Freesurfer September 2008

freesurfer@nmr.mgh.harvard.edu

70 participants
96 discussions

LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

4 4

mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

2 1

design matrix : inter-run effetcs
by Andersson Frederic 02 Dec '08

02 Dec '08

Hi, Computing individual fMRI analysis (several runs) and looking at the design matrix (X.mat), I saw that only one regressor represents each condition. I was expecting that the number of regressors concerning a condition would be the number of runs (as SPM). There are "inter-run effect" regressors but is this better if I affect a different value for each of run and each condition (see examples below). Other question concerning design matrix : only 3 movement parameters included in the design matrix. Why 3 rather than the 6 computed during movement correction? Concerning inter-run effects and movement parameters, is there any advantage of reducing the number of regressors but having a less ideal model? >>> 1 condition = 1regressor 0 = rest 1=conditionA 2=conditionB Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 1 15 1 18 1 18 1 18 1 21 1 21 1 21 1 24 1 24 1 24 1 27 1 27 1 27 1 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 2 42 2 45 2 45 2 45 2 48 2 48 2 48 2 51 2 51 2 51 2 54 2 54 2 54 2 57 0 57 0 57 0 >>> 1 condition = 1regressor / run 0=rest 1=conditionA run#1 2=conditionB run#1 3=conditionA run#2 4=conditionB run#2 5=conditionA run#3 6=conditionB run#3 Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 3 15 5 18 1 18 3 18 5 21 1 21 3 21 5 24 1 24 3 24 5 27 1 27 3 27 5 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 4 42 6 45 2 45 4 45 6 48 2 48 4 48 6 51 2 51 4 51 6 54 2 54 4 54 6 57 0 57 0 57 0 Frédéric ANDERSSON.

