Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

pre-processing functional data error
by Yangmei LUO 09 Nov '12

09 Nov '12

Hi there, I am a newbie and I used data collected from SIEMENS 3T to practice. It works well when I tried to preprocess structural data using freesurfer. However, there is a problem when I tried to convert the functional data in DICOM into NII using freesurfer. The problem I can not solve, so I turn to you. Could you give me some advice on how to solve this problem? Any help is appreciated! The command I run: * export FREESURFER_HOME=/usr/local/freesurfer /usr/local/freesurfer/bin/mri_convert --in_type dicom --out_type nii I0001.dcm s105.run1.nii* and the result in terminal is */usr/local/freesurfer/bin/mri_convert --in_type dicom --out_type nii I0001.dcm ..nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from I0001.dcm... Starting DICOMRead2() dcmfile = /home/fsl/data/emotion/s105/run1/I0001.dcm dcmdir = /home/fsl/data/emotion/s105/run1 Ref Series No = 3 Found 231 files, checking for dicoms Found 228 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 0 Vs: -nan -nan -nan Second Sorting Counting frames nframes = 228 nslices = 1 ndcmfiles = 228 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=2000.00, TE=30.00, TI=0.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.999945, 0.0104718) k_ras = (nan, nan, -nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is -nan, matrix is: -3.000 -0.000 nan nan; -0.000 -3.000 nan nan; 0.000 0.031 -nan -nan; 0.000 0.000 0.000 1.000;* Thank you very much! Best wishes, Yangmei

2 1

pre-processing error?
by Julia Nantes 08 Nov '12

08 Nov '12

Hello, I am having trouble with the pre-processing step. When I enter the recon-all <subject-id> command I get an error: [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all -s ms_018 ERROR: nothing to do When I enter 'recon-all -s ms_018 -qcache' I get a long list of output but I don't think it worked correctly: [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# recon-all -s ms_018 -qcache Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 root wheel 87913 Nov 8 10:52 /Applications/freesurfer/subjects/ms_018/scripts/recon-all.log Darwin Lisa-Koskis-iMac.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer/ Previous: /Applications/freesurfer /Applications/freesurfer/subjects/ms_018/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Thu Nov 8 11:46:43 EST 2012 INFO: File lh.thickness does not exist! Skipping creation of smoothed data for lh.thickness #-------------------------------------------- #@# Qdec Cache lh area fsaverage Thu Nov 8 11:46:43 EST 2012 INFO: File lh.area does not exist! Skipping creation of smoothed data for lh.area #-------------------------------------------- #@# Qdec Cache lh area.pial fsaverage Thu Nov 8 11:46:43 EST 2012 INFO: File lh.area.pial does not exist! Skipping creation of smoothed data for lh.area.pial #-------------------------------------------- ....etc recon-all -s ms_018 finished without error at Thu Nov 8 11:46:43 EST 2012 done My goal is to eventually be able to bring up my T1 images with the qdec application and segment the motor cortex. When I use the tkmedit command it works correctly (I have converted my files to .mgz already). Do you know if it is a pre-processing error that is preventing me from getting the qdec application to work with my own brain images? I cannot open files in qdec currently. Many thanks, Julia

2 1

FW: FreeSurfer remote access question
by Li, Hua 08 Nov '12

08 Nov '12

Hello, We recently installed freesurfer on an Ubuntu 12.04 workstation for doctors in Emergency room which will be used for CT scan analysis. In such case, remote access is required for multiple users. No difficulty was encountered when we tested tkmedit bert orig.mgz locally. However, it shows error message "GLUT: Fatal Error in tkmedit.bin: visual with necessary capabilities not found." When it was tried remotely. Is there any way that this can be resolved? Thank you. Best, Hua Li System Administrator 3D Imaging Service Massachusetts General Hospital Tel: 1-(617)-726-9465

3 2

Re: [Freesurfer] Total cerebral volume.
by Douglas N Greve 08 Nov '12

08 Nov '12

Hi Zheng, there is something wrong with your math. When I sum up all the columns in your table from Left-Lateral-Ventricle to CC_Anterior, I get 215952 for the first row (you get only 67548). Can you double check your calculations? doug On 10/28/2012 11:53 PM, Zheng Hui wrote: > Forgot to attach the excel file. Sorry for that. > > From: zhenghui <zheng.hui(a)duke-nus.edu.sg > <mailto:zheng.hui@duke-nus.edu.sg>> > Date: Monday, October 29, 2012 11:52 AM > To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Subject: [Freesurfer] Total cerebral volume. > > Hi Doug, > > Thanks for replying. But our datasets do showed that > Sum(all structures (after ICV in the list) except ventricle, CSF, > cerebellum and brainstem) is much smaller SubCortGrayVol. The former > is only about 30-40% of the later. We are using FS 5.1.0 without the > SupraTentorialVol fix.I attached the aseg file for your reference (the > last three columns in the sheet). > > Thanks, > Zheng Hui > > On 10/24/2012 09:01 AM, Zheng Hui wrote: > > > > Hi freesurfer, > > > > We are trying to calculate the total cerebral volume which excludes > cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use > > > > CortexVol + CorticalWhiteMatterVol + SubCortGrayVol > > Or > > CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in > the list) except ventricle, CSF, cerebellum and brainstem) > This should give very close to the same value. I don't think it makes a > difference. > > > > > > Also, I saw Doug's post about the bug fixing for SupraTentorialVol. > To re-run the segstats for longitudinal subjects, any extra step other > than "recon-all –long tpN baseID –segstats" and does it affect any > other structure or just SupraTentorialVol? > It should not affect other structures. > doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

