Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Salvaging brainmasks
by Rakshathi Basavaraju 01 Feb '23

01 Feb '23

External Email - Use Caution Dear FS, A few of my brainmasks were excessively stripped and I used watershedding to correct them. Many I could set right. But a few scans despite playing around with different h values if I cannot restore the cut parts of the brainmask what is to be done in that case? Should I discard the same? Thanks, Dr. Rakshathi Basavaraju (M.D. Psychiatry) Assistant Professor (Department of Health Research-sponsored return-home research fellowship) Principal Investigator - OPCINSS Department of Psychiatry National Institute of Mental Health and Neurosciences (NIMHANS) Bengaluru, Karnataka, India-560029 Phone: +91-9480829898/+91-80-26972156/+91-80-26995320

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FreeSurfer load nifti error
by Siamak Sorooshyari 01 Feb '23

01 Feb '23

External Email - Use Caution Dear FreeSurfer, I am using the FieldTrip software to process MEG data, it involves my using the function ft_read_mri() in MATLAB to read in the anatomical MRI file. I have tried feeding into this function a .nii.gz as well as the unzipped .nii version. In the latter case I get an error: ERROR: D:\...\anat\sub-0249_ses-01_run-1_T1w.nii, read in 21626880 voxels, expected 10813440 I contacted the FieldTrip folks and they mentioned that it's a FreeSurfer issue. I think I've isolated the issue to the load_nifti.m file with the "nitemsread" variable and "nvoxels" variables not matching in value. I am not clear why this would happen, how can this be fixed? Best, Siamak

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Correlating two modalities in group-level surface-based analyses
by Betsy Bartlett 01 Feb '23

01 Feb '23

External Email - Use Caution Hello, Does Freesurfer offer the option for group-level surface-based vertex-wise analyses comparing two imaging modalities? For example, I want to find clusters of vertices where cortical thickness and a PET, DTI, or fMRI measure mapped onto the surface are significantly correlated in my cohort of subjects. If this is possible in Freesurfer, is there any existing documentation you could point me to for setting up the fsgd and contrast files? Thank you!

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License issue
by Sayre, Christopher 31 Jan '23

31 Jan '23

External Email - Use Caution Hello all, I have gotten my license.txt file and I have copied it to the $FREESURFERHOME Directory. When attempting to use freesurfer I am getting the following error. Error parsing licensing file, expected 4 values. Looking at the file there are 4 lines in the file. Does anyone have any ideas? Thanks, Chris Sayre Systems Engineer Fralin Biomedical Research Institute at VTC<https://secure-web.cisco.com/1PzAXQtNRov_9n6NeWXa7FjyosKE41mO7DpnfmPqJRkLlS…> Health Sciences and Technology 2 Riverside Circle, Roanoke, VA 24016 O: 540-526-2012 | E: csayre(a)vtc.vt.edu<mailto:csayre@vtc.vt.edu> Recent Media Stories<https://secure-web.cisco.com/1y6if2h3SmT5W2Rm9gz7mb-HZ2jABcD5Hd70fNAPhelxxY…> | Facebook<https://secure-web.cisco.com/1KgborgQJrN48EUgjnrUvqAZP2tewy53jjaVf4BctRQ2Ct…> | Twitter<https://secure-web.cisco.com/1yw6tLfQz5sl-rBmwJc4G5o1evZt5c9y7niDmL2gyEa6o2…> | Instagram<https://secure-web.cisco.com/1Z0qi8rSf3A-X6MOlIQq2Z8hZFZz5h9HAXd2CDvXEMc5u4…> | LinkedIn<https://secure-web.cisco.com/1nH3SOkljui4g5BNqYv1yGRm9toe1_4mvU7fJbMfYcvVvE…> [signature_1749735209]

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Re: [Freesurfer] [SPAM]: Re: License issue
by Sayre, Christopher 31 Jan '23

