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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 ================================================

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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

2 1

WM edit problems
by Charles Frank 10 Jul '12

10 Jul '12

Freesurfer experts, I am having problems generating a corrected wm boundary after editing the wm.mgz volume. After control points were placed and ran with the command autorecon2-cp, I noticed that the yellow line became overzealous and included gm in some of the slices. To fix this I followed the tutorial “fixing Non-white matter classified as white matter”. I fixed all the slices that had the problem in a certain area. However, after running autorecon2-wm and autorecon3 the edits to the wm.mgz volume remain and yellow line does not change....i.e. The edits that were made remained, but had absolutely no effect on the wm boundary. I am using version 5.0. I have included some screen shots of a certain area that was targeted correction. These shots are taken after the data was ran through autorecon2-wm and autorecon3. Any suggestions of what I'm doing wrong would be very appreciated. Thanks Chuck

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(no subject)
by Charles Frank 10 Jul '12

10 Jul '12

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no-aseg for make_average_subject
by Leon 10 Jul '12

10 Jul '12

Hi, FreeSurfer experts I want to generate an average surface and volume using make_average_subject command based on some of my non-human primate data, which do not have aparc.annot data. I wonder if it is possible with FS. From the archive, I found some emails entitled "no seg", in which a --no-seg switch was used and may help on solving this problem. However, from my FS v5.0, I could not find this switch in either the make_average_subject or make_average_surface/volume commands. Could someone tell me how I could turn on this switch and try if it will help to generate a surface without aparc.annot files? Thank you very much in advance! Leon

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