3 2

FW: [Freesurfer] Talairach_with_skull.lta accuracy
by Jeff Sadino 09 Oct '08

09 Oct '08

Hello, I am trying to validate the ICV value by lining up the nu_noneck image with the RB image. These are the commands I am using: mri_convert nu_noneck.mgz --apply_transform transforms/talairach_with_skull.lta nu_noneck5.mgz tkmedit -f nu_noneck5.mgz & tkmedit -f /apps/freesurfer/average/RB_all_withskull_2006-02-15.gca & When I compare these two, they don't line up. The RB image is all blurry (Maybe it's a combination of several subjects and is supposed to be like that). Any suggestions as to how to line up the noneck transformed imaged to the RB image is greatly appreciated! I also attached three files to show what's happening in my transform process. Thanks, Jeff ---------------------------------------- > Date: Fri, 5 Sep 2008 20:31:55 -0400 > From: fischl(a)nmr.mgh.harvard.edu > To: jsadino(a)hotmail.com > Subject: RE: [Freesurfer] Talairach_with_skull.lta accuracy > > can you send this to the list so others can respond? Where did you get the > tmp.reg file? If you have transformed them already you shouldn't need > tkregister2 (or a registration file in general) to compare them. > > On Fri, 5 Sep 2008, > Jeff Sadino wrote: > >> >> Thank you very much for your help. Your knowledge and quick responses are very much appreciated. >> >> I converted my image into transformed space, but it still does not match the RB image. These are the commands I used: >> >> mri_convert nu_noneck.mgz --apply_transform > transforms/talairach_with_skull.lta nu_noneckt3.mgz >> >> tkregister2 --targ > /apps/freesurfer/average/RB_all_withskull_2006-02-15.gca --reg tmp.reg > --lta /data/040002_S04_bakj/mri/transforms/talairach_with_skull.lta --mov > /data/040002_S04_bakj/mri/nu_noneckt3.mgz >> >> Again, my main goal is to verify the ICV value, so to do that I need to verify that the lta file is transforming the nu_noneck image onto the RB image...I think. >> >> What step am I missing? >> >> Thank you >> Jeff >> >> >> ---------------------------------------- >>> Date: Fri, 5 Sep 2008 13:09:21 -0400 >>> From: fischl(a)nmr.mgh.harvard.edu >>> To: jsadino(a)hotmail.com >>> CC: greve(a)nmr.mgh.harvard.edu >>> Subject: RE: [Freesurfer] Talairach_with_skull.lta accuracy >>> >>> that won't generate a transformed volume, just display it in the >>> transformed space. That is, the volumes you sent were in their native >>> space and would have no reason to be aligned. The neck removal seems to >>> have been fine in both cases. >>> On Thu, 4 Sep 2008, Jeff Sadino wrote: >>> >>>> >>>> ps, sorry, I forgot to include my command: >>>> >>>> >>>> tkregister2 --targ /apps/freesurfer/average/RB_all_withskull_2006-02-15.gca --mov /data/${file}/mri/nu_noneck.mgz --lta /data/${file}/mri/transforms/talairach_with_skull.lta --reg tmp.reg >>>> >>>> I believe this will transform the nu_neck.mgz image via the talairach matrix, so that it matches the RB image. >>>> >>>> btw, we processed the scans using freesurfer 3, but the tkregister2 that came with freesurfer 3 did not include the --lta tag, so I am using the tkregister2 from freesurfer4. >>>> >>>> Thanks! >>>> >>>> ---------------------------------------- >>>>> Date: Thu, 4 Sep 2008 21:49:27 -0400 >>>>> From: fischl(a)nmr.mgh.harvard.edu >>>>> To: jsadino(a)hotmail.com >>>>> CC: freesurfer(a)nmr.mgh.harvard.edu >>>>> Subject: Re: [Freesurfer] Talairach_with_skull.lta accuracy >>>>> >>>>> Hi Jeff, >>>>> >>>>> why do you say that one is bad? We don't resample, so neither one will be >>>>> aligned with the atlas unless you apply the transform. >>>>> >>>>> We are aware that the eTIV measures have more variability than we would >>>>> like, and we're looking into it, but don't have a good solution from only >>>>> T1 images. >>>>> >>>>> cheers, >>>>> Bruce >>>>> On Thu, 4 Sep 2008, >>>>> Jeff Sadino wrote: >>>>> >>>>>> >>>>>> Hello all, >>>>>> >>>>>> According to aseg.stats, our ICV values fluctuate on the same subject across scans, sometimes by up to 10% I have been validating the talairach_with_skull.lta accuracy by comparing the nu_neck.mgz to the RB_all_withskull_2006-02-15.gca template. I read on the boards that it is not all that necessary that the brains match, that it is more important for the skulls to match. The RB is blurred (I don't fully understand where the RB comes from, I think from 22 subjects that the freesurfers combined into one?), so am I matching up the whitest areas of the RB to the skull on the nu_neck image? I noticed also that the bottom of the brains rarely match at all to the RB image...is this normal? Are there any other parts of the image that need to be checked for validity? >>>>>> >>>>>> I attached two nu_noneck.mgz files, one was good and the other bad. Are these images typical? >>>>>> >>>>>> Thank you for your help, >>>>>> Jeff >>>>>> >>>>>> _________________________________________________________________ >>>>>> See how Windows Mobile brings your life together?at home, work, or on the go. >>>>>> http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/ >>>> >>>> _________________________________________________________________ >>>> Get more out of the Web. Learn 10 hidden secrets of Windows Live. >>>> http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!5… >>>> >>>> >>>> >> >> _________________________________________________________________ >> See how Windows connects the people, information, and fun that are part of your life. >> http://clk.atdmt.com/MRT/go/msnnkwxp1020093175mrt/direct/01/ >> >> >> _________________________________________________________________ See how Windows Mobile brings your life together—at home, work, or on the go. http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/

3 2

Re: [Freesurfer] volumes in wmparc.stats vs. aparc.stats
by bell0368＠umn.edu 08 Oct '08

08 Oct '08

I was wondering how the calculations of the wm volume were performed as well. The six values below are volume values from aseg I believe. I assume mris_wm_volume does more than sub-divide these regions into the wm parcellations, but probably also includes partial volume estimations along the wm/gm surface, is this correct? I basically have the same question for the gm volume values in aparc.stats; do they include partial volume calculations from the gm/pial and gm/white borders? Which binary is used to create these values for gm in aparc.stats... is it mri_segstats (with --pv)? I was assuming it would be an mris (surface) calculation as well. I am asking because if you use tkmedit to view the ?h.surface files and load the aparc+aseg or wmparc segmentation volumes in also, the surfaces and the segmentations don't seem to line up. Is there a way to create a segmentation volume that includes partial-volumed voxels at the gray/white and gray/pial boundries? Thanks for your help. Chris Bell the interior voxels are only included in the volume if they are one of the following in the aseg.mgz: case Left_Cerebral_Cortex: case Right_Cerebral_Cortex: case Left_Cerebral_White_Matter: case Right_Cerebral_White_Matter: case Left_WM_hypointensities: case Right_WM_hypointensities: cheers, Bruce On Tue, 15 Jul 2008, Marin Richardson wrote: OK, so aparc.stats is better for cortical gray matter. I want to look at the parcellated white matter volumes as well - is the only/best option to use the wm volumes from wmparc.stats? Also, when using mris_wm_volume to calculate total white matter, I saw the result defined as the volume within the white matter surface minus non-WM structures? Can you tell me which regions are and are not included? Marin Doug Greve <[EMAIL PROTECTED]> 7/15/2008 12:02 PM >>> It is better to use the aparc as it is derived from surface measurements, which have sub-voxel resolution. The wmparc.stats are generated by counting 1mm^3 voxels. doug Marin Richardson wrote: Hi all, I noticed that the gray volumes for parcellated cortical regions in wmparc.stats are different from those for the same region in aparc.stats (e.g. ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = 9466 in lh.aparc.stats). Why are the values different and which one is a better measure to use? Thanks, Marin