31 Jan '23

External Email - Use Caution Sorry about this. I had the file in infant freesurfer not freesurfer. Thanks! Thanks, Chris Sayre Systems Engineer Fralin Biomedical Research Institute at VTC <https://secure-web.cisco.com/1xTR8rYicZ5IJQQ-EDdPxqiRFVPcQgQU3PxDQ-bKeHRqmq…> Health Sciences and Technology 2 Riverside Circle, Roanoke, VA 24016 O: 540-526-2012 | E: csayre(a)vtc.vt.edu Recent Media Stories <https://secure-web.cisco.com/1X0SxrdDhW8WynbglsFvb5d-KExa5VkkxfLE4RXMOtW3rS…> | Facebook <https://secure-web.cisco.com/1POh1UQ_drq7IQg3r0U3ptDsyC9fXQpBnyVL6e_sk-uE9U…> | Twitter <https://secure-web.cisco.com/1BSCgANoqITXW9nuyuHYk92CX1ic6ZVJaE31KyazuDCe-3…> | Instagram <https://secure-web.cisco.com/1Mohb5jnD26o8u-5ioqVpGCirRdW3oouBwjgv1nEKD9OU2…> | LinkedIn <https://secure-web.cisco.com/1oqguQ3Daqsim8yYL17-2EM94tV_RZUoXOCqNoIEVsrOHe… YvMDqBYIxCONZiVXRp62-hhA8UDdYuf54awmUfim6bpYxztPhMzokB7M3xSZbR6c0SnfuBFf809Y6DQ/https%3A%2F%2Fwww.linkedin.com%2Fcompany%2F19066634%2F> On 1/31/23, 1:28 PM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Wighton, Paul" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of PWIGHTON(a)mgh.harvard.edu> wrote: Hi Chris, What version of FreeSurfer are you using? There are some issues with the license file with really old (<6.0) versions, but the 5.3-HCP version should work. https://secure-web.cisco.com/1zb7C3gxbLxG8sPZPC56xwWH2dMAzSsksDVAdvrFlFy13N… -Paul ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Sayre, Christopher <csayre(a)vtc.vt.edu> Sent: Tuesday, January 31, 2023 12:21 PM To: Freesurfer support list Subject: [Freesurfer] License issue External Email - Use Caution Hello all, I have gotten my license.txt file and I have copied it to the $FREESURFERHOME Directory. When attempting to use freesurfer I am getting the following error. Error parsing licensing file, expected 4 values. Looking at the file there are 4 lines in the file. Does anyone have any ideas? Thanks, Chris Sayre Systems Engineer Fralin Biomedical Research Institute at VTC<https://secure-web.cisco.com/1PzAXQtNRov_9n6NeWXa7FjyosKE41mO7DpnfmPqJRkLlS…> Health Sciences and Technology 2 Riverside Circle, Roanoke, VA 24016 O: 540-526-2012 | E: csayre(a)vtc.vt.edu<mailto:csayre@vtc.vt.edu> Recent Media Stories<https://secure-web.cisco.com/1y6if2h3SmT5W2Rm9gz7mb-HZ2jABcD5Hd70fNAPhelxxY…> | Facebook<https://secure-web.cisco.com/1KgborgQJrN48EUgjnrUvqAZP2tewy53jjaVf4BctRQ2Ct…> | Twitter<https://secure-web.cisco.com/1yw6tLfQz5sl-rBmwJc4G5o1evZt5c9y7niDmL2gyEa6o2…> | Instagram<https://secure-web.cisco.com/1Z0qi8rSf3A-X6MOlIQq2Z8hZFZz5h9HAXd2CDvXEMc5u4…> | LinkedIn<https://secure-web.cisco.com/1nH3SOkljui4g5BNqYv1yGRm9toe1_4mvU7fJbMfYcvVvE… _hGiOA4dLta9Nuf7V-gX7lyFMqpwz-CngNiVnT1P4rKxiH30l0Ln5HdS0Xdh4uo2p0QCjKbUd_jqmQ/https%3A%2F%2Fwww.linkedin.com%2Fcompany%2F19066634%2F> [signature_1749735209]

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Opening for research engineer position based in Tours (Loire Valley, France)
by briend 31 Jan '23

31 Jan '23

External Email - Use Caution Dear colleagues, Apologies for double posting, The INSERM-U1253 & University of Tours research unit based in Tours (Loire Valley, France) invites applications for a research engineer position to begin as soon as possible on cognitive neuroscience methodologies. A good command of written and spoken French is requested of all applicants. Prospective candidates should also contact directly Marie Gomot (marie.gomot(a)univ-tours.fr) Please include the following documents in your application (as a single PDF-file): Cover letter and curriculum vitae. For more information, and to apply: Follow this link* Frederic Briend * https://secure-web.cisco.com/1f7AdKWFpC1jtfmp6TJI2MWV2Ug2R8yxHmHoVS5EM8BAOv…

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Re: [Freesurfer] Skull stripping with external brainmask
by Iglesias Gonzalez, Juan E. 30 Jan '23

30 Jan '23

Dear Narlon, I believe you can add -xmask [mask_volume_file] to your recon-all command. To generate such external mask, maybe you could use mri_synthseg with the --robust flag and binarize the output? Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Boa Sorte Silva, Narlon" <narlon.silva(a)ubc.ca> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, January 30, 2023 at 01:14 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Skull stripping with external brainmask External Email - Use Caution Hi there, I just wanted to follow-up on this. Thanks! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon On Jan 18, 2023, at 7:33 PM, Boa Sorte Silva, Narlon <narlon.silva(a)ubc.ca> wrote: Dear FreeSurfer experts, I dealing with some issues regarding skull stripping in FreeSurfer (v7.1.1). It seems like the conventional approaches (e.g., adjusting -wsthresh) doesn’t seem to help. As well, applying these preprocessing steps to the raw T1w BEFORE processing in FreeSurfer doesn’t seem to help either. I have tried: intensity truncation, N4 bias field correction, data normalization (with different combinations). Considering that we’re analyzing data from a large dataset (>500 scans * multiple timepoints), manual editing may not feasible. Therefore, to address poor skull stripping, I was wondering if it is possible to use a brain mask created outside FreeSurfer for the same subject to help with skull stripping. I saw in previous emails in the Archive that the steps below could work. Can someone confirm if this is still true and would work for v7.1.1? 1. run recon-all (as one normally would) 2. apply mri_mask to mask the T1.mgz with external brain mask volume (in native space) 3. name the output “brainmask.mgz” and move it to "subjid/mri/“ 3. re-run recon-all starting from -autorecon2 -autorecon3 Thanks for your help! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon

