[Freesurfer] question about Correction for Multiple Comparison
Hi all: A few days ago, i have asked about some questions about Correction for Multiple Comparison. But i'm still confused about it. The version of FS is 5.1.0. when i performed Correction for Multiple Comparison using command line with 'mris_glmfit-sim', it usually took many hours to complete. However, when i performed this in qdec, it only took a few seconds. Moreover, i couldn't find command with ''mris_glmfit-sim' in the terminal except for the 'mri_surfcluster' command. I wander whether the 'mri_surfcluster' command can be used for the Correction for Multiple Comparison? Any suggestions will be appreciