Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

QA_tools missing signal to noise calculation
by Knut J Bjuland 15 Oct '12

15 Oct '12

Hi, I have downloaded the latest QA_tools v1.1 from http://surfer.nmr.mgh.harvard.edu/fswiki/QATools. However, when I ran recon_checker, I did not get a signal to noise calculations. I ran recon_checker with -s-dir subjectfile and -snaps-detailed. Is there any option that I missed? Is it possible to download a newer version from cvs? Knut J

2 2

Lobe measures
by Mahinda Yogarajah 15 Oct '12

15 Oct '12

Dear Experts, I apologise for the repost but I was wondering if anyone could guide me with respect to deriving lobar measures and whether the commands below are correct . Thanks. M GM Lobar Values (1) mri_annotation2label --subject subject1 --hemi ?h --lobesStrict lobesfile (2) mri_anatomical_stats –mgz –cortex ../label/?h.cortex.label –f ../stats/?h.lobesfiles.stats –b –a ../label/?h.lobesfile.annot subject1 ?h white Q: Is this valid? Q:Do I need to include that part of the command in italics (-cortex...?hcortex.label) - is it not redundant given the use of the ?h.lobesfile.annot - using one or the other does give a different result at the top of the stats file (namely NumVert, WhiteSurfArea, and mean thickness which disappears if ?h.cortex.label is not passed) - why is this ? WM Lobar Values (1) mri_annotation2label --subject subject1 –hemi ?h --lobesStrict lobesfile (2) mri_aparc2seg --s subject1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.lobar.mgz --ctxseg aparc+aseg.mgz --annot ?h.lobesfile.annot Q: Is this valid ? Q: Do I need all the items in italics (hypo...rip...volmask) - they are present in the recon-all logfile but not in some forum posts on similar topics. (3a) mri_segstats --seg mri/wmparc.lobar.mgz --sum stats/wmparc.lobar.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject1 --surf-wm-vol --surf-ctx-vol --totalgray --ctab newcolourtable --etiv OR (3b) mri_segstats --seg mri/wmparc.lobar.mgz --sum stats/wmparc.lobar.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/norm.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject1 --surf-wm-vol --ctab newcolourtable --etiv Q: Which of these should I be using - the latter is based on the recon-all log file, while the former is based on forum posts - what are the differences. Thanks. Mahinda

2 1

Question about inferior temporal lobe topological/control points anomalies
by pietro de rossi 15 Oct '12

15 Oct '12

Dear FreeSurfer users and developers, I'm getting very frequently some bilateral inferior temporal lobe topological/control points anomalies. I attach an example with and without segmentation on. It seems to me that they are not affecting the pial surface's shape (inferior aspect of right temporal lobe attached in first picture. Should I edit and rerun recon? Thank you very much Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

2 1

set a breakpoint in malloc_error_break to debug Bus error in recon-all
by pietro de rossi 15 Oct '12

15 Oct '12

Hi free surfer users and developers, for the first time I got this error after running recon-all: CORRECTING DEFECT 76 (vertices=36299, convex hull=8085) mris_fix_topology(74305) malloc: *** mmap(size=1148719104) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin HG-01881507-DM7.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 recon-all -s 122 exited with ERRORS at Sat Oct 13 22:31:01 EDT 2012 What can I do to fix the problem? Thanks in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

2 4

ERROR: inputs have mismatched dimensions! when running recon -i dicom -i dicom -s
by Knut J Bjuland 15 Oct '12

15 Oct '12

Hi, When I import one subject with recon -i dicom -i dicom -s subjec, I get this error message ERROR: inputs have mismatched dimensions! I think it is caused by the fact that there is a different number of slices into the two series. One series has 256x256x125 white the other has 256x256x128. How can I detect if there is missing slices in the series with 125 slices? What would you recommend me to do? Is is possible to ask recon-all to bypass this error message and import both series? Knut J output k_ras = (-1, 0, 0) writing to /home/knutjb/freesurfer/subject_dir/subject/mri/orig/001.mgz... ERROR: inputs have mismatched dimensions! /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D/MR.9677.100 is 256 x 256 x 125 while /home/knutjb/freesurfer/subject_dir/dicom/subject_dicom/t1_mpr_sag_3D2/MR.9677.235 is 256 x 256 x 128 Linux dmed4960 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

