Freesurfer

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30132 discussions

Re: [Freesurfer] Combining linear transformations
by Martin Reuter 11 Jul '12

11 Jul '12

Hi Usman , Try validating each step by applying each transform. I usually use mri_convert -at For it. Best MartinUsman Khan <usman(a)bwh.harvard.edu> wrote:Hi Martin, Thanks for the quick reply. I tried the following commands, but it looks like the volumes are still out of line. Is there something I am missing? to get from hc_subfield --> nu.mgz --> t1_cbv #register and create transforms 1) mri_vol2vol --mov hc_subfield.mgz --targ nu.mgz --reg-final xfm_hcsubfield_to_nu.dat --regheader 2) mri_robust_register --mov nu.mgz --dst t1_cbv.mgz --lta xfm_nu_to_t1.lta --satit #convert output from (1) from reg-final.dat to .lta 3) tkregister2 --noedit --mov hc_subfield.mgz --targ nu.mgz --reg xfm_hcsubfield_to_nu.dat --ltaout test.lta 4) mri_concatenate_lta test.lta xfm_nu_to_t1.lta final.lta #apply lta file, using t1_cbv as target and hc_subfield as --mov file 5) mri_vol2vol --mov subfield --targ t1_cbv.mgz --reg final.lta --out test.mgz On Tue, Jul 10, 2012 at 6:10 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Usman, you need to convert the reg to lta (using tkregister2) and then you can use mri_concatenate_lta . Cheers, Martin On Tue, 2012-07-10 at 17:36 -0400, Usman Khan wrote: > Hi FreeSurfer, > I have two images. One MPRAGE (1x1x1mm) and a T1-weighted > (0.682x0.682x3mm) image used for CBV mapping. We have run FS, with > hippocampal subfields on the MPRAGE and would now like to transform > the posterior probability maps to the T1-weighted CBV space. > > > I have been using > 1) mri_vol2vol with --regheader to map the posterior_* subfield files > to nu.mgz space > 2) mri_robust_register to coregister the nu.mgz file to the > T1-weighted CBV image > > > Is there any way to combine the .reg and .lta files from (1) and (2) > to transform the subfield posterior probability maps directly from > their 0.5mm^3 space to the T1-weighted CBV space? I have been > reluctant to create an intermediate volume between steps 1 and 2, as > resampling the subfield probability maps into 1x1x1mm nu.mgz space > will result in loss of resolution to the 0.68x0.68 (coronal) space in > the T1-weighted CBV scan. > > > Any help would be appreciated > > > Usman > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] error message for recon-all
by Muriel Bruchhage 11 Jul '12

11 Jul '12

It worked! Thank you so so much! Best, Muriel On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: > Hi Bruce, > > Thank you very much for your fast response. > > Unfortunately though, I still get an error response when typing in "recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02" > > recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 > 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/MRI_04_2012/GID02/2_T1_3DSAG/DICOM > Actual FREESURFER_HOME /Applications/freesurfer > Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 > /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02 > \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz \n > mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz > corRead(): can't open file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/COR-.info > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM... > Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 > > recon-all -s GID02 exited with ERRORS at Wed Jul 11 18:32:26 CEST 2012 > > For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > Thank you very much in advance for all your help! > > Best, > Muriel > > > On Jul 11, 2012, at 6:20 PM, Bruce Fischl wrote: > >> Hi Muriel >> >> the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i <path to dicom file>. And one acquisition is usually sufficient these days depending on the coil and field strength. We don't use T2s at the moment. >> >> cheers >> Bruce >> >> >> On Wed, 11 Jul 2012, Muriel Bruchhage wrote: >> >>> Hi, >>> I am new to freesurfer and tried to run recon-all on it (I am using a >>> MacBook Pro with Lion if that is of any importance). >>> What I have been done so far: >>> 1) I set my Freesurfer environment in my .tcshrc file to: >>> setenv FREESURFER_HOME /Applications/freesurfer/ >>> source $FREESURFER_HOME/SetUpFreeSurfer.csh >>> source $FREESURFER_HOME >>> setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ >>> 2) I converted my original T1 DICOM files into one MGZ file using the >>> mri_convert command (mri_convert <first dicom>.dcm 001.mgz). Both files can >>> be found under $SUBJECTS_DIR/GID02/2_T1_3DSAG - the MGZ file under a MGZ >>> folder and the DICOMs under a DICOM folder >>> ($SUBJECTS_DIR/GID02/2_T1_3DSAG/MGZ or $SUBJECTS_DIR/GID02/2_T1_3DSAG/DICOM >>> respectively). >>> 3) I tried the recon-all command with both the setenv >>> $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/ andwith $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1 >>> _3DSAG/MGZ where the MGZ file actually lies. >>> Does the fact that I only have one .mgz file have an influence on my data >>> processing? Would a T2 scan count as a second structural scan? >>> As I always get this error message: >>> 1) for running it with recon-all -all -subjid GID02 on setenv SUBJECTS_DIR >>> /Applications/freesurfer/subjects/MRI_04_2012/ >>> [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% ls >>> GID02 GID251 GID51_2 GID70 GID753 >>> GID100 GID28 GID53 GID701 GID76 >>> GID117 GID33 GID549 GID710 VBM >>> GID12 GID47 GID61 GID72 fsaverage >>> GID140 GID51 GID62 GID75 >>> [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% cd >>> GID02/2_T1_3DSAG/MGZ/ >>> [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% ls >>> 001.mgz >>> [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all >>> -subjid 001.mgz >>> ERROR: cannot find /Applications/freesurfer/subjects/MRI_04_2012/001.mgz >>> [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all >>> -subjid GID02 >>> 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/MRI_04_2012 >>> Actual FREESURFER_HOME /Applications/freesurfer >>> -rw-rw-r-- 1 mbruchhage wheel 33313 Jul 11 12:13 >>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log >>> Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu >>> Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 >>> #-------------------------------------------- >>> #@# MotionCor Wed Jul 11 17:54:17 CEST 2012 >>> ERROR: no run data found in >>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/mri. Make sure to >>> have a volume called 001.mgz in >>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/mri/orig. >>> If you have a second run of data call it 002.mgz, etc. >>> See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion >>> Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu >>> Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 >>> recon-all -s GID02 exited with ERRORS at Wed Jul 11 17:54:17 CEST 2012 >>> For more details, see the log file >>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log >>> To report a problem, >>> see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> 2) for running it with recon-all -all -subjid 001.mgz on setenv SUBJECTS_DIR >>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ >>> [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all >>> -subjid 001.mgz >>> mkdir:/Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz: >>> Not a directory >>> cp:/Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz/ >>> scripts/build-stamp.txt: Not a directory >>> cat:/Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz/ >>> scripts/build-stamp.txt: Not a directory >>> INFO: FreeSurfer build stamps do not match >>> Subject Stamp: >>> Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 >>> INFO: SUBJECTS_DIR is >>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ >>> Actual FREESURFER_HOME /Applications/freesurfer >>> /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz: >>> Not a directory. >>> Thank you very much in advance and greetings from Oslo, >>> Muriel Bruchhage >>> >> >> >> 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. >

