Freesurfer

freesurfer@nmr.mgh.harvard.edu

13 participants
30061 discussions

data quality check before analysis
by yunus soleymani 14 Oct '23

14 Oct '23

External Email - Use Caution Hi there, My name is Yunus and I'm currently working on my Ph.D. thesis, which involves analyzing the HCP database volumetrically using Freesurfer. However, before I begin with the software, I was wondering if there is a tool in Freesurfer that can perform a quality check on the data to identify any possible artifacts or noise that might affect the analysis. Could you please let me know if such a tool exists in Freesurfer? Your help would be much appreciated. Thank you and Best Regards,Yunus. --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------

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Convert in subject space after cw256
by Maurilio Genovese 13 Oct '23

13 Oct '23

External Email - Use Caution Hi all, I am trying to convert freesurfer reconall output back in original subject space so I am following this guide: https://secure-web.cisco.com/1gX-L0rMewLeZ04f3aHxi6QsxMjCpOru8m6oGdCmStPD1u… However some of my images have a very large fov so I use the cw256 option. In those cases converting back results in rawavg.mgz is not enough, because the fov of rawavg.mgz is already downscaled, so I think I need to go back to 001.mgz. Can someone help me to understand how to go from the cw256 cropped space to the original space? Thanks Maurilio

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(no subject)
by Maurilio Genovese 13 Oct '23

13 Oct '23

External Email - Use Caution Hi all, I am trying to convert freesurfer reconall output back in original subject space so I am following this guide: https://secure-web.cisco.com/1hdoEYpcNfh6v9Yoq-8Iexo7oO3DXo3uI45KMmpjSSOcdu… However some of my images have a very large fov so I use the cw256 option. In those cases converting back results in rawavg.mgz is not enough, because the fov of rawavg.mgz is already downscaled, so I think I need to go back to 001.mgz. Can someone help me to understand how to go from the cw256 cropped space to the original space? Thanks Maurilio

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Re: [Freesurfer] ERROR: could not configure recon-all parameters
by 윤혜정 12 Oct '23

12 Oct '23

External Email - Use Caution Hi, On top of the email I sent earlier, I also get the next error line that says: ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: Undefined error: 0 -----Original Message----- From: hyejung7890(a)amc.seoul.kr To: <freesurfer(a)nmr.mgh.harvard.edu>; Cc: Sent: 2023. 10. 13. (금) 08:35 (GMT+09:00) Subject: ERROR: could not configure recon-all parameters Good day, I get the following error message when I run recon-all: ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file I went through a bit of the mail archive and unlike the others I don't see ASCII error message in mine. Additionally, I was wondering if the thickness of MR slices would affect recon-all process at all? I appreciate your help. Best wishes, Alice

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ERROR: could not configure recon-all parameters
by 윤혜정 12 Oct '23

12 Oct '23

External Email - Use Caution Good day, I get the following error message when I run recon-all: ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file I went through a bit of the mail archive and unlike the others I don't see ASCII error message in mine. Additionally, I was wondering if the thickness of MR slices would affect recon-all process at all? I appreciate your help. Best wishes, Alice

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Postdoctoral position in Neuroimaging and Aging at Albert Einstein College of Medicine
by Mark Wagshul 12 Oct '23

