Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30133 discussions

(no subject)
by Hugh Pemberton 24 Jan '14

24 Jan '14

Hi freesurfer crew, I found some details through this website http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/i… about cortical thickness maps with freesurfer. I have done some reading but can't really make much sense of how I might do this for a single subject through freesurfer. I have already done autorecon 2 and 3 and so have the cortical thickness stats but would like to put it into a map such as this one: [image: [Click to enlarge image]]<http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/f…> Could you possibly advise on how I might go about this? Would be much appreciated. Many thanks and all the best, Hugh

3 2

Source Code not accessible
by Thomas Frank 24 Jan '14

24 Jan '14

Hello, I tried to get freesurfer's source code after registering and receiving the password for the read-only-cvs. The login command from https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS is simply failing with a timeout like this: # cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login Logging in to :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:2401/usr/fscvsroot CVS password: cvs [login aborted]: connect to fsvm.nmr.mgh.harvard.edu(155.52.242.23):2401 failed: Connection timed out The timeout happens even when I do not use the correct password. Does anyone has any suggestions? Best regards, Thomas

2 1

Editing-related Wiki pages
by Harms, Michael 24 Jan '14

24 Jan '14

2 1

converting binary cortical GM ribbon mask to mative T1 space
by Alexopoulos, Dimitrios 24 Jan '14

24 Jan '14

Hi, We'd like to map the cortical GM ribbon on our original single volume native space anatomical T1. The dataset has been run through recon-all -all. The 'rawavg.mgz' or '001.mgz' is the native space T1 and 'ribbon.mgz' is the cortical GM mask in freesurfer space, correct? I converted the ribbon.mgz to native T1 space using: mri_label2vol --seg ribbon.mgz --temp rawavg.mgz --o ribbon-in-rawavg.mgz --regheader ribbon.mgz Is this the correct procedure? Thanks. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email.

2 1

converting binary cortical GM ribbon mask to native T1 space
by Alexopoulos, Dimitrios 24 Jan '14

24 Jan '14

We'd like to map the cortical GM ribbon on our original single volume native space anatomical T1. The dataset has been run through recon-all -all. The 'rawavg.mgz' or '001.mgz' is the native space T1 and 'ribbon.mgz' is the cortical GM mask in freesurfer space, correct? I converted the ribbon.mgz to native T1 space using: mri_label2vol --seg ribbon.mgz --temp rawavg.mgz --o ribbon-in-rawavg.mgz --regheader ribbon.mgz Is this the correct procedure? Thanks. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email.

1 0

FW: poor grey/white distinction in superior part of scan
by Matt Glasser 24 Jan '14

24 Jan '14

From: Christine Smith <cnsmith(a)ucsd.edu> Date: Thursday, January 23, 2014 3:58 PM To: Matt Glasser <matt(a)ma-tea.com> Subject: Re: [Freesurfer] poor grey/white distinction in superior part of scan Please note that the left and right sides of the brain are flipped for freesurfer vs the dicom picture. Please find attached a dicom picture that is oriented the same way as freesurfer. Sorry for any confusion. On Thu, Jan 23, 2014 at 1:56 PM, Christine Smith <cnsmith(a)ucsd.edu> wrote: > Dear Matt, > > Please find attached two pictures. One is of the brain from reconstructed > dicom files (using AFNI). The other one is a pic from tkmedit of the same > subject and approximately the same slice of brain. Notice that the freesurfer > image is very bright. Look at the white matter and pial lines (i.e., cortical > thickness) in the upper left hand part of the image and see how thin the > cortex appears. Notice also, that there is very little grey/white contrast in > this same area in the brain image reconstructed from dicoms. > > Please let me know if there are any other pictures you might desire or > information you might need. > > Christine > > > On Thu, Jan 23, 2014 at 11:33 AM, Matt Glasser <matt(a)ma-tea.com> wrote: >> Some pictures would probably be helpful to know what the issue is. >> >> Peace, >> >> Matt. >> >> From: Christine Smith <cnsmith(a)ucsd.edu> >> Date: Thursday, January 23, 2014 1:05 PM >> To: <freesurfer(a)nmr.mgh.harvard.edu> >> Subject: [Freesurfer] poor grey/white distinction in superior part of scan >> >> Hello, >> >> I am emailing to inquire about whether poor grey/white contrast in one part >> of a scan (i.e., the posterior and superior part of the scan; ~parietal >> cortex) can be addressed. The contrast in other parts of the scan looks good >> and freesurfer does a great job of distinguishing white from grey. For the >> parietal cortex area the cortex appears very thin. In addition, the entire >> brain appears 'white' or bright, even though the brain doesn't look this >> bright if you reconstruct it from dicoms. >> >> We have now obtained 4 scans like this, so it isn't just one person with >> thinning cortex. >> >> How can I make an adjustment to only this superior part of the brain and >> leave the rest of it alone? Or do I need to make an adjustment to the >> intensity early on for the entire scan and then basically start over with >> editing? >> >> Best, >> Christine >> >> -- >> Christine N. Smith, Ph.D. >> Department of Psychiatry >> University of California, San Diego >> _______________________________________________ Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listin >> fo/freesurfer The information in this e-mail is intended only for the person >> to whom it is addressed. If you believe this e-mail was sent to you in error >> and the e-mail contains patient information, please contact the Partners >> Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail >> was sent to you in error but does not contain patient information, please >> contact the sender and properly dispose of the e-mail. > > > > -- > Christine N. Smith, Ph.D. > Department of Psychiatry > University of California, San Diego -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego

