Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Desikan and Killiany atlas
by Valentina Mancini 14 Feb '20

14 Feb '20

External Email - Use Caution Dear Freesurfer experts, we used the Desikan and Killiany atlas to build individual head models in order to project surface EEG data in the inverse space. We would like to plot on the cortical surface the regions of the D&K atlas where we find a different functional activation. As I understand, there is a way to plot statistically significant results with tksurfer, but in our case we cannot show our statistical values because we should take into account also epochs and frequency and we can do that only with a time-frequency plot. Is there a simple way to get a figure of the cortical surface with a set of predetermined regions of the D&K atlas highlighted only for visualization purpose? Best regards, Valentina Mancini

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Coordinates transformation from conformed space to the original FLAIR image
by Xiaojiang Yang 13 Feb '20

13 Feb '20

External Email - Use Caution Hi everyone, I have used both T1 and (T2) Flair images as inputs to recon-all, and I have generated some coordinates (ROI) that I can transform to the original T1 images. Basically, I use the two matrixes obtained from the mri_info -- vox2ras commands: Sr = mri_info --vox2ras $SUBJECTS_DIR/$subject/mri/orig/001.mgz Sc = mri_info --vox2ras $SUBJECTS_DIR/$subject/mri/T1.mgz For a given point Coordinate=(x, y, z, 1) in the conformed space, I get the coordinates in the original T1 space using the formula: t1_Coordinate = inv(Sr) * Sc * Coordinate. The above formula works fine. But I also want to get the transformed coordinates in the Flair image space. I have used a similar way: Srf = mri_info --vox2ras $SUBJECTS_DIR/$subject/mri/orig/FLAIRraw.mgz Sc = mri_info --vox2ras $SUBJECTS_DIR/$subject/mri/T1.mgz flair_Coordinate = inv(Srf) * Sc * Coordinate. But the above calculation is not correct. Does anyone have an idea of how to get this flair coordinate? Thank you!!! Xiaojiang

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freesurfer error in matlab
by Miguel Ángel Rivas Fernández 12 Feb '20

12 Feb '20

External Email - Use Caution Dear Freesurfer devs, I am trying to run FreeSurfer in Matlab and I received the following error message dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib I tried to fix this error disabling the SIP but this did not work. Maybe could be due to the gcc compiler? Any help would be appreciated Thanks in advance Best regards, -- *Miguel Ángel Rivas Fernández*

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ERROR: nu_correct
by Graduate Imaging 12 Feb '20

12 Feb '20

External Email - Use Caution Hi, I've been processing some 3T MRI scans through Freesurfer and recently implemented the use of the -3T flag for nu-correction. I have processed about 200 scans and the majority of them have gone through with out an issue. However there are a handful that I received and error: nu_correct message in the recon-all log. I've visually inspected these images and there appears to be nothing wrong with them. I've attached the error code below. Does anyone know what might be causing this? Furthermore, one of these images had actually been processed without a 3T flag prior without issues so it appears to be intrinsic to flag. Assertion failed: (pxp->bf_refcount <= 0), function ncio_px_sync, file ./posixio.c, line 798. nu_evaluate: crashed while running minc_modify_header (termination status=6) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct

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Hippocampal segmentations -- how to make manual adjustments
by Kathy Reding 12 Feb '20

12 Feb '20

External Email - Use Caution I would like to manually adjust the hippocampal segmentations created by the hippocampal/amygdala sub-field segmentation pipeline. The hippocampal head boundary with the amygdala was poorly defined in my subjects (1mm isotropic images), and I would like to manually adjust this boundary. 1) I used the longitudinal pipeline (subjects had three visits each). Ideally, I would like to do this once per subject (i.e., on the subject average), but am not sure if that is possible, or if the subject average boundaries would maintain their accuracy once applied to each individual visit. If this is not possible, I would like to adjust only a single image per subject/visit (outline of the whole hippocampus) and apply it to two of to the three available segmentation (HBT, CA), or more importantly, extract the volumes in a similar manner to the FS provided sub-field output. 2) I would like to know how the alveus is assigned in the CA and HBT segmentations. It appears to be included in the hippocampus in my images, and I am curious if this is an error. Should it be excluded? Best, Kathy Reding

