Freesurfer August 2023

freesurfer@nmr.mgh.harvard.edu

89 participants
126 discussions

Is there an inverse function to mris_flatten?
by Phillip Tran 04 Aug '23

04 Aug '23

External Email - Use Caution Hello FreeSurfer team, I'm new to FreeSurfer and would greatly appreciate your help. My objective is to reverse the flattening process of mris_flatten. I successfully got flatmaps by using mris_flatten on "bert" inflated hemispheres with manual relaxation cuts (in Freeview/tksurferfv as opposed to deprecated tksurfer) as directed by these instructions: https://secure-web.cisco.com/1A7xoXmR8WDKrZnRfFGHzLvRwUtKyRcCICrInChTpRemfC… I also have a small 2-D patch of non-MRI image data that's been registered to and fused with the hemisphere flatmap. Is there an inverse function or procedure for mris_flatten? E.g.: I would input a .dcm/.jpg/etc. containing the patch-fused flatmap, then get in response the original inflated hemisphere with the fused patch appropriately deformed to fit the 3d shape. Then, is there potentially a way to return the patch-fused inflated hemisphere back into the pial surface from which it was inflated? FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Ubuntu version: 22.04.2 Jammy Jellyfish Thank you for your time, Phillip

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using synthsr with HCP Pipeline
by KennethSPrice 03 Aug '23

03 Aug '23

External Email - Use Caution Hello all, I am currently struggling through the HCP Pipeline! I want to use clinical scans processed with synthsr in the HCP Pipeline. 1.) Is this even possible? 2.) Is there a way to get a T2 output with synthsr? 3.) In lieu of the HCP Pipeline, could you use SythSR scans with the HCP Database to do a normal group analysis? Thanks, Ken

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[FreeSurfer] recon fix the surfaces of the brain
by Krystal Xiwing Yau 03 Aug '23

03 Aug '23

External Email - Use Caution Dear FreeSurfer experts, I am fixing the error generated by recon-all. Please see the capture below: [cid:a7289c63-1b2b-407c-9dec-a9ff5e082daa] Fig.1 Under-segmentation of white and pial surfaces still not fixed after running the command with the flags -autorecon2-cp -autorecon3 for the subject [cid:baf96016-01d2-4d50-ac8e-ce6067c1dec6] Fig.2 The same image for the subject, with the visible wm. The tutorial <https://secure-web.cisco.com/1eFs9sHrAZSKhe4nUQhj-OHr9PCuaQnsYS1AVa0FxCl5k_…> from the FsTutorial indicated that adding control points to the white matter area only. Moreover, the pial surface expends from the white surface. Thus, it is not possible to add control points on the cortex. Would somebody can help with fixing such error, please? Thank you very much! Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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7 zip pass code please
by Lewis, Jeramy 02 Aug '23

02 Aug '23

External Email - Use Caution Hello, I am stuck downloading and installing freesurfer. It is requiring a pass code to open the 7zip file to install. Please provide the pass code so I can continue. Jeramy Lewis, PhD Mallinckrodt Institute of Radiology Washington University School of Medicine 4525 Scott Ave, Room 3224 G St. Louis, MO 63110 mobile: 720-885-2044 e-mail: jeramy(a)wustl.edu<https://secure-web.cisco.com/14UiD4O4jlVflixdtoLKMb1QHbpWKEUDpJyazsQNyeP99x…> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Freeview sudden termination
by Jacob Bunyamin 02 Aug '23

02 Aug '23

External Email - Use Caution Hi, I am running freesurfer/7.3.2 and had an issue with freeview sudden termination. The error message is *sub-002/label/aparc.annot.ctabMRISreadAnnotationIntoArray: vertex index out of range: 538980362 i=2020300A, in_array_size=132205* *annot file: /fs04/wr47/Project/Data/NIFTI/Freesurfer7.3.2/sub-002/label/aparc.annot.ctab* *terminate called after throwing an instance of 'int'* It happened when I tried to load any annotation. I can load pial surfaces. I worked in a cluster computer if that helps. Thank you, Kind regards, Jacob -- *Jacob Bunyamin* PhD Student *Department of Neuroscience* Central Clinical School, Monash University 99 Commercial Road Melbourne VIC 3004 *E:* jacob.bunyamin(a)monash.edu

