Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Regarding: "mri_segstats error"
by Joel Bruss 09 Jun '11

09 Jun '11

I ran across the same issue reported in: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17687.html The initial question was why mri_segstats did not work and complained: "Error: could not open stats/aseg/stats for writing" If you try to, literally, copy and paste the same command listed in the aseg.stats file: mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --inintensity-name norm--in-intensity-units MR --etiv --subject 004 you'll get the error message, even if you source the freesurfer setup file (/usr/freesurfer/SetUpFreeSurfer.csh). In order to run the command, one needs to type out the complete path to each referenced file: mri_segstats --seg ${SUBJECTS_DIR}/'subject"/mri/aseg.mgz --sum ${SUBJECTS_DIR}/'subject"/stats/aseg.stats --pv ${SUBJECTS_DIR}/'subject"/mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask ${SUBJECTS_DIR}/'subject"/mri/brainmask.mgz --in ${SUBJECTS_DIR}/'subject"/mri/norm.mgz --inintensity-name norm--in-intensity-units MR --etiv --subject 004 (obviously replace ${SUBJECTS_DIR}/'subject" with the correct path and subject ID). I apologize for the lengthy response but I felt the referenced thread ended without truly addressing the problem. Also, when running into the exact same error I was left scratching my head trying to figure it out. Hopefully someone else finds this useful.

2 1

Re: [Freesurfer] Middle line issue
by Wayne Su 09 Jun '11

09 Jun '11

Anybody can help me out? What caused the middle line (both pial and wm boundary) shifted to right side even the wm mask is good? Please see the attached images. Thank you very much. Wayne On 07/06/11 2:58 PM, "Wayne Su" <wsu(a)interchange.ubc.ca> wrote: > > >> Hello, >> I have a subject with very big ventricle. I managed to edit wm.mask and >> aseg.mgz, and rerun the recon-all autorecon2, but the middle line separating >> left/right ventricles is still not right (attached). Is there any way to >> correct it? I¹m using FS 5.1. Thanks. >> >> Wayne >>> >> > > > _______________________________________________ > 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.

2 2

Reading ascii files with tksurfer
by Emma Robinson 09 Jun '11

09 Jun '11

Hi, Can I read ascii surface files using tksurfer? I have tried loading them as surfaces and overlays but without success. Alternatively is there a tool for vtk to surface conversion? Thanks in advance Emma Robinson

2 1

segmentation error
by Alfredo Damasceno 08 Jun '11

08 Jun '11

Hello freesufers, I was inspecting my images for segmentation erros and I found some images where the temporal cortex is correcly identified as cortex but the pial surface line is not correctly outlining this structure (blue arrows in attached figure). How should I proceed to correct it? Thanks in advance Alfredo

2 1

choroid plexus
by Tracy Butler 08 Jun '11

08 Jun '11

Is there a good method to segment choroid plexus and calculate volume? I know it's an aseg label. Thanks, Tracy

3 2

problem with annotation to label
by kwa1＠rice.edu 08 Jun '11

08 Jun '11

Hello, I am deriving a cortical region of interest label from FS from a series of normal controls. I have tried two different methods of obtaining these labels to see which is more consistent but neither are really acceptable. I am interested in the temporal pole label so first I did the normal mri_annotation2label for each subject but I don't know if it is a problem with segmentation or with vertex assignment, the TP labels can be wide and ranging and not consistent. Additionally, I tried taking the fsaverage subject and doing a label2label to map that TP label on to all the subjects but that was not good either. Does anyone know potentially what the problem can be and do you have any suggestions about how I can automatically derive a temporal pole label without having to get into manually drawing them (which would introduce a whole new array of issues with reliability). Thank you very much, Kareem

2 2

Mri_glmfit-sim conceptual question
by John Richey 08 Jun '11

08 Jun '11

Dear freesurfer experts, I have a question about the conceptual use of mri_glmfit-sim. I wish to apply permutation based cluster-correction to my between-groups results (patients vs controls), and it is not clear to me which volume should be the input for this type of simulation. For example, the acceptable input for mri_glmfit-sim appears to be only the ".ces" map, which is not present in my between-groups directory, but only in my lower-level one-sample group means (osgm). This raises the question of whether to run the permutation algorithm 1) one time on the .ces map that results from the total sample OSGM (i.e. patients + controls), or 2) separately on OSGM for patients and then controls. Probably I am mistaken but neither seem to be conceptually correct, as I am mainly interested in the cwp for clusters emerging in the between-groups contrast. Any help would be greatly appreciated!

