Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

fixing bad tal registrations
by Garth Coombs 16 Mar '10

16 Mar '10

Hi, I recently ran into a problem with some of my tal registrations during the recon-all process (see below message to Martino's Tech). In order to fix the problem, it was suggested that we run bbregister outside of the recon-all stream and then feed that registration into the subsequent recon stages. Does this make sense, and how would I go about doing this? I'm not sure what the --mov file should be, or if there is a way to specify fstal as the reference structural. Thanks for your help! -Garth Hi Doug & FreeSurfers, I recently re-ran a large number of recons and have been checking to make sure they all ran correctly, and I have come up with a couple of questions about the talairach transform/recon checking. For some of my recons, the green line outlining the white matter on the individual brain extends slightly further than the cortex surface of the fstal brain. While it looks relatively well aligned (e.g. ventricles, brain stem), the fstal brain looks slightly too small for the subject's brain. Additionally, the green outline tends to extend into the skull of fstal in the sagittal plane. An example is: setenv SUBJECTS_DIR /autofs/space/brownie_003/users/gcoombs/ SUBJECTS_DIR/ tkregister2 --mgz --fstal --surf orig --s amac_anat or tkregister2 --mgz --fstal --surf orig --s amra_anat In order to fix these talairach transforms, it seems like the best option would be to scale the brain; however, we will be doing a cortical thickness analysis on this group, and we do not want to scale the brain if it will somehow affect the outcomes. Is this something we should worry about? Another question we have is about general recon quality control: when checking that the recons ran smoothly, what should we look for? I look to make sure that the pial and white matter surface lines don't include dura or any other matter and that they follow the structures correctly, skull stripping, and intensity normalization, but is there anything else that is particularly important? Any advice would be greatly appreciated! Thanks, Garth

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DTI Analysis
by Ryan 16 Mar '10

16 Mar '10

Hello all, I'm doing a volumetric group analysis of DTI data and am now stuck. I ran mri_preproc, mri_info, and mri_glmfit to create sig.mgh. I run the following command and load sig.mgh as an overlay: tkmedit fsaverage brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white I'm wondering if this is the correct usage for the sig.mgh file, and if someone could point me in the right direction for what steps are next? Thank you. -Ryan

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Correction at the cluster level in Freesurfer
by Olivier Colliot 16 Mar '10

16 Mar '10

Hi Freesurfers, I was wondering if there exists a procedure in Freesurfer to have corrections for multiple comparisons at the cluster level (as in SPM for example). Many thanks Olivier

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optseq2 installation
by Florence POMARES 16 Mar '10

16 Mar '10

Forget the previous message, we can run it now. Thank you for your response De : Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Date : 15 mars 2010 18:51:19 HNEC À : Florence POMARES <florence.borgetto(a)univ-st-etienne.fr> Cc : freesurfer(a)nmr.mgh.harvard.edu Objet : Rép : [Freesurfer] optseq installation what do you mean it is not recognized? To make it executable, you need to run chmod a+x optseq2 to run it, either put it into your PATH, or cd to where it is located and run ./optseq2 the "./" is necessary if it is not in the PATH doug Florence POMARES wrote: Dear Doug, Thank you for your answer. We run it from shell (a comand window of X11 because we are connected to the server by the way of a MacIntosh) but it isn't recognized. How can we make it executable ? We just upload optseq2 on the Linux server... Le 12 mars 10 à 20:30, Florence POMARES a écrit : Début du message réexpédié : *De : *Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu >> *Date : *12 mars 2010 20:09:57 HNEC *À : *Florence POMARES <florence.borgetto(a)univ-st-etienne.fr <mailto:florence.borgetto@univ-st-etienne.fr >> *Cc : *freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu > *Objet : **Rép : [Freesurfer] optseq installation* Did you make it executable? They are run from the shell, not matlab. doug Florence POMARES wrote: Dear Optseq Developpers, Few years ago we used to design our paradigm with optseq. We would like to use it again but we can't install it. We went on the web site : http://surfer.nmr.mgh.harvard.edu/optseq/ we download the linux version 2 we upload it to the our old linux server with matlab optseq and optseq2 aren't recognize as command. we also tried to install the cywin version on a PCwindows with cygwin and matlab. but when we execute the optseq2.exe it says that it doesn't find the input point of _isnand in the library of the dynmic links cywin1.ddl we don't know what to do. would you please help us ? thank you