2 6

Tksurfer display issue
by leemon albert 15 Oct '12

15 Oct '12

Hi, everyone. The tksurfer can't initial a window in iOS 10.7.5. Has anyone met this before? Last login: Mon Oct 15 10:57:04 on ttys001 -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl $ system_profiler SPSoftwareDataTypeSoftware: System Software Overview: System Version: Mac OS X 10.7.5 (11G63) Kernel Version: Darwin 11.4.2 Boot Volume: Macintosh HD Boot Mode: Normal Secure Virtual Memory: Enabled 64-bit Kernel and Extensions: Yes Time since boot: 1:56 $ tksurfer bert lh pial subject is bert hemi is lh surface is pial surfer: current subjects dir: /Applications/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/canlab06 checking for nofix files in 'pial' Reading image info (/Applications/freesurfer/subjects/bert) Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Applications/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=132501, faces=264998 surfer: single buffered window surfer: tkoInitWindow(bert) then it stopped here and does#t have any respond. I tried several times with different subjects, but failed with the same issue. Does anyone have any ideas? Thanks a lot. Best Wishes Meng

1 0

Error with mris_calc
by Christopher Coello 15 Oct '12

15 Oct '12

Dear Freesurfer community, Using freeview, I can visualize that two binary volumes are overlaying in some parts. freeview -v binF1.mgz -v binF2.mgz When using the command mris_calc -o out.mgz binF1.mgz mul binF2.mgz to create the intersection of these two volumes, I obtain a file with only zeros. To debug, I added the two volumes mris_calc -o out.mgz binF1.mgz add binF2.mgz I was surprise to see that one of the volumes (binF1) is shifted of tens of voxels along an axis. When doing mris_calc -o out.mgz binF2.mgz add binF1.mgz, the binF2 is shifted. Is that a bug ? mris_calc : v.1.37.2.4 2011/04/04 freeview : v1.0 2011/05/22 Best, Christopher -- Christopher Coello, Ph.D. Preclinical PET/CT unit http://www.med.uio.no/imb/english/research/about/infrastructure/pet/ Institute of Basic Medical Sciences Faculty of Medicine, University of Oslo tel. +4745154516

5 5

Re: [Freesurfer] WM/GM boundary changes and control points
by EK Kim 15 Oct '12

15 Oct '12

I've been struggling to upload the file to the ftp server, but failed in several times. Sorry for bothering you, but I will send an e-mail when the uploading is done. Best, EK 2012/10/14 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > I found EK_test.zip, but neither tar nor unzip knows how to uncomress it. > What format is it? Or maybe it's corrupted... > > > On Sat, 13 Oct 2012, EK Kim wrote: > > Bruce, and other experts, thank you for your time :) >> >> I'm now uploading the data folder (before cp and after cp) to the >> freesurfer incoming directory. >> >> >> We obtained the 3D-SPGR axial images using 3T GE system which have >> 8HRBRAIN receiving coil. >> Data acquisition matrix is 320-by192, FOV is 200-by-200. >> >> Other parameters; >> slice thickness =1.5 >> TR=5.924 >> TE=1.472 >> Flip angle: 20 >> Inversion Time=400 >> Imaging Frequency 127.88 >> Percent Phase FOV =80 >> >> Sincerely, >> >> EK >> >> >> >> 2012/10/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi EK >> >> that is a really low-contrast image. Can you tell me about the >> acquisition parameters and resolution? Also, I can't >> diagnose your problem from just the volume I'll need the entire >> (tarred and gzipped) subject directory. Finally, >> please cc the list on these emails so that others can help you! >> >> Bruce >> On Thu, 11 Oct 2012, EK Kim wrote: >> >> I uploaded the files to transfer/incoming folder. >> >> >> Best, >> >> EK >> >> 2012/10/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> If you upload the subject to our FTP site I will take a >> look >> Bruce >> >> >> >> On Oct 10, 2012, at 9:29 PM, EK Kim <ksea03(a)gmail.com> wrote: >> >> Thank you for your answer. >> I'm not sure I understand your question right, >> but I just processed the file using following procedures. >> 1. recon-all -autorecon1 -nuintensitycor-3T (because mine was >> 3T) >> 2. skullstripping brain mask using gcuts >> 3. adding control points (only on the left hemisphere) >> 4. recon-all -autorecon2-cp >> and this figure was made by a commnad line, [tkmedit wm.mgz >> -aux >> brain.mgz -surfs]. >> Best, >> EK. >> >> 2012/10/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> what was the name of the file that you transferred? >> On Wed, 10 Oct 2012, EK Kim wrote: >> >> I already uploaded this problem 2 days >> ago, reprocessing the subject to make >> sure about control points. >> However when I added the control points >> to the left hemisphere, >> the right hemisphere surface was changed >> severely. >> I used the command line, recon-all >> -autorecon2-cp -s subjectID. >> Could you tell me why does it occur and >> how to deal with it? >> >> >> Best, >> >> EK >> >> >> >> >> 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<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. >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >> >> >>

