Freesurfer February 2022

freesurfer@nmr.mgh.harvard.edu

83 participants
132 discussions

Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital 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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Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG
by Donatas Sederevicius 28 Aug '22

28 Aug '22

External Email - Use Caution A new pre-print paper comparing two FreeSurfer’s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selection of the processing method. https://www.biorxiv.org/content/10.1101/2020.10.13.335737v1

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SAMSEG and statistics
by k3ops＠free.fr 27 Aug '22

27 Aug '22

External Email - Use Caution Hi FreeSurfer community, I recently discovered the SAMSEG application in the FreeSurfer 7.2.0 release and started to give a try on few subjects were FreeSurfer was having a hard time to segment brain structures (due to poor contrast). So I have few questions to harmonize the SAMSEG and FreeSurfer statistical files: 1. "samseg.stats" file is not compliant with the "asegstats2table" application so I was not able to generate a final CSV file with volumetric results Is there another solution? 2. "samseg.stats" file does not provide large brain structures like "BrainSegNotVent" or "SupraTentorialNotVent", is there a way to get them calculated? 3. "samseg.stats" file does not provide left/right or global cortical thickness, is there a command line to execute to get these extra values? Thanks. Best, Florent

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Paracingulate
by Roxanna Korologou-Linden 27 Apr '22

27 Apr '22

External Email - Use Caution Hi, I have been reading papers referring to the paracingulate cortex. What does this correspond to in the Desikan-Killiany atlas used in FreeSurfer? I am trying to compare my results to previous studies. I would appreciate your insight. Thanks, Roxanna

2 1

classes for GLM analysis
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 27 Mar '22

27 Mar '22

External Email - Use Caution Hi all, I am doing an analysis and generating the FSGD. I understand sex and race are classes in this context, but something I was also hoping to regress out is the effects of scanner/sequences. We have a large participant size, so we have around 10+ scanner/sequences, which makes for a large amount of classes combinations, with some having just 1 (if not zero) fitting into a class. Would you proceed with this nonetheless? If not, should scanner/sequence be something that we consider? Should we find some other way to adjust site (I don't think we can z-score...). Or can we consider site/scanner as a continuous variable Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Trac-all -prep -c error
by Kaplan, Elizabeth 17 Mar '22

17 Mar '22

External Email - Use Caution Hello All, I am attempting to process images using tracula, however I am running into an error when attempting to run the "trac-all -prep -c" command line. Parcellation was ran on FS 7.2.0, However, I am running the command on freesurfer dev version due to an earlier resolved error reading index file: https://secure-web.cisco.com/1NrhFqWiJIFbTxyFpNb7jAq78TXhI1EKDKQf_a4RRwqAAO… Trac-all exits on the command: CMD mri_binarize --i /autofs/cluster/lazar/Projects/DTIanalysis/Subjects_DTI_t1t2/AG010_1308_T1_LAZAR_recon.long.AG010_1308/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /autofs/cluster/lazar/Projects/DTIanalysis/Subjects_DTI_t1t2/AG010_1308_T1_LAZAR_recon.long.AG010_1308/dlabel/anatorig/aparc+aseg_mask.nii.gz The Trac-all.log reads "mri_binarize done", see attached, and the outputs from the mri_binarize command are present. I used the longitudinal configuration file example on the wiki, attached below. Any guidance on how to navigate the issue would be greatly appreciated! Thank you!

