Freesurfer

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30130 discussions

Finding Intracranial volume
by Mirsol Choi 01 Nov '23

01 Nov '23

External Email - Use Caution Hi fellow freesurfers! I am a Masters student currently working with diffusion images. I would like to ask you experts how I can obtain ICV from my T1/T2 or diffusion images. Is there a certain output from recon-all that produces intracranial volume? Or is there a different command I must use? Thank you all so much for your time. I look forward to hearing from you. Peter

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NIH R25 Course : Training in Advancd Statistical Methods in Neuroimaging and Genetics, Salt Lake City, Utah, April 15-26, 2024. Extended deadline!
by ROBERT CARY WELSH 01 Nov '23

01 Nov '23

External Email - Use Caution Hi everybody, We are pleased to announce that the application portal is still open for the NIH funded 2024 session of the course, “Training in Advanced Statistical Methods in Neuroimaging and Genetics”. We hope you pass this email on to your local neuroimaging community. The course will start on Monday, April 15, 2024 and finish on April 26, 2024 and is to be held in person, in Salt Lake City, Utah, United States at the University Guest House Conference Center. Our course also includes an ongoing (throughout the year) continuing education portion. The course is an intensive 2-weeks, about 8 hours per day of a mix of lectures and hands-on computer labs. neurostatsbootcamp.org<http://secure-web.cisco.com/1GCutdK2bppCWbDssYqZS8SY5rngQjhQqY0KSWKrPj_Czf8…> Due to recently increased funding, we are pleased to announce we can drop our tuition this year to $2250 (from $3000). Strictly financial need scholarships will also still be offered. Tuition includes hotel accommodations at the University Guest House (arrival on April 14 with departure on April 26), breakfast, lunch, day time snacks, three dinners out as a group, and the planned evening activities. All course attendees will arrange for their own transportation to Salt Lake City. The course cost does include a daily pass to the Salt Lake City Trax light rail/commuter system. (Please note that the course instructors' effort is supported by the NIH grant thus avoiding that cost being passed on to the course attendees. This course is strictly not-for-profit.) Because of the limited size and advanced nature of the course, attendance is by application only – please make sure to fully read the website instructions. In general, applicants must be a US citizen, permanent resident, or working with an appointment at a US institution, though we do have the ability to accommodate 3 to 6 individuals that do not meet this criteria. We anticipate the total class size to be between 22 and 25 students. There are opportunities for scholarships which can partially offset hotel accommodations. These are based on true financial need and you will be instructed how to apply if you are admitted to the course. We look forward to seeing you in SLC in 2024! Priority application deadline is Nov 1, 2023; decisions around Dec 5th. Late application deadline is Dec 1, 2023; decisions by Jan 5th, 2024. For more information email us at neurostats(a)g.ucla.edu<mailto:neurostats@g.ucla.edu> or advancedstatisticscourse(a)utah.edu<mailto:advancedstatisticscourse@utah.edu> Robert and Anna ------------------------------ Robert Welsh, PhD Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics rcwelsh(a)g.ucla.edu<mailto:rcwelsh@g.ucla.edu> robert.c.welsh(a)utah.edu<mailto:robert.c.welsh@utah.edu> Anna Docherty, PhD Associate Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics anna.docherty(a)utah.edu<mailto:anna.docherty@utah.edu> Christina Caldera Course Administrator neurostats(a)g.ucla.edu<mailto:neurostats@g.ucla.edu>

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mri_cvs_register failure
by Antonín Škoch 01 Nov '23

01 Nov '23

External Email - Use Caution Dear experts, I have encountered a total failure of mri_cvs_register --mov my_subject --mni The resulting output file final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz looks like in the attachment. Could you please give me a hint, where could be a problem, or how to troubleshoot the mri_cvs_register routine? Regards, Antonin Skoch

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Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs
by Huang, Yujing 31 Oct '23

31 Oct '23

It looks like seg2recon is also looking for FREESURFER. Set it to your Freesurfer install directory, same as FREESURFER_HOME. From: Maya Yablonski <mayay(a)stanford.edu> Sent: Tuesday, October 31, 2023 7:08 PM To: Huang, Yujing <YHUANG43(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs External Email - Use Caution Thanks! That seems to do the trick and it started running, but crashed after a few minutes. The log file shows the last thing that ran was this command: seg2recon --s sub-xx --seg PATH/sub-xx/mri/synthseg.rca.mgz --i /PATH/sub-xx/mri/orig.mgz --threads 1 followed by this error: FREESURFER: Undefined variable. Should I define this variable in addition to FREESURFER_HOME and SUBJECTS_DIR? Where should it point to? Thanks for the help! Maya

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TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz
by Lauren Stephens 31 Oct '23

31 Oct '23

External Email - Use Caution Hi FreeSurfers, 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 two 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! Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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Using Synthseg segmentations to fix recon-all outputs
by Maya Yablonski 31 Oct '23