1 1

Re: [Freesurfer] WM/GM boundary changes and control points
by EK Kim 13 Oct '12

13 Oct '12

Bruce, and other experts, thank you for your time :) I'm now uploading the data folder (before cp and after cp) to the freesurfer incoming directory. We obtained the 3D-SPGR axial images using 3T GE system which have 8HRBRAIN receiving coil. Data acquisition matrix is 320-by192, FOV is 200-by-200. Other parameters; slice thickness =1.5 TR=5.924 TE=1.472 Flip angle: 20 Inversion Time=400 Imaging Frequency 127.88 Percent Phase FOV =80 Sincerely, EK 2012/10/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi EK > > that is a really low-contrast image. Can you tell me about the acquisition > parameters and resolution? Also, I can't diagnose your problem from just > the volume I'll need the entire (tarred and gzipped) subject directory. > Finally, please cc the list on these emails so that others can help you! > > Bruce > > On Thu, 11 Oct 2012, EK Kim wrote: > > I uploaded the files to transfer/incoming folder. >> >> >> Best, >> >> EK >> >> 2012/10/11 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> If you upload the subject to our FTP site I will take a look >> Bruce >> >> >> >> On Oct 10, 2012, at 9:29 PM, EK Kim <ksea03(a)gmail.com> wrote: >> >> Thank you for your answer. >> I'm not sure I understand your question right, >> but I just processed the file using following procedures. >> 1. recon-all -autorecon1 -nuintensitycor-3T (because mine was >> 3T) >> 2. skullstripping brain mask using gcuts >> 3. adding control points (only on the left hemisphere) >> 4. recon-all -autorecon2-cp >> and this figure was made by a commnad line, [tkmedit wm.mgz -aux >> brain.mgz -surfs]. >> Best, >> EK. >> >> 2012/10/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> what was the name of the file that you transferred? >> On Wed, 10 Oct 2012, EK Kim wrote: >> >> I already uploaded this problem 2 days >> ago, reprocessing the subject to make >> sure about control points. >> However when I added the control points >> to the left hemisphere, >> the right hemisphere surface was changed >> severely. >> I used the command line, recon-all >> -autorecon2-cp -s subjectID. >> Could you tell me why does it occur and >> how to deal with it? >> >> >> Best, >> >> EK >> >> >> >> >> 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<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. >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >>

2 1

talairach.xfm error frequency
by Eric Cunningham 12 Oct '12

12 Oct '12

Greetings, I am trying to determine how bad a talairach.xfm registration has to be to warrant a manual edit. I have found that even minor edits can have noticable (9%) effects on major subcortical volumes (such as thalamus or hippocampus). Very few registrations seem to have completely failed, but most seem like they could be made better by a tweak here or there. At what point would I just be adding randomness by manually editing? About what percent of a given dataset would you expect to manually edit? Much appreciated, -Eric Cunningham

2 5

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