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slanted
by Borzello, Mia 11 Jul '12

11 Jul '12

Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using "rotate" does help. How should I correct this? Thanks, Mia

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error message for recon-all
by Muriel Bruchhage 11 Jul '12

11 Jul '12

Hi, I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance). What I have been done so far: 1) I set my Freesurfer environment in my .tcshrc file to: setenv FREESURFER_HOME /Applications/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh source $FREESURFER_HOME setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ 2) I converted my original T1 DICOM files into one MGZ file using the mri_convert command (mri_convert <first dicom>.dcm 001.mgz). Both files can be found under $SUBJECTS_DIR/GID02/2_T1_3DSAG - the MGZ file under a MGZ folder and the DICOMs under a DICOM folder ($SUBJECTS_DIR/GID02/2_T1_3DSAG/MGZ or $SUBJECTS_DIR/GID02/2_T1_3DSAG/DICOM respectively). 3) I tried the recon-all command with both the setenv $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/ and with $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ where the MGZ file actually lies. Does the fact that I only have one .mgz file have an influence on my data processing? Would a T2 scan count as a second structural scan? As I always get this error message: 1) for running it with recon-all -all -subjid GID02 on setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/ [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% ls GID02 GID251 GID51_2 GID70 GID753 GID100 GID28 GID53 GID701 GID76 GID117 GID33 GID549 GID710 VBM GID12 GID47 GID61 GID72 fsaverage GID140 GID51 GID62 GID75 [Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% cd GID02/2_T1_3DSAG/MGZ/ [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% ls 001.mgz [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid 001.mgz ERROR: cannot find /Applications/freesurfer/subjects/MRI_04_2012/001.mgz [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid GID02 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/MRI_04_2012 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 mbruchhage wheel 33313 Jul 11 12:13 /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# MotionCor Wed Jul 11 17:54:17 CEST 2012 ERROR: no run data found in /Applications/freesurfer/subjects/MRI_04_2012/GID02/mri. Make sure to have a volume called 001.mgz in /Applications/freesurfer/subjects/MRI_04_2012/GID02/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 recon-all -s GID02 exited with ERRORS at Wed Jul 11 17:54:17 CEST 2012 For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 2) for running it with recon-all -all -subjid 001.mgz on setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ [Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid 001.mgz mkdir: /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz: Not a directory cp: /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz/scripts/build-stamp.txt: Not a directory cat: /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz/scripts/build-stamp.txt: Not a directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz: Not a directory. Thank you very much in advance and greetings from Oslo, Muriel Bruchhage

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cortical thickness and ICA of resting state fMRI
by Mojdeh Zamyadi 11 Jul '12

11 Jul '12

Hi all, I was wondering if anyone knows about any articles that compare/relate cortical thickness analysis with resting state ICA results? More specifically, I'm looking for articles that study cortical thickness changes in different regions of brain and its possible relation to group clusters found using ICA analysis of resting state fMRI. Thanks, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto ON M5G 1X8

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annot 2 surf
by Arnaud Messé 11 Jul '12