2 1

pet partial volume correction
by corinna bauer 08 Jun '11

08 Jun '11

Hi all, I am wondering if partial volume is taken into account when calculating average uptake values of pet data. I know that aseg.stats takes partial volume into account and I am wondering if there is something similar in place for pet data? From what I gather, most people when using FreeSurfer correct for partial volume effects by regressing out cortical thickness, but no basis for this correction method has been provided. Any insight would be appreciated. n.b. to obtain the pet uptake values I used mri_segstats --seg mri/aparc+aseg.mgz --sum pet.segstats.dat --i $petanat --ctab rois.txt Thank you, Corinna

2 1

FS5.1 OSX dyld: Library not loaded
by Michael O'Sullivan 08 Jun '11

08 Jun '11

I've encountered the same problem described below despite downloading the new version posted on 26th May. I downloaded freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.dmg today from http://www.freesurfer.net/fswiki/Download I'm running Mac OS X version 10.6.7 (Intel) On attempting to test the installation as described in the instructions with tkmedit bert orig.mgz I get the message dyld: Library not loaded: /usr/pubsw/packages/tcltktixblt/current/lib/libtk8.4.dylib Referenced from: /Applications/IRIS/freesurfer/tktools/tkmedit.bin Reason: image not found Trace/BPT trap Is this the same library dependency issue, i.e. it's not fully fixed in the latest download at least not for my OS? I couldn't find any more recent posts but am new to the list, so apologies if I have. Thanks Mike Nick Schmansky Thu, 26 May 2011 05:59:24 -0700 Hyunwoo (and Mac users), A new build of v5.1 for the Mac (Leopard and Snow Leopard) has been posted. If you downloaded the one posted on May 24th, you will need to get this new one, as the one from May 24th depended on libgfortran, which is not installed natively. Sorry for any inconvenience. N. On Wed, 2011-05-25 at 14:57 -0400, Nick Schmansky wrote: > Hyunwoo (and Mac users), > > We're going to have to post a new build of v5.1 later today which fixes > this problem. In general, our goal is to have a Mac build that doesnt > require special libraries, like libgfortran, but both our build and test > machines had that lib for other reasons, so it slipped through the > cracks during testing. > > I'll post to the list when its ready. It will be identical in usage to > the current Mac 5.1, just without the libgfortran dynamic lib > dependency. > > Nick > > > On Wed, 2011-05-25 at 16:30 +0000, Hyunwoo Lee wrote: > > Dear FreeSurfer > > > > Hello, I am currently trying the following freesurfer version: > > freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwi…> > > and I noticed the following. > > During the first step ( recon-all -i invol1 -i invol2 -subjid > > your_subject_name ), the console displays the following messages: > > ------------------------------------------------------------------------------- > > 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 ******* > > Actual FREESURFER_HOME /Applications/freesurfer > > Darwin mrs.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:17:16 > > PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386 > > dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib > > Referenced from: /Applications/freesurfer/bin/mri_robust_register > > Reason: image not found > > Trace/BPT trap > > dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib > > Referenced from: /Applications/freesurfer/bin/mri_robust_register > > Reason: image not found > > Trace/BPT trap

2 2

Re: [Freesurfer] subcortical mask to MNI152 space
by Douglas N Greve 08 Jun '11

08 Jun '11

Hi Elisa, sorry about that. Yes, use the $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat instead. doug Elisa Golfinopoulos wrote: > Hi Doug, > > Thanks for responding to my inquiry. My version of Freesurfer (v.5) > does not contain > > mni152.mni305.cor.subfov2.dat > > in the average folder. I did notice that the most recent version of > freesurfer has the reg.2mm.mni152.dat > > in the same folder as the subcortical mask. > > Thanks so much for your help! > Take good care. > Elisa > > > On Tue, Jun 7, 2011 at 6:15 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Eventhough they are both in "MNI" space, there is still a > registration that has to be applied. Try something like this: > > > mri_vol2vol --mov > $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz \ > --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ > --reg $FREESURFER_HOME/average/mni152.mni305.cor.subfov2.dat \ > --o ./subcort.mask152.nii > > Elisa Golfinopoulos wrote: > > Hi, > > I would like to normalize the subcort.mask.mgz to MNI152 > space. I have attempted to use the command: > > mri_vol2vol --mov $FREESURFER_HOME/subjects/ > fsaverage/mri.2mm/subcort.mask.mgz > --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz > --o ./subcort.mask152.nii > --reg $FREESURFER_HOME/average/mni152.register.dat > > but when I check the registration with the MNI152 template I > find that the 152 normalized subcortical mask does not align > with the template. The problem is somewhat resolved when I > specify a 180 degree rotation along the x axis (though there > still appears to be some translation error). However, I feel > uncomfortable using rotations/translations without > understanding why the registration is incorrect in the first > place. > > In fact, this problem is making me question whether a > transformation is really necessary since, technically, both > the mask and the target are in MNI space and the registration > of the original MNI 305 subcortical mask with the MNI152 > template looks more accurate than the 152 normalized mask. Any > help that you can offer would be greatly appreciated. > > Cheers, > Elisa > > > -- > Elisa Golfinopoulos > Speech Laboratory > Cognitive and Neural Systems > Boston University > Phone: 617.353.6181 <tel:617.353.6181> <tel:617.353.6181 > <tel:617.353.6181>> > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > > > -- > Elisa Golfinopoulos > Speech Laboratory > Cognitive and Neural Systems > Boston University > Phone: 617.353.6181 <tel:617.353.6181> > -- 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