2 2

Surface-based normalization, smoothing and averaging
by Shigetoshi Takaya 08 Nov '12

08 Nov '12

Dear Freesurfer experts, I would like to have your help. I have a volume data of a certain parameter on white/grey matter boundary (X.nii). What I want to do are as follows: Step 1: I want to register it onto a standard space using surface-based alignment and smooth it. Step 2: I want to generate the averaged images of several subjects on the standard inflated surface. My questions are follows: Q1) For Step 1, I guess I need to convert the image using mri_vol2surf (X.nii --> X.mgh), then use mri_surf2surf and mris_smooth. If it is the case what should I use for <target subject name> for mri_sur2surf? Q2) How to do Step 2? Thanks in advance, Shige

2 1

Re: [Freesurfer] fs-fast preprocessing resting state
by Douglas N Greve 08 Nov '12

08 Nov '12

Hi Chris, the problem is that you do not have FSLDIR defined. Assuming you have FSL installed, then setenv FSLDIR /place/where/fsl/is/installed doug On 11/06/2012 09:09 PM, Chris McNorgan wrote: > Hi Doug, > > Attached are two plain-text files: fslog2.txt contains the redirected > terminal output after executing: > preproc-sess -s sub00294 -fsd rest -per-run -surface self lhrh -mni305 > -fwhm 0 &> ~/fslog2.txt > > 294files.txt contains the output of `find` for all files in the > project directory related to this participant *after* executing > preproc-sess, in case any clue can be found in this information (I > omitted files in the log/ directory). > > > Thanks, > Chris -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

process exited abnormally
by Varghese Chikku 08 Nov '12

08 Nov '12

Dear all, I am trying to run recon all and FS will either exists with this.... * child process exited abnormally*.......or just a blank window appears with leaving the system to freeze.So i have to power off the VM and start all over again. Does it have to do with the system requirements.I am using VM,. Thanks a lot, chikku

2 2

Rejoindre mon réseau sur LinkedIn
by Barnali Basu via LinkedIn 08 Nov '12

08 Nov '12

LinkedIn ------------ Barnali Basu souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Barnali Basu http://www.linkedin.com/e/-qq80um-h99hrngj-3q/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Barnali Basu http://www.linkedin.com/e/-qq80um-h99hrngj-3q/rso/29278335/BhlY/name/664711… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-h99hrngj-3q/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

1 0

freeview
by Catherine Bois 07 Nov '12

07 Nov '12

Hi, I am trying to use freeview to look at wm/brainmask etc however the command wont work. The command Im suing is freeview -v wm1_edits_before/mri/wm.mgz:colormap=heat:opacity=0.4 wm1_edits_before/mri/brainmask.mgz \ -f wm1_edits_before/surf/lh.white:edgecolor=blue wm1_edits_before/surf/lh.pial:edgecolor=red \ wm1_edits_before/surf/rh.white:edgecolor=blue wm1_edits_before/surf/rh.pial:edgecolor=red (but i am exchanging paths for my own data). However, it keeps saying that operation console failed, and for some reason, even though Ive set the subject directory to where the files are kept it keeps looking in my home directory. I recently attended a course in freesurfer, but this problem was not explained? Grateful for help.

2 1

Re: [Freesurfer] qcache error
by Douglas N Greve 06 Nov '12

06 Nov '12

Do you have write permissions to the output dir? I noticed a perm error in the log. The recon-all.log file has the permission: -rw-rw-r-- 1 guest phd doug On 11/06/2012 03:53 PM, Berg, S.F. van den wrote: > Hi Doug and Bruce > > There is enough disc space. A text file is attached, this file is created with the "recon-all -s 0050 -qcache |& tee mylog.txt" command. I try the "recon-all -s 0050 -qcache" command. The command start to run but finished with errors. > > Have you got any idea of the problem in this case? Also the recon-all.log file is attached (subject 0050). > > Thanks, > > Stan > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: 05 November 2012 19:37 > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] qcache error > > Do run out of disk space? Also, please send terminal output in a text > file rather than as a snapshot. You can do this with > > recon-all ... |& tee mylog.txt > > doug > > On 11/05/2012 10:21 AM, Berg, S.F. van den wrote: >> Dear Freesurfer experts, >> >> I have got a problem with the qcache function. I have already runned >> 150 subjects with the recon-all command. Before i can work with the >> statistical program qdec i have to smooth the subjects. I want to >> smooth them with the command: recon-all -s<subject> -qcache. The >> command start to run but finished with errors. A overview of the >> terminal output is attached to this email in JPEG format. What is the >> problem in this case? >> >> further information about freesurfer version: >> >> recon-all -version: Id: recon-all, v 1.373 2011/03/15 00:43:47 mreuter >> Exp $ >> >> We run FreeSurfer-Linux-centos5_x86_64-dev-201110315 under Debian >> Squeeze. >> >> Thanks a lot, >> >> Stan van den Berg >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

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