Freesurfer August 2019

freesurfer@nmr.mgh.harvard.edu

100 participants
144 discussions

WM surface including too much gray matter
by Brian Biekman 05 Aug '19

05 Aug '19

External Email - Use Caution To whom it may concern: I'm dealing with an issue in my subjects' recon-all output where the white matter surface extends into the gray matter, especially in the parietal and posterior temporal regions. This is caused by the wm.mgz including too much gray matter. This issue occurs to some degree in every subject's scans. This can be fixed with extensive wm volume edits but since this appears to be a systematic problem, I wanted to find a solution that could be applied to every subject, possibly in the recon-all pipeline. I've tried using an expert parameters 2 different ways to no avail. I've changed the -wlo values in mri_segment but it removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried adding the -prune and -gentle flags to mri_normalize but that appears to make the problem worse. Is there a better approach to try? If necessary, I can send a subject's recon-all output. -- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman(a)uh.edu Brian.Biekman(a)times.uh.edu

4 9

Re: [Freesurfer] [External] Re: mri_deface fails on pediatric brain
by Soichi Hayashi 05 Aug '19

05 Aug '19

External Email - Use Caution We run on our freesurfer through singularity/docker container, and we are currently using Centos7 as the base image to build our freesurfer container, but we can run it on any other Linux based OSes. As far as our hardware goes, we run on variety of hardware including HPC system, public and private cloud platforms and a few dedicated desktop machines at our labs. Thanks! Soichi On Sun, Aug 4, 2019 at 10:55 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Soichi > > I have a fix for you. Can you let us know what kind of hardware/software > env you are running in and we will send it to you? > > cheers > Bruce > > > On Sun, 4 Aug 2019, Soichi Hayashi wrote: > > > > > External Email - Use Caution > > > > Bruce, > > I've uploaded one of the failed subject to surfer.nmr.mgh.harvard.edu > ftp > > server (named t1.nii.gz).Thank you for looking into this problem. > > > > Soichi > > > > On Sun, Aug 4, 2019 at 10:35 AM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > > > > wrote: > > This message was sent from a non-IU address. Please exercise > > caution when clicking links or opening attachments from > > external sources. > > ------- > > > > Hi Soichi > > > > mri_deface isn't really supported anymore, but if you upload a > > subject > > that fails I'll take a look. I would have thought in the ABCD > > subject age > > range it would work > > > > cheers > > Bruce > > On Sat, 3 Aug 2019, Soichi Hayashi wrote: > > > > > > > > External Email - Use Caution > > > > > > Hello. > > > > > > We are running mri_deface on subjects from ABCD (Adolescent > > Brain Cognitive > > > Development) study and many of the subjects are failing on > > mri_deface. > > > > > > $ mri_deface t1.nii.gz > > > $FREESURFER_HOME/average/talairach_mixed_with_skull.gca > > > $FREESURFER_HOME/average/face.gca defaced.nii.gz > > > logging results to defaced.nii.log > > > reading > > > > > '/usr/local/freesurfer/average/talairach_mixed_with_skull.gca'... > > > reading 't1.nii.gz'... > > > changing type of input volume to 8 bits/voxel... > > > MRIchangeType: Building histogram > > > bounding unknown intensity as < 10.3 or > 1461.6 > > > total sample mean = 111.8 (0 zeros) > > > spacing=8, using 2055 sample points, tol=1.00e-03... > > > resetting wm mean[0]: 143 --> 144 > > > resetting gm mean[0]: 89 --> 89 > > > input volume #1 is the most T1-like > > > using real data threshold=11.0 > > > skull bounding box = (54, 38, 18) --> (205, 255, 220) > > > using (104, 110, 119) as brain centroid... > > > mean wm in atlas = 144, using box (85,83,94) --> (122, > > 136,143) > > > to find MRI wm > > > before smoothing, mri peak at 79 > > > robust fit to distribution - 80 +- 8.7 > > > distribution too broad for accurate scaling - disabling > > > WARNING2: gca.c::GCAhistoScaleImageIntensities: > > > h_mri->nbins=111, mri_peak=140 > > > after smoothing, mri peak at 0, scaling input > > intensities by > > > inf > > > GCAhistoScaleImageIntensities: could not find wm peak > > > Numerical result out of range > > > > > > > > > Should talairach_mixed_with_skull.gca template work with > > pediatric > > > subjects? Or is there a different template we must choose? Or > > maybe any > > > parameters that we could tweak to get it work better? > > > > > > Thanks! > > > Soichi > > > > > > > > > > > >

4 3

Re: [Freesurfer] Using Freesurfer Commands for Neonate
by Mahshid Fouladivanda 05 Aug '19

05 Aug '19

External Email - Use Caution Dear Lilla, Thanks for your help. I have used the same command in the recon-all.log file (seen bellow), but I have a doubt for the highlighted part in the command: "mri_aparc2aseg --s SBJ1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gcamri/aseg.auto_noCCseg.label_intensities.txt" which used a predefined file from freesurfer folder. Actually, I used the mri_aparc2aseg command with some changes, seen bellow: mri_aparc2aseg --s mysubj --annot aparc --o $SUBJECTS_DIR/mysubj/mri/parc.mgz so, I am wondered if it reads the ' /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca' automatically. I would appreciate it of you could help on how to correct this part. Regards, Mahshid