12 Oct '23

External Email - Use Caution Postdoctoral position in Neuroimaging and Aging at Albert Einstein College of Medicine A postdoctoral research fellow position is available immediately in the departments of Neurology and Radiology at the Albert Einstein College of Medicine in NY. The position will offer unique opportunities to utilize multi-modal neuroimaging data collected on normal and neurological populations that are well characterized in terms of cognitive, motor, and emotional function. The post-doctoral fellow will be expected to devote significant time and effort to writing empirical research articles. In addition, there will be opportunities to learn and become involved in collecting, processing, and analyzing novel neuroimaging data combining different methods (MRI, fNIRS, EEG). We are seeking an enthusiastic and highly-motivated individual with experience in neuroimaging analysis methodologies. Experience and knowledge of aging and neurodegenerative diseases is desirable. Successful candidates will have a PhD in biomedical engineering, physics, computer science, cognitive neuroscience or related disciplines, and experience in conducting experiments and performing advanced data analysis with structural and/or functional MRI methods (e.g. DTI/NODDI, resting state). Candidates will have a solid background in relevant data processing packages (e.g., FSL, SPM, Freesurfer), programming in either Matlab, Python or similar environments and should be comfortable with data analysis in a Linux environment. The ideal candidate will also have familiarity with computational and statistical methods related to imaging analyses. A strong work ethic, excellent organizational and communication skills is expected as well as the ability to work in an interdisciplinary environment. Willingness to learn new techniques or software environments and a strong foundation in neuroanatomy is plus. Excellent writing skills, a good publication record, and ability to work independently will be strongly favorable. The Albert Einstein College of Medicine is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, protected veteran or disabled status, or genetic information. Einstein seeks candidates whose skills, and personal and professional experience, have prepared them to contribute to our commitment to diversity and excellence, and the communities we serve. Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu<mailto:mark.wagshul@einsteinmed.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz
by Eric Paul Kraybill 12 Oct '23

12 Oct '23

External Email - Use Caution To Whom it may concern, I am trying to troubleshoot an error during TRACULA preprocessing and the issue seems related to the creation of aparc+aseg+thalnuc.nii.gz. The subregion segmentation prior to trac-all -prep was successful and mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz and other Thalamic Nuclei files were generated. In the archives I saw that three others have experienced a similar issue without a resolution in the thread. I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6. I have attached the log file, log error, and my configuration file. Any help would be greatly appreciated, and I hope to hear from you soon. Thank you, Eric

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VM image Freesurfer 7.2.0 download
by Tsai, Perry 11 Oct '23

11 Oct '23

External Email - Use Caution Hello, I'm hoping to download the Ubuntu virtual machine disk image of Freesurfer 7.2.0 in order to install onto a new computer. On the website, it appears this link was removed and being updated as of 9/11/23. Is there any timeline on when this download will be available again? Or could I get the previous download file another way? Thanks! *********************EMAIL DISCLAIMER********************* This email and any files transmitted with it may be confidential and are intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient or the individual responsible for delivering the e-mail to the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is strictly prohibited. If you have received this e-mail in error, please delete it and notify the sender or contact Privacy Office 312.355.5650.

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Hippocampus Segmentation Troubleshoot - Matlab crash
by Mirsol Choi 11 Oct '23

11 Oct '23

External Email - Use Caution Hi there, I am a Master's student who is looking to segment the hippocampus and analyze diffusion data of the segments. I am trying to utilize the segmentation function with this command: segmentHA_T1.sh subj01 But I am met with this error saying that Matlab has crashed. The crash log is attached to this email. I have freesurfer version 7.1.1, running on MacOs 11.7.10. I have followed your website instructions to download Matlab R2014b. Following the installation process of Matlab, I was met with this message: Installing Product: MATLAB Compiler Runtime - Core 8.4 (Oct 08, 2023 11:29:15) Installing Product: MATLAB Compiler Runtime - GPU 8.4 (Oct 08, 2023 11:29:21) Notes: On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable: /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/bin/maci64: (Oct 08, 2023 11:29:21) Exiting with status 0 (Oct 08, 2023 11:29:21) End - Successful. Finished R2014b installed successfully in /Applications/freesurfer/7.1.1/MCRv84 And so I have appended the path using this code into my bashrc profile: export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/bin/maci64 I am wondering if I can get some help with running the hippocampus segmentation protocol . Thank you so much for your time, I greatly appreciate your support.

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Comparison between groups
by Iara Senem 11 Oct '23

11 Oct '23

External Email - Use Caution Hello! I'm a beginner on FS, hope you can help me. I already ran recon-all and I got aseg and aparc stats into an Excel spreadsheet. Using statistical software (SPSS) I found some differences between controls and patients in some cortical thickness regions. I'd like to know how I can put those differences in a picture. How can I analyze the differences between these groups and get an image on Freeview? Thank you. -- ____________________________________________________ Iara Senem Doutoranda da FMRP-USP Departamento de Neurociências e Ciências do Comportamento da FMRP Neuropsicóloga/Psicóloga - CRP 06/142554 Fone: +55 (16) 98209-1817

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