2 1

Fwd: QDEC error
by Wanda Truong 23 Jan '14

23 Jan '14

---------- Forwarded message ---------- From: Wanda Truong <wanda.truong.87(a)gmail.com> Date: 23 January 2014 16:57 Subject: QDEC error To: freesurfer(a)nmr.mgh.harvard.edu Hello, I am having trouble with my group analysis using QDEC. I have 3 groups, 72 subjects, and 4 covariates. This is the error I get: Loading data table /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/qdec.table.dat... Number of columns: 438 fsid column: 1 Number of factors: 437 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. I've attached my qdec.table.dat file and fsgd file as well. I initially created the columns using excel and I copied and pasted it into a .txt. file. Could this be the problem? If so, what would be a better method? Thanks very much, Wanda -- Wanda Truong, MSc -- Wanda Truong, MSc

2 1

Corrections to the segmentation lead to giant defects
by Thomas Fink 23 Jan '14

23 Jan '14

Dear Freesurfer experts, We are using FS 5.1 and have several participants with errors in the segmentation of the hippocampus and other regions of the cortex. So far we did corrections to the hippocampus but in 10 out of 13 participants we got error messages listed below: Seven participants: ----- CORRECTING DEFECT 0 (vertices=74686, convex hull=1605) Excessive topologic defect encountered: could not allocate 390335770 edges for retessellation Cannot allocate memory Darwin NPSY.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 ----- One participant: ----- mhtVoxelList_Add(189, 240, 290, 260205): complete list too big! mhtVoxelList_Add(189, 240, 290, 260205): complete list too big! No such file or directory marking ambiguous vertices... Too many intersected faces for face 255461 (126442, 128896, 128873) No such file or directory Darwin NPSY.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 ----- One participant: ----- CORRECTING DEFECT 14 (vertices=33317, convex hull=1285) mris_fix_topology(26738) malloc: *** mmap(size=1212047360) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin NPSY.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 ----- One participant: ----- Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 414500 ambiguous faces found in tessellation segmenting defects... Bus error Darwin NPSY.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 ----- The error log says in all cases that there is something wrong with the cerebellum. When we open the ?h inflated.nofix file then we see the cerebellum added (see attached file) in the hemisphere we made the edits. We have no clue if or what we are doing wrong and here are the steps we did: - open the files (tkmedit subject norm.mgz -aseg.mgz - Tool -> Configure Segmentation Brush info -> select the hippocampus -> add voxels - File -> save segmentation - run recon with "recon-all -autorecon2 -noaseg –autorecon3 -subjid subject -nuintensitycor-3T" So far we had no problems with our subjects for all the previous steps (recon after wm, pial, .... edits) and it did run smoothly. Any help would be greatly appreciated. Thomas Fink Mail: Thomas.Fink(a)psy.lmu.de

2 1

Help Thickness Reproducibility
by Thiago Junqueira 23 Jan '14

23 Jan '14

Dear FreeSurfers I am having some troubles to run step 4 of protocol to thickness reproducibility. The error message is below: nf04:~> mris_surface_stats -nsmooth 100 -surf_name /home/nf04/subjects/t_pac01/su > > rf/lh.white -out_name > > /home/nf04/subjects/groupstudy/lh_std_60.mgh -absmean > /home/nf04/subjects/groupstudy/lh_absmean_60.mgh -mean > /home/nf04/subjects/groupstudy/lh_mean_60.mgh -absstd > /home/nf04/subjects/groupstudy/lh_absstd_60.mgh > > /home/nf04/subjects/groupstudy/tpac02_lh_thicknes_diff_resampled_to_tpac01.mgh > Perform 100 steps of smoothing of input data > using /home/nf04/subjects/groupstudy/lh_std_60.mgh as output file > using /home/nf04/subjects/groupstudy/lh_absmean_60.mgh as output file > for > abs-mean > using /home/nf04/subjects/groupstudy/lh_mean_60.mgh as output file for > mean > using /home/nf04/subjects/groupstudy/lh_absstd_60.mgh as output file > for > std-of-abs-mean > reading > > /home/nf04/subjects/groupstudy/tpac02_lh_thicknes_diff_resampled_to_tpac01.mgh... > Smooth input data by 100 steps > ERROR: MyMRISsmooth: Surf/Src dimension mismatch > Stats over surface (76117 vertices): mean = 0.368766, std = 1.02826, > absmean = 0.790395, absstd = 0.754038 > > I would appreciate so much any help. > > Many thanks > Thiago Junqueira Medical Physicist, Msc Student in Neuroimage Neuroimage Lab and Medical Physics Lab University of Campinas Phone: +55 19 8809-9476

2 1

mri_surfcluster
by krista kelly 23 Jan '14

23 Jan '14

Hi all, I have obtained laterality indices using xhemi analyses and would like to use FDR instead of the mri_glmfit-sim suggested in the xhemi instructions. I know to get the FDR threshold from tksurfer, but I want to restrict the clusters to a certain cluster size. Based on a previous thread ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html ) I think this should be done using mri_surfcluster but I am having trouble with the actual commands. I've tried this but it doesn't seem to work: mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54 --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf fsaverage_sym --hemi lh the error = srcsubjid must be supplied If I'm performing this on a group file (not individual subject), what would I even input as the subjid? Or do I have this totally wrong? Thanks! Krista

2 3

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