1 0

FreeSurfer Import File
by Jiajun Luo 05 Aug '19

05 Aug '19

External Email - Use Caution Hi, I am beginner for FreeSurfer... I want to run recon-all on my MRI T1 data. I have a series of dcm files for an individual and these dcm files are archived in a tgz file. What should I import to FreeSurfer for recon-all? A single dcm file, or some selected dcm files, or all dcm files, or the archived tgz file? Do I need to convert these dcm files to certain types of files? Thank you! Jiajun

3 2

Gray Matter Intensity at each vertex
by Axelson, Eric D 05 Aug '19

05 Aug '19

External Email - Use Caution Is there a way to extract the gray matter intensity value at each vertex of a surface file (lh/rh.curv/pial/etc)? ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

2 1

Re: [Freesurfer] Estimation of surface based smoothing
by Greve, Douglas N.,Ph.D. 05 Aug '19

05 Aug '19

There is no set value for surface or volume. Typically we apply 5-10mm. Surface-based smoothing is more gentle than volume-based, so you can apply larger kernels. On 8/5/2019 2:59 AM, Matthieu VANHOUTTE wrote: External Email - Use Caution Hi Douglas, I was talking about the FWHM smoothing to apply before statistical analysis. I know the FWHM to apply to a volume-based study but wonder what should be apply regarding the surface-based study? Best, Matthieu On 04/08/2019 22:53, Greve, Douglas N.,Ph.D. wrote: can you be more specific? What kind of effects? On 8/4/2019 4:29 PM, Matthieu Vanhoutte wrote: External Email - Use Caution Dear experts, Knowing the size of the effects on volume-based data, does anyone would know a way to estimate the size of the effects on surface data? Best, Matthieu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

subcortical structure accuracy
by Zeng,Victor (BIDMC - Psychiatry) 05 Aug '19

05 Aug '19

?Hi all, For the sake of time, for one dataset we have that we want to extract hippocampal/amygdala/thalamus subfields from, we ran it without manually editing any portions of the brain. We're going to visually QC it, but do you anticipate any trouble with the accuracy of the segmentation considering we didn't remove any portions of the brainmask for dura/blood vessels and etc. Obviously, if we detect that a blood vessel is running through the amgydala, we would remove that and rerun the subfield extraction. Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

1 0

Re: [Freesurfer] Recon-all Error in output - ERROR: nu_correct
by Gregory Mierzwinski 05 Aug '19

05 Aug '19

External Email - Use Caution Hello, Even though this is an old post, the entire solution to this has not been posted and I couldn’t find it anywhere. I hit this error, and I had to (1) make sure the SUBJECT_DIR environment variable was pointing to a directory that is not on the shared Neurodebian folder, and (2) that the data given as input through `-i` was not on the shared folder. Greg

2 1

mri_vol2label with fs v5.3
by Alshelh, Zeynab 05 Aug '19

05 Aug '19

Hi freesurfers, I am currently using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and I need to run $mri_vol2label which I have been informed works with fs v6.0. Is there any way I can use this command or a is there a similar command on v5.3? Thanks in advance, ---- Zeynab Alshelh, PhD | Postdoctoral Research Fellow Pain and Neuroinflammation Imaging Laboratory Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129 +1 (617) 794 6838 zalshelh(a)mgh.harvard.edu | www.nmr.mgh.harvard.edu

2 1

A Question Regarding Topology Correction
by Maedeh Khalilian 05 Aug '19

05 Aug '19

External Email - Use Caution Dear Bruce, The other day I asked you about doing topology correction on my own segmentation(I have put my first e-mail and you response in the following so u can track easier). according to what you suggested, I have created a synthetic T1 volume based on my own segmentation. Now I wonder what to do exactly as the second step. Should I use "mris_fix_topology"? I would be grateful if you could help me with that. Best, Maedeh "Dear FreeSurfer experts, I know that FreeSurfer does segmentation, surface reconstruction and topology correction through its routine pipeline using "recon-all" . However, I have some T2w brain MR images and I have done the segmentation and extracted WM, GM, and CSF with my own algorithm. Now I need to remove back to back (i.e. a part of topology correction) which is caused in sulci due to the segmentation. In other word, after doing my segmentation, I wanna open the closed concavities in CSF that were open originally. Now I wanna know if I can do the topology correction using FreeSurfer while I have done the segmentation by myself? I would be grateful if you could help me with that. Best, Maedeh Hi Maedeh in principle you can, although it would be a lot easier if you just had a reasonable quality T1. If not, you will need to create all the files that recon-all expects to exist prior to the topology correction step (wm.mgz, norm.mgz, orig.mgz, ....). Maybe the easiest thing to do would be to use your gray/white/csf segmentation to create a synthetic T1 volume? Set all the wm voxels to 110, all the gray to 70 and all the csf to 20, or something like that? cheers Bruce"

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2019