmV4wLBq2ngukhOIFRTuNMes-ZVlDOudKnAn…) but I still cannot find a solution to this problem. Any insights are greatly appreciated. Thanks for the help. Andrew ---- Andrew Beaudin, PhD | Postdoctoral Scholar University of Calgary | Cumming School of Medicine Department of Clinical Neurosciences HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1 Phone: (403) 210-6273

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Original image and the mask file dimension mismatch
by priya padma 16 Nov '22

16 Nov '22

External Email - Use Caution Hello Team, I have a nifti file of dimension (256, 256, 156) but once I run the freesurfer recon-all the subregions mask "*aparc.DKTatlas+aseg.mgz*" has a dimension of (256,256,256) due to this I am unable to view the segmentation overlaid on the original image in any dicom viewer. May I know why freesurfer changes the dimension of the original image and the mask ? Is there any solution for this? Any help will be highly appreciated. Thank you. -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

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about using -norandomness flag with recon-all
by Xin Qi 16 Nov '22

16 Nov '22

External Email - Use Caution Hello Freesurfer Team: Because of ensuring that results are exactly the same from run to run, norandomness flag is used with recon-all. To better understand the randomness, we have a few questions listed below. 1. Which algorithms inside the recon-all use the seeded random number? And what randomness is about? 2. Is there a way to use a seed value to ensure the same data can be reproduced? 3. Whether we are compromising anything by going with the non-random option? Thank you very much for your time and looking forward to hearing from you. Best regards Xin

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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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