[Freesurfer] no-octave
Dears, Mkanalysis-sess does not accept -per-run and It looks like mkcontrast-sess cannot initiate Matlab in the terminal. I have installed octave and addpath and save path both /home/fsl/Desktop/freesurfer/matlab /home/fsl/Desktop/freesurfer/fsfast/toolbox I will appreciate in advance if you possibly could help me to solve the problem. Best Regards, Elahe' Windows 7 and vmware10 Linux version: --- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/fsl/Desktop/freesurfer FSFAST_HOME /home/fsl/Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/fsl/Desktop/freesurfer/subjects MNI_DIR /home/fsl/Desktop/freesurfer/mni FSL_DIR /usr/local/fsl Current working directory: *pwd* */home/fsl* *which freesurfer* */home/fsl/Desktop/freesurfer/**bin/freesurfer* *which mkanalysis-sess* */home/fsl/Desktop/freesurfer/fsfast/bin/mkanalysis-sess* *which mkcontrast-sess* */home/fsl/Desktop/freesurfer/fsfast/bin/mkcontrast-sess* Command lines: *mkdir FIVA* *cd FIVA* *mkdir MT_Localizer* *cd MT_Localizer* *mkdir subj1sess1 * *cd subj1sess1* *unpacksdcmdir -src /home/fsl/Desktop/MTLocalizer/IMAGES -targ . -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii -run 11 bold nii f.nii* Within subj1sess1, made a text file named subjectname, and wrote subj001 (the name of my anatomical subject). *cd ..* *preproc-sess -s subj1sess1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run* *plot-twf-sess -s subj1sess1 -fsd bold -mc* *tkregister-sess -s subj1sess1 -fsd bold -per-run -bbr-sum* *tkregister-sess -s subj1sess1 -fsd bold -per-run* For each run, a paradigm file (paradigm.par) is included. *mkanalysis-sess -a MT.lh -surface self lh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 **-nskip 4 **-polyfit 2 -spmhrf 0 -mcextreg -per-run* *'ERROR flag -per-run unrecognized'* It does not accept -per-run so I omitted that. *mkanalysis-sess -a MT.lh -surface self lh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg* *mkanalysis-sess -a MT.rh -surface self rh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg * *mkcontrast-sess -analysis MT.lh -contrast M_S -a 2 -c 1 * Non-Null Conditions INFO: Found 1 Delays Condition Weights: -1. 1. mkcontrast -anadir MT.lh -wcond -1. 1. -sumconds -o MT.lh/12.mat -wdelay 1 -no-octave $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $ cmtxfile MT.lh/12.mat nconds2, wcond -1. 1. ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.05 rdelta rtau ERROR running mkcontrast mkcontrast -anadir MT.lh -wcond -1. 1. -sumconds -o MT.lh/12.mat -wdelay 1 -no-octave ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis
Hi Emma, Could you clarify what would be the disadvantages that you've heard about? I ask because we've studied and tried to clarify many aspects of the analysis of surface area in this paper http://www.sciencedirect.com/science/article/pii/S1053811912002996. Maybe if there's something not covered there we could try to comment then. Thanks! All the best, Anderson On 10 October 2014 22:19, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis
Hi Donna, In that same paper we also comment on the differences between expansion/contraction and absolute areal measurements assessed at each face of the surface (i.e., facewise), which can, after interpolation, be converted to vertexwise to facilitate analysis using current tools (e.g., mri_glmfit or qdec), without loss of areal quantities. All the best, Anderson On 11 October 2014 04:05, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only ... which is similar, but not identical to the local gyrification index? If so, would you use this measure on surfaces before or after registration to a target atlas? Donna On Oct 10, 2014, at 4:19 PM, Emma Thompson vonecono...@gmail.com wrote: Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] v5.1 control point mri_ca_normalize bug
correct (the thing to do is comment-out the addition of the control points). n. On Wed, 2014-10-08 at 17:05 -0400, Bruce Fischl wrote: I don't think you want to run with -nocanorm. Just commenting out the addition of the -f $ControlPointsFile should be sufficient. Right Nick? On Wed, 8 Oct 2014, Marx, Gabe wrote: Hi Bruce, I appreciate the response! I am sorry, I am a bit confused. The release notes state: An option is to disable the running of mri_ca_normalize when re-running the -autorecon2 or -autorecon2-cp stage after adding control points by adding the flag -nocanorm to the end of recon-all. We will continue to investigate a more automated solution to detection of this problem. The more permanent workaround for v5.1 users is to edit their recon-all script making the following change, which will disable usage of control points with ca_norm: # find these lines: set cmd = (mri_ca_normalize) if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) # and comment-out the second line like this: set cmd = (mri_ca_normalize) #if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) # then re-run your subjects with the flags: -autorecon2 -autorecon3 -clean-aseg Are you saying the -nocanorm flag will result in inaccurate data? Thanks! Gabe -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, October 08, 2014 8:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug Hi Gabe this wasn't really a bug per-se, just induced some behavior that people didn't like. You can't skip the mri_ca_normalize step or the aseg won't be accurate. The aseg patch I believe just starts autorecon2-cp after the aseg hs been created, but Nick or Zeke can correct me if I'm wrong. cheers Bruce On Mon, 6 Oct 2014, Marx, Gabe wrote: Hello Freesurfer experts, I had a question regarding the v5.1 control point mri_ca_normalize bug. I read the release notes and know that this bug can be worked around by adding the –nocanorm flag to my recon-all however I have become worried about the ramifications of skipping mri_ca_normalize in my pipeline. Would someone be able to give me a better description as to what mri_ca_normalize is doing and what I am sacrificing by taking it out of my pipeline? Furthermore, in regards to the patch for the recon-all script to fix this bug, what is the patch doing exactly? If I had some data in which I used the –nocanorm flag and other data in which I used the patch would I still be able to make valid analysis if I merged them? Would there be significant inconsistencies? Thanks! Best, Gabe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] skewed CT viewed in tkregister2
Hi, Any insight on this problem I'm having with tkregister2? I haven't been able to resolve this yet. My original posting is below with the output from bugr. Thanks! Mia From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Monday, October 06, 2014 11:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] skewed CT viewed in tkregister2 Hi Freesurfers I'm having trouble viewing a CT in tkregister2. Here is the output from bugr: FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects PWD: /autofs/space/huygens_001/users/mia/subjects/BI20v2_SurferOutput/mri ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/BI20v2_SurferOutput/mri 1. BI20 2. tkregister2 --s BI20v2_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig 3. the coronal/saggital/horizontal views were skewed 4.attached. Thanks a lot, Mia ___ Freesurfer mailing list Freesurfer@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.
