Freesurfer August 2021

freesurfer@nmr.mgh.harvard.edu

73 participants
101 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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Tracula 7.2 using older structural outputs
by Alexopoulos, Dimitrios 21 Nov '21

21 Nov '21

External Email - Use Caution HI, Can you run Tracula 7.2 using older structural outputs generated with FS 6.0 and 7.1.1? Jim ________________________________ 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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Re: [Freesurfer] Base correction, longitudinal analysis
by Eszter Boros 01 Nov '21

01 Nov '21

External Email - Use Caution Thank you for your answer! I think I should clarify this question a little bit. So this is about correcting the Base. And run recon-all *after *correcting the Base. What command should I use here? if I want to regenerate only the Base after correcting it? Because the common below does not work: (ERROR: must specify subjects for base subject using -base-tp) recon-all -base OAS2_0057 -autorecon-pial But if I use "recon-all -base OAS2_0001 -tp OAS2_0001_MR1 -tp OAS2_0001_MR2 -all" that just creates a new Base based on the cross MR1 and MR2. My question is how can I regenerate the corrected Base? What command should I use? Thank you so much! All the best, Eszter Boros Eszter Boros <boros.eszter0226(a)gmail.com> ezt írta (időpont: 2021. aug. 8., V, 19:04): > Dear FreeSurfer Team, > > I am working on a longitudinal pipeline and after correcting the Cross and > generating the Base, I can still see some pial problems sometimes (on the > Base). > > I read on the Freesurfer website that it is possible to correct and > regenerate only the Base, but when I use this command: > > recon-all -base OAS2_0057 -autorecon-pial > > /where OAS2_0057 is the name of the Base/ > > I get the following error message: > > ERROR: must specify subjects for base subject using -base-tp > > > Why is this not working? I am using Freesurefer 7.1.1. > > Thank you so much! > > All the best, > Eszter Boros > >

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WM or Pial edits to correct surfaces
by Alexopoulos, Dimitrios 27 Sep '21

27 Sep '21

External Email - Use Caution Hi users, We're having some issues with running some of our 2-3yo data (0.8mm isotropic) through FS7 with and without the -hires flag. There are persistent issues with the frontal lobe regions where the pial has not extended to outer surface as illustrated below. The WM surface contour look reasonable but the pial has underestimated the outer cortex resulting in an incorrect surface (below). I don't think control points will work (low intensity values in the 50-60s), and no WM to add to the WM.mgz. Any suggestion on how to push the pial surface out to capture the cortical surface?? Thx. Jim [cid:image004.png@01D752FB.04011E10] [cid:image005.jpg@01D752FB.04011E10] [cid:image001.png@01D752F8.E6507AC0] [cid:image002.png@01D752F8.E6507AC0] [cid:image006.png@01D752FB.04011E10][cid:image007.jpg@01D752FB.04011E10] ________________________________ 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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lme_mass_F error
by Emmanuel Nwosu 24 Sep '21

24 Sep '21

External Email - Use Caution Dear All I am running the longitudinal post processing statistical analysis and this error comes up each time I run the lme_mass_F. Does anyone have an idea of why this is happening and how to resolve it. Any help will be appreciated *************************************************************************************************** F_lstats = lme_mass_F(tlstats,CM); Computing F statistics, degrees of freedom and P-values ... Error using lme_mass_F (line 92) The source code (/matlab filepath/lme_mass_F.m) for the parfor-loop that is trying to execute on the worker could not be found. Caused by: Undefined function 'fcdf' for input arguments of type 'double'. Error using remoteParallelFunction (line 84) Worker unable to find file. Undefined function 'fcdf' for input arguments of type 'double' **************************************************************************************************** Kind regards Emmanuel

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Announcing FreeSurfer version 7.2
by Douglas N. Greve 23 Sep '21

23 Sep '21

We are please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check out https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes doug

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Segmentation of thalamic nuclei: LGN volume
by Marco Aiello 20 Sep '21

20 Sep '21

External Email - Use Caution Dear Freesurfer experts, I'm running (FS 7.1.1) segmentThalamicNuclei.sh on T1 scan from recon-all. On a sample of about 100 subjects I've found an average volume of 250 mm^3 and 290 mm^3 for LGN-left and LGN-right, respectively. Consistent with literature, I would expect an LGN volume around the order of 100 mm^3. Do you have any suggestions to address this issue? Best, Marco An example of left thalamic nuclei stats on a subject: # Left Thalamic nuclei volume statistics as created by segmentThalamicNuclei.sh 1 1 0 179.160119 AV 2 2 0 89.639229 CeM 3 3 0 40.504433 CL 4 4 0 298.704524 CM 5 5 0 29.204221 LD 6 6 0 323.610060 LGN 7 7 0 172.804240 LP 8 8 0 16.699212 L-Sg 9 9 0 370.292762 MDl 10 10 0 1028.359432 MDm 11 11 0 99.816768 MGN 12 12 0 16.307111 MV(Re) 13 13 0 4.583480 Pc 14 14 0 46.055844 Pf 15 15 0 8.414055 Pt 16 16 0 274.769665 PuA 17 17 0 276.059756 PuI 18 18 0 197.470981 PuL 19 19 0 1329.257389 PuM 20 20 0 540.769724 VA 21 21 0 48.461021 VAmc 22 22 0 879.500725 VLa 23 23 0 1143.223136 VLp 24 24 0 33.606403 VM 25 25 0 1224.126516 VPL 26 26 0 8671.400807 Whole_thalamus

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Mask Correlation Analysis Area by Yeo Network
by Haley Park 06 Sep '21

06 Sep '21

External Email - Use Caution Hello, I would like to run a correlation analysis but limit the analysis area to three of the seven networks of the Yeo 2011 network parcellations. Would this be possible? Would I do it via a --mask option in mri_glmfit? Thank you, Haley

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Freesurfer August 2021