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Recon-all autorecon2 exited with error
by Benjamin Ineichen 12 Feb '20

12 Feb '20

External Email - Use Caution Dear Freesurfer experts, I edited the brainmask.mgz to erase some dura which caused problems with the pial surface in a subject. I then re-ran recon-all using: recon-all -qcache -s test1_edit -autorecon2 However, the recon-all finished with errors. Attached the log and error files. What is the problem? Thanks! /Ben -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01

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Re: [Freesurfer] Problem with registration (PetSurfer)
by Marina Fernández 12 Feb '20

12 Feb '20

External Email - Use Caution Doug, the full terminal output from the terminal after running tkregisterfv was: freeview -transform-volume -viewport cor -v /usr/local/freesurfer/subjects/s_001/mri/orig.mgz:visible=0:name=orig.mgz(targ) /home/sleep2014/0_Analisis_Marina/PET/s_001_PET.nii:name=s_001_PET.nii(mov):reg=/home/sleep2014/0_Analisis_Marina/PET/s_001.reg.lta --surface /usr/local/freesurfer/subjects/s_001/surf/lh.white:edgecolor=yellow --surface /usr/local/freesurfer/subjects/s_001/surf/rh.white:edgecolor=yellow Warning: Transformation can only apply to volumes for now. If your data includes ROI/Surface/Way Points, please do not use this feature yet. MatrixAsciiReadFrom: could not scanf parms Source temporarily unavailable LTAchangeType: src geometry must be valid Source temporarily unavailable terminate called after throwing an instance of 'int' Abort Thanks for your attention. Marina.

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freeview slow/choppy
by Octavian Lie 11 Feb '20

11 Feb '20

External Email - Use Caution Dear All, I recently changed from ubuntu 16.04 to 18.04 LTS, then reinstalled Freesurfer. As opposed to prior behavior, freeview image manipulation (mainly mouse-based rotations) are exceedingly choppy and slow. The screen briefly freezes after moving the mouse to rotate a volume, then jumps to the final volume position. Any thoughts? Thank you, Octavian

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Job opening: Full/Part-time medical imaging scientist: PWI/DWI/ASL/SWI
by shi yao wang 11 Feb '20

11 Feb '20

External Email - Use Caution Dear list members, Please check the attached job ad for a medical imaging scientist position at Atlanta, GA. We need experts for medical imaging analysis, especially for PWI, DWI/DTI, ASL or SWI. The position could be part-time and projected based. Best regards Dr. Pauli Email: pauil.ma(a)szdrbrain.com

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Re: [Freesurfer] Question re: hippocampal/amygdala subfields
by Iglesias Gonzalez, Juan E. 11 Feb '20

11 Feb '20

That is correct, Tegan! And welcome to FreeSurfer ;-) Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Tegan Hargreaves <thargrea(a)stjosham.on.ca> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, February 11, 2020 at 14:55 To: "'freesurfer(a)nmr.mgh.harvard.edu'" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Question re: hippocampal/amygdala subfields External Email - Use Caution Hi all, I am fairly new to FreeSurfer and am implanting the hippocampal/amygdala subfields script in our participants. As there are two versions of the hippocampal script (i.e., version 10 that is only hippocampus and version 21 which is both), I wanted to confirm that I should be using FS v6.0 (stable) for recon-all, and then running only the hippocampal/amygdala (v21) script through the dev version of FS. I don’t believe that I should be running the exclusively hippocampal script anymore, as the guide states it is now obsolete, but I just wanted to confirm. Thank you so much! Best, Tegan Tegan Hargreaves, MSc Research Assistant Peter Boris Centre for Addictions Research | St. Joseph’s Healthcare Hamilton 100 West 5th Street, Hamilton, ON L8P 3P2 P: 905-522-1155 ext. 36368 | E: thargrea(a)stjoes.ca<mailto:thargrea@stjoes.ca> ________________________________ Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and/or privileged information. Any unauthorized review, use, copying, saving, disclosure, re-transmission or distribution is strictly prohibited. If you are not the intended recipient or this information has been inappropriately forwarded to you, please contact the sender by reply e-mail or the Privacy Office via privacy(a)stjoes.ca. Thank you. ________________________________

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