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A doubt regarding autorecon after watershedding
by Rakshathi Basavaraju 30 Jan '23

30 Jan '23

External Email - Use Caution Dear FS, I intend to examine cortical thickness correlates of negative symptoms in my schizophrenia sample. I ran recon-all and corrected a few brainmasks which were excessively stripped by watershedding with different h values (ran autorecon-pial for those watershedded). I am attaching a few screenshots of scans where the segmentation is erroneous and the aseg omits the right temporal and parietal or cerebellar regions. How do I set this right? [image: Screenshot 2023-01-27 at 3.37.46 PM.png] [image: Screenshot 2023-01-27 at 3.29.47 PM.png][image: Screenshot 2023-01-27 at 3.26.29 PM.png][image: Screenshot 2023-01-27 at 3.32.08 PM.png] Dr. Rakshathi Basavaraju (M.D. Psychiatry) Assistant Professor (Department of Health Research-sponsored return-home research fellowship) Principal Investigator - OPCINSS Department of Psychiatry National Institute of Mental Health and Neurosciences (NIMHANS) Bengaluru, Karnataka, India-560029 Phone: +91-9480829898/+91-80-26972156/+91-80-26995320

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Fw: error: Numerical argument out of domain; error: MRIhistogramLabelRegion: constant image\00
by adriana.jorge＠unibe.ch 30 Jan '23

30 Jan '23

External Email - Use Caution Here follows my previous email, with the logs. Best, Adriana ________________________________ From: Jorge, Adriana (ARTORG) Sent: Tuesday, January 10, 2023 2:31 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: error: Numerical argument out of domain; error: MRIhistogramLabelRegion: constant image\00 Hi FreeSurfer Developers, I'm trying to obtain brain parcellations/segmentations of a subject's brain, using T1 and T2 images, but when I execute the recon-all command, I get the following error message: error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image error: Numerical argument out of domain error: MRIhistogramLabelRegion: constant image Segmentation fault Linux sharky 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux recon-all -s Test_withT2 exited with ERRORS at Tue Jan 10 13:17:00 CET 2023 The FreeSurfer version I'm currently using is the freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275, but I have also tried the exact same process (same command and same data) in the freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 version and got the exact same error message. When I tried running the recon-all again with the freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b version, no error was reported and the recon-all outputs were correct. Recon-all works for versions reesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275 and freesurfer-linux-ubuntu18_x86_64-7.3.0-20220718-7725d89 if I use only the T1 image. The recon-all logs for the 2 failed and the 1 successful attempts are attached here. Can you help me figure out what the issue is? Why can't I run the recon-all using both T1 and T2 in the latest versions? Best, Adriana Jorge

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What if FS fails
by Rakshathi Basavaraju 30 Jan '23

30 Jan '23

External Email - Use Caution What is to be done if we get such an error message for recon-all: (copied from recon-allstatus log) status file for recon-all Tue Jan 3 22:43:36 IST 2023 #@# MotionCor Tue Jan 3 22:43:41 IST 2023 #@# Talairach Tue Jan 3 22:43:53 IST 2023 #@# Talairach Failure Detection Tue Jan 3 22:47:14 IST 2023 #@# Talairach Tue Jan 3 22:47:15 IST 2023 #@# Talairach Failure Detection Tue Jan 3 22:50:31 IST 2023 #@# Talairach Tue Jan 3 22:50:32 IST 2023 #@# Talairach Failure Detection Tue Jan 3 22:53:29 IST 2023 Darwin JAGADISHAs-Mac-mini.local 21.2.0 Darwin Kernel Version 21.2.0: Sun Nov 28 20:29:10 PST 2021; root:xnu-8019.61.5~1/RELEASE_ARM64_T8101 x86_64 recon-all -s subj39_anat exited with ERRORS at Tue Jan 3 22:53:30 IST 2023 Dr. Rakshathi Basavaraju (M.D. Psychiatry) Assistant Professor (Department of Health Research-sponsored return-home research fellowship) Principal Investigator - OPCINSS Department of Psychiatry National Institute of Mental Health and Neurosciences (NIMHANS) Bengaluru, Karnataka, India-560029 Phone: +91-9480829898/+91-80-26972156/+91-80-26995320

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