11 Jul '12

Dear all, There is a way to convert annot file into surface? -- Arnaud Messé, PhD Laboratoire d'imagerie fonctionnelle (LIF) UMRS 678 Inserm/UPMC CHU Pitié-Salpêtrière 91 boulevard de l'Hôpital F-75634 Paris Cedex 13 +33(0)1538284 03 (fax: 48) Arnaud.Messe(a)imed.jussieu.fr http://www.imed.jussieu.fr

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Fwd: pars triangular and BA44 segmentation bug?
by Gabor Perlaki 11 Jul '12

11 Jul '12

Dear Bruce, Did you also identified a strong rightward asymmetry (with pars triangular and BA44) in your data analyzed by freesurfer 5.1? Just, to be sure, that this is not an issue only with our data. I'd like to use the TRACULA as well, and because tracula uses the cortical parcellation of our subjects I'm not sure that it is worth to start TRACULA now, or waiting for your cortical parcellation fix. Sorry for disturbing you again with the same issue, but it is very important for us to know, that it is a real issue with the cortical parcellation or we messed up something, and if it is a real issue, which labels we shouldn't use for statistical analysis. Thank you in advance for your answer, Gabor 2012/6/25 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > sure. Thanks for pointing out the BA44 issue. We'll put together a fix in > the next couple of weeks > Bruce > > On Mon, 25 Jun 2012, Gabor Perlaki wrote: > > Dear Bruce, >> >> I've checked the pars triangularis. It was right-lateralized in 79 >> subjects >> and left-lateralized in only 19 subjects. >> >> Thanks, Gabor >> >> 2012/6/23 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> the structures don't need a threshold. Do you know that pars >> triangularis is left lateralized? For the BAs will get you a >> solution >> >> On Sat, 23 Jun 2012, Gabor Perlaki wrote: >> >> Dear Bruce, >> >> We don't used any thresholding by ourselves, we just >> took BA44 volumes out >> of the text-file in the stats directory. >> Should we use thresholded values instead of the >> volumes reported by the text >> files in the stats directory? >> Could we use the volumes reported by the aparc.stats >> and aseg.stats files >> for any statistical analyses, or do we need >> threshold that structures as >> well? >> >> >> Thanks, >> Gabor >> >> 2012/6/23 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Gabor >> >> are you thresholding the BA4 label? In 5.2 we >> will distribute >> some tools to automatically threshold the >> labels so that the >> predicted area has the average area of the >> input labels. The >> right BA44 had more spatial spread than the >> left, so you might >> be including a lot of low probability vertices. >> >> cheers >> Bruce >> >> On Sat, 23 Jun 2012, Gabor Perlaki wrote: >> >> Dear Bruce, >> >> In the paper "Left-right asymmetry in >> volume and >> number of neurons in adult >> Broca's area." by Katrin Amunts, 10 >> subjects (5 men >> and 5 women) were >> studied, and the volume of BA44 was >> greater in the >> left hemisphere than in >> the right in all ten cases. So, it is >> very strange >> that the volume of BA44 >> was greater in the right hemisphere in >> all of the 80 >> subjects analyzed by >> Eniko. >> >> Thanks, >> Gabor >> >> >> >> >> 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. >> >> >> >> >> >> >>

2 1

fsgd file
by Jacobs H (NP) 11 Jul '12

11 Jul '12

Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cognitive scores (continuous) and age (continuous). How can I compare two continuous variables? I have tried to list them as two variables in the fsgd (so not class): e.g: Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ age) Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a surface sig file. However, when I look at the scatterplot in tksurfer, I cannot see the two cognitive variables at the same time. Is there a better way to do this? Thanks a zillion times :) Best wishes Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

1 0

Combining linear transformations
by Usman Khan 10 Jul '12

10 Jul '12

Hi FreeSurfer, I have two images. One MPRAGE (1x1x1mm) and a T1-weighted (0.682x0.682x3mm) image used for CBV mapping. We have run FS, with hippocampal subfields on the MPRAGE and would now like to transform the posterior probability maps to the T1-weighted CBV space. I have been using 1) mri_vol2vol with --regheader to map the posterior_* subfield files to nu.mgz space 2) mri_robust_register to coregister the nu.mgz file to the T1-weighted CBV image Is there any way to combine the .reg and .lta files from (1) and (2) to transform the subfield posterior probability maps directly from their 0.5mm^3 space to the T1-weighted CBV space? I have been reluctant to create an intermediate volume between steps 1 and 2, as resampling the subfield probability maps into 1x1x1mm nu.mgz space will result in loss of resolution to the 0.68x0.68 (coronal) space in the T1-weighted CBV scan. Any help would be appreciated Usman

3 3

Finding name of labels
by Sam Carpenter 10 Jul '12

10 Jul '12

Hi all, I have a simple problem that hopefully has a simple solution. I'm going through an annotation file, trying to find the names of select labels. In the tksurfer window at the bottom right it displays the name of the label file that the curser window is hovering over, BUT it only displays the first part of the name, does anybody know how to get the full name of a selected or highlighted label within a loaded annotation file? Thanks in advance. -Sam

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