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error with trac-all -prep in FS7.2 tracula
by Alexopoulos, Dimitrios 17 Mar '22

17 Mar '22

External Email - Use Caution Hi all, We are reprocessing some of our data with FS 7.2 to evaluate the new updates to Tracula, however, we are getting errors from the trac-all -prep -c configfile step. The last 20 lines of output are shown below. Anyone have any comments on how to correct this? ------------------------------------- trac-preproc exited with ERRORS at Fri Feb 11 18:18:29 CST 2022lines: 1DIAGNOSTIC, 24, -4.743908838687e-01, 5.860622007851e-05, 4.2190e+01, 1.4997e+00, 1DIAGNOSTIC, 25, -4.743823138430e-01, 4.831431802083e-05, 4.3721e+01, 1.5312e+00, 1DIAGNOSTIC, 26, -4.744830990496e-01, 3.946018283887e-05, 4.5293e+01, 1.5718e+00, 1DIAGNOSTIC, 27, -4.744857576549e-01, 3.343839305766e-05, 4.6879e+01, 1.5857e+00, 1DIAGNOSTIC, 28, -4.744568952592e-01, 2.896457797682e-05, 4.8446e+01, 1.5669e+00, 1DIAGNOSTIC, 29, -4.744930355970e-01, 2.351784987169e-05, 5.0045e+01, 1.5996e+00, 1DIAGNOSTIC, 30, -4.744428763349e-01, 1.764564796251e-05, 5.1621e+01, 1.5762e+00, 1DIAGNOSTIC, 31, -4.744390742695e-01, 1.211632175497e-05, 5.3234e+01, 1.6130e+00, 1DIAGNOSTIC, 32, -4.744465209349e-01, 6.742111363235e-06, 5.4833e+01, 1.5989e+00, 1DIAGNOSTIC, 33, -4.743750058790e-01, 8.816157837238e-07, 5.6420e+01, 1.5867e+00, Elapsed time (stage 2): 58.59 Total elapsed time: 71.08 ConvertTransformFile 3 /data/shimony/shimony2/neonatal/wunder_9_10yo/freesurfer7.2/neo289e/dmri/xfms/diff2syn0GenericAffine.mat /data/shimony/shimony2/neonatal/wunder_9_10yo/freesurfer7.2/neo289e/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux hopper 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux That piece of code is part of the ANTS library. When I look at the code this is what I see (or don't see for that matter) # Register FA nonlinearly to FA template with SyN set cmd = $ANTSPATH/antsRegistrationSyNQuick.sh <-- This ANTs code has $ANTSPATH set cmd = ($cmd -d 3) set cmd = ($cmd -m $dwidir/dtifit_FA.nii.gz) set cmd = ($cmd -f $intertrg) set cmd = ($cmd -o $xfmdir/diff2syn) echo $cmd |& tee -a $LF |& tee -a $CF if ($RunIt) then $cmd |& tee -a $LF if ($status) goto error_exit endif # Convert affine transform to .lta set cmd = ConvertTransformFile <-- This ANTs code DOES NOT have $ANTSPATH ________________________________ 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.

2 2

TRACULA trac-all -prep finishes with errors
by Goeckner, Bryna 17 Mar '22

17 Mar '22

External Email - Use Caution Hi FreeSurfer Developers, I am attempting to run data for several subjects through TRACULA using trac-all -prep, but some of them have finished with errors. I have checked registration for all of them and it looks ok. I am including a link to my config file, and the trac-all.log and trac-all.error files for one subject: https://secure-web.cisco.com/1fMOW2H4XkhFM0lHgtKrt25eEfHZNAPKOFCoBf2ppUW5T2… FreeSurfer version: freesurfer-linux-centos6_x86_64-7.2.0-20210720-aa8f76b Any help you can give me is greatly appreciated. Thanks! Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program

2 2

recon-all outpputs for deep learning
by REEM ABU BAKR BAHATHIQ 13 Mar '22

13 Mar '22

External Email - Use Caution Hello Freesurfer experts I want to apply deep learning to structural brain images processed by Recon-all. My goal is to demonstrate the morphological variation(e.g., gray matter volumes or cortical thickness) of brain regions in structural magnetic resonance imaging using convolutional neural networks (CNN). Then interpret those models on the basis of the region of interest. But I'm still distracted by the model input . I searched before but still couldn't decide which Recon-all output I should use to perform the task. I think I'll use the folder(mri) but I'm not sure which file. can any one guide me . Thanks,

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Freesurfer February 2022