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optseq2 installation
by Florence POMARES 16 Mar '10

16 Mar '10

Dear Doug, The command is still not known. I think that our linux platform is too old... Just to be sure : - optseq2 need matlab ? - optseq2 can be run even if Freesurfer and FS-FAST are not installed ? thank you. other wise, do you know another program doing similar things than optseq ? regards De : Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Date : 15 mars 2010 18:51:19 HNEC À : Florence POMARES <florence.borgetto(a)univ-st-etienne.fr> Cc : freesurfer(a)nmr.mgh.harvard.edu Objet : Rép : [Freesurfer] optseq installation what do you mean it is not recognized? To make it executable, you need to run chmod a+x optseq2 to run it, either put it into your PATH, or cd to where it is located and run ./optseq2 the "./" is necessary if it is not in the PATH doug Florence POMARES wrote: Dear Doug, Thank you for your answer. We run it from shell (a comand window of X11 because we are connected to the server by the way of a MacIntosh) but it isn't recognized. How can we make it executable ? We just upload optseq2 on the Linux server... Le 12 mars 10 à 20:30, Florence POMARES a écrit : Début du message réexpédié : *De : *Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu >> *Date : *12 mars 2010 20:09:57 HNEC *À : *Florence POMARES <florence.borgetto(a)univ-st-etienne.fr <mailto:florence.borgetto@univ-st-etienne.fr >> *Cc : *freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu > *Objet : **Rép : [Freesurfer] optseq installation* Did you make it executable? They are run from the shell, not matlab. doug Florence POMARES wrote: Dear Optseq Developpers, Few years ago we used to design our paradigm with optseq. We would like to use it again but we can't install it. We went on the web site : http://surfer.nmr.mgh.harvard.edu/optseq/ we download the linux version 2 we upload it to the our old linux server with matlab optseq and optseq2 aren't recognize as command. we also tried to install the cywin version on a PCwindows with cygwin and matlab. but when we execute the optseq2.exe it says that it doesn't find the input point of _isnand in the library of the dynmic links cywin1.ddl we don't know what to do. would you please help us ? thank you

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How to transform brain.mgz back to native space
by liang wang 16 Mar '10

16 Mar '10

Hi FS experts, I find that FS does make a great skullstrip and extract a perfect brain (ie. brain.mgz). I am thinking to register this brain to MNI152 standard space using FSL. Does anyone know how to transfer the brain (256.^3, 1mm ) to subject-specific native space (224*256*176, 1mm). Thanks in advance. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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Clusterwise Correction for Multiple Comparisons
by liyari5018 16 Mar '10

16 Mar '10

Hi all, I used QDEC compare differences between normal subjects and patients, the activation can be seen without correction, after correction by FDR ,all disappeared.I read about the Clusterwise Correction for Multiple Comparisons of the manual. I am confused about the meaning of Correction. I use the simulation when an error is as follows: ############################################################################################# ERROR: dimension mismatch between X and contrast /usr/local/freesurfer/subjects/sad/qdec/Untitled/tmp.mri_glmfit-sim-2797/lh-Avg-Intercept-area.mtx X has 8 cols, C has 2 cols ############################################################################################# Why is that? Also could you please give some recommendations on the correction. Thanks for your reply, i 'll be very grateful to you for your help. LJ

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modification made to longitudinal results
by Guang Zeng 16 Mar '10

16 Mar '10

Hi, there, I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should I use? recon-all -s subj.long.baseid .... or recon-all -long subj baseid .... Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/

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gaussian and mean curvature in qdec
by Ana Catarino 16 Mar '10

16 Mar '10

Hello, I have 2 groups, normal and patients, and was using qdec to compare groups for several measures (thickness, curv, sulc, etc), but couldn't do it for Gaussian (white.K) and mean curvature (white.H). I get the following error: Error in Analyze: Couldn't open file $SUBJECTS_DIR/AS1/surf/lh.white.K.fwhm10.avgsubject.mgh How can I create the ?h.white.K.fwhm??.avgsubject.mgh file for every subject? Many Thanks, Ana Catarino

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recon-all fails because of mri_label error
by Guang Zeng 15 Mar '10

15 Mar '10

Hi, there, recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions? gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010 _________________________________________________________________ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:…

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