4 7

qdec cannot find subjects in qdec.table.dat
by David Qixiang Chen 02 Oct '08

02 Oct '08

Hi, I'm running freesurfer in Ubuntu hardy 2.6.24-19 I've ran into a problem with loading data tables in qdec. I've followed the instructions in tutorial 2a and created associated data tables, but qdec always returned the error: ERROR: QdecProject::VerifySubjects: Couldn't find subject '<sdi>' in SUBJECTS_DIR sh: Syntax error: Bad fd number I've even tried to load the tutorial example files, and had the same errors returned back to me, please assist: Here's the error output: Loading data table /media/STORAGE/buckner_data/tutorial_subjs/group_analysis_tutorial/qdec/qdec.table.dat... Number of columns: 189 fsid column: 1 Number of factors: 188 Number of subjects: 40 Reading discrete factor levels from config file /media/STORAGE/buckner_data/tutorial_subjs/group_analysis_tutorial/qdec/gender.levels...'Male','Female', done. Data table /media/STORAGE/buckner_data/tutorial_subjs/group_analysis_tutorial/qdec/qdec.table.dat loaded. sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '004' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '008' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '017' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '021' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '039' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '040' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '045' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '049' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '067' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '073' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '074' in SUBJECTS_DIR Thanks - David Qixiang Chen

2 1

Default LGI settings
by Martin Kavec 02 Oct '08

02 Oct '08

Hi, I wonder how are the default FS settings to calculate LGI finetuned? More towards large-scale changes, such as in neonal>pediatric cortex, or would it be possible to study rather focal changes, say on a sulcus/gyrus level? Which parameters should I change to become sensitive to "smaller" LGI changes? Thanks a lot for input, Martin

2 1

localGI exits with error
by j janssen 02 Oct '08

02 Oct '08

Hi, i am using version 4.0.5. for two brains out of a larger study, localGI exits with errors, the error message is similar in both brains and looks like: lGI for vertex number 49901 of the outer mesh is 1.9168 lGI for vertex number 50001 of the outer mesh is 2.4523 ratio saved at 50001 lGI for vertex number 50101 of the outer mesh is 3.2668 ... remeasuring lGI value for vertex iV = 50201. It may take a few minutes. WARNING -- Problem for vertex iV = 50201, lGI value is aberrantly high (lGI=43.3799)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. mris_euler_number ?h.pial gives 0 defects. i ran localGI on both brains several times and got the same error message at the same vertex number (for lh). empirically, surfaces look reasonable. a similar message was posted some time ago: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07281.html but no reply. any ideas? thanks, -joost

2 1

convert single-frame dicoms to a multi-frame dicom?
by Qianqian Fang 30 Sep '08

30 Sep '08

hi I know that mri_convert and a few other tools are able to convert a series of dicom files into a 4D (multi-frame?) nifti file. However, is there a way, either using freesurfer or other tools you know, can convert a the dicoms, or a 4D nifti, to a 4D (multi-frame) dicom? thanks Qianqian

2 1

Volume processing question
by Tommaso De Marco 30 Sep '08

30 Sep '08

Hi, I'm a freesurfer user beginner. I need to discretize the gray matter in a cubic mesh. I have extracted the $h.pial and $h.white surfaces, and I would know if it is possible in freesurfer to discretize the volume suttended by these surfaces. I have seen that there are some files called $h.volume; what kind of information is stored in these files? Is it possible to open them in a matlab environment or with tksurfer? Regards Tommaso De Marco

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer September 2008