31 Oct '23

External Email - Use Caution Hello, I am working with a pediatric sample for which we are seeing many segmentation errors using the standard recon-all pipeline (version 7.3.2). Running synthseg on the same input files improves the segmentations dramatically, and I would like to be able to fix the surface files (?h.white, ?h.pial) according to the synthseg segmentation. I could not find how to do this in the documentation? Can I place the synthseg.nii.gz file somewhere and rerun recon-all? or autorecon? Would appreciate any pointers to the right way to go about this! Alternatively, I ran recon-all-clinical and that also seems to work well on our data, however the output folder is not identical to the standard recon-all folder, so I can not use that with other preprocessing pipelines that rely on freesurfer output (e.g. fmriprep). I would appreciate any advice on how to leverage the synthseg outputs instead of manually editing the segmentations! Thank you, Maya

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Freesurfer crash when loading "volume" surf
by Mirsol Choi 27 Oct '23

27 Oct '23

External Email - Use Caution Hi there, I have processed a t1 image using recon-all function, and when I try to open the surface file "lh.volume" or "rh.volume", freesurfer crashes everytime. This crash also occurs for other surface files as well, such as "lh.area.pial". Attached is the error message, do you know how I can go about this? For your reference I am using a macOS, running freesurfer 7.4.1. Thank you, I look forward to hearing from you. [image: Screen Shot 2023-10-26 at 6.41.05 PM.png] [image: Screen Shot 2023-10-26 at 6.41.55 PM.png]

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Re: [Freesurfer] Freesurfer crash when loading "volume" surf
by fsbuild 27 Oct '23

27 Oct '23

External Email - Use Caution If you have been launching Freeview using the Finder by double clicking on the icon, then try running it from the command line in a terminal to open a file, e.g. in bash or zsh ... $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh… output deleted ... … set the environment variable FS_LICENSE to point to your license file, e.g., put license.txt file you received via email after you registered into your home directory under /Users/<your userid> ... $ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou(a)somedomain.com.   <— email address you used to register with $ which freeview/Applications/7.4.1/bin/freeview … test displaying a known to be good volume … $ freeview  $SUBJECTS_DIR/bert/mri/brain.mgz If the above works, then try opening your file(s) from the command line instead of the volume file listed above. - R. On Oct 26, 2023, at 20:42, Mirsol Choi <mirsol(a)ualberta.ca> wrote:        External Email - Use Caution        Hi there, I have processed a t1 image using recon-all function, and when I try to open the surface file "lh.volume" or "rh.volume", freesurfer crashes everytime. This crash also occurs for other surface files as well, such as "lh.area.pial". Attached is the error message, do you know how I can go about this?For your reference I am using a macOS, running freesurfer 7.4.1.Thank you, I look forward to hearing from you. <Screen Shot 2023-10-26 at 6.41.05 PM.png><Screen Shot 2023-10-26 at 6.41.55 PM.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Linear Mixed Models for Functional Data
by Emily Iannazzi 26 Oct '23

26 Oct '23

External Email - Use Caution Hi there, We are trying to conduct functional linear mixed model analyses on our longitudinal (2 timepoint) data but are having trouble applying the structural documentation to functional data, particularly with the functions fs_read_label.m, fs_read.surf.m, and fs_read_Y.m. For instance, in the function [Y,mri] = fs_read_Y(‘lh.thickness.sm10.mgh’), which file should we be reading for functional data (instead of cortical thickness)? Additionally, do any of the subsequent steps (building design matrix, model specification, parameter estimation) require further information to be adapted for functional data? Any help would be greatly appreciated, Emily -- Emily Iannazzi (she/her) Adult Clinical Psychology University of Washington

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Stools error query
by Elizabeth Haris 25 Oct '23

25 Oct '23

External Email - Use Caution Hi there, I am running into a problem when using qatools.py to qa my recon-all. Some of my participants process ok, but with others I get the error below. Any advice on what to do to address this? Many thanks, Elizabeth ERROR: Computing white and gray matter SNR for orig.mgz ... Traceback (most recent call last): File "/Applications/freesurfer_v7.1.0/python/scripts/qatools.py", line 17, in <module> qatoolspython.run_qatools(subjects_dir, output_dir, subjects, shape, screenshots, fornix, outlier, outlier_table) File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/qatoolspython.py", line 883, in run_qatools _do_qatools(subjects_dir, output_dir, subjects, shape, screenshots, fornix, outlier, outlier_table) File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/qatoolspython.py", line 663, in _do_qatools wm_snr_orig, gm_snr_orig = checkSNR(subjects_dir, subject, SNR_AMOUT_EROSION, ref_image="orig.mgz") File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/checkSNR.py", line 83, in checkSNR b_wm_data[x,y,z] = 1 IndexError: index 256 is out of bounds for axis 2 with size 256

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