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mri_fdr questions
by Finn, Quentin 02 Aug '23

02 Aug '23

External Email - Use Caution Freesurfer experts, I have a surface overlay that represents -log_10(p) for a statistical test that I ran using tools other than mri_glmfit. Does mri_fdr still give accurate fdr thresholds, or does it require some of the additional files generated by mri_glmfit ? thank you! Houston Methodist. Leading Medicine. U.S. News & World Report has named Houston Methodist Hospital the Best Hospital in Texas* for 12 years in a row and recognized us on the Honor Roll seven times. For more than 100 years, we have provided patients with the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine. *In a two-way tie houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Password request for virtual machine installation
by 深水阳光 02 Aug '23

02 Aug '23

External Email - Use Caution Dear technical personnel: Greeting,  I want to obtain the password so that I can extract the virtual machine file 'FS_7_2_0_ubuntu_18_04_06.ova.zip' Thanks for your time! 深水阳光 hdfghdjghdg(a)foxmail.com  

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Freeview update for FS v6.0.0 on MacOS
by Ha Manh Luu 01 Aug '23

01 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I have installed FreeSurfer v6.0.0 in my MacOS 12.6.7 but I got Freeview crashed due to PETSC error (which has been fixed in FreeSurfer v7.1.1). For the consistency with my previous work, I do not want to upgrade to Freesurfer V7.x in my MAC. I updated the latest freeview from this website: https://secure-web.cisco.com/1GU54Krzar0viM1rYGXBq6dM7Sopf4ca6PYKueDS2-Ie8D… freesurfer-macOS-darwin_x86_64-dev-freeview.tar.gz 2023-07-29 08:52 37M After updating the Freeview, it works for me but whenever I load a pial surface, I got this error message: error: mincRead(): error reading volume from file /Applications/freesurfer/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc I'm not sure this is serious or just relating to the rendering. Could anyone tell me how to fix this? 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: MacOS Darwin 12.6.7 3) freeview: mincRead(): error reading volume from file /Applications/freesurfer/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc 4) FreeSurferColorLUT.txt: see attached Thanks, Ha

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mris_preproc error: cannot allocate memory
by MANSSOUR Wassima 01 Aug '23

01 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I'm conducting the Surface Based Group Analysis explained on the tutoriel (https://secure-web.cisco.com/1_YynvwS-dkAnt9HfkAib_JfSy9UZxarfHbzK2t54zb7qC…) but I keep getting the error: "Cannot allocate memory" while running the mris_preproc command. I'm using the data of 355 subjects stored on an external hard drive, and a pc of 23G RAM, but it stops at the 334 subject. I've already tried with a windows and mac of 16G RAM and got the error, so moved to the other one but still getting the same issue. Does anyone have any thoughts on how to trouble-shoot this? or any other alternative solution to run the mris_preproc on all the subjects? FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platforme: Debian 3.16.7 Thank you for your help, -- Wassima MANSSOUR Master Student at INSEA Rabat M2SI - Information Systems & Intelligent Systems IMRB intern-France wmanssour(a)insea.ac.ma<mailto:wmanssour@insea.ac.ma> wassima.manssour(a)u-pec.fr<mailto:wassima.manssour@u-pec.fr>

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FreeSurfer Pass Code request
by Lewis, Jeramy 01 Aug '23

01 Aug '23

External Email - Use Caution Greetings, I am a postdoc researcher at Washington University School of Medicine in MR imaging and I'm in the process of installing FreeSurfer. I've reached the point where I need a pass code in order to complete the process. I'm installing on a Windows 10 PC utilizing virtual machine Ubuntu. Any assistance is greatly appreciated, [cid:354939e4-69d8-4702-a37f-63865ecb8c58] Jeramy Lewis, PhD Mallinckrodt Institute of Radiology Washington University School of Medicine 4525 Scott Ave, Room 3224 G St. Louis, MO 63110 mobile: 720-885-2044 e-mail: jeramy(a)wustl.edu<https://secure-web.cisco.com/1WGU-kNnE_nPRi0BEIYhcyX3DsBTEe952B3lsHQ44v8CKN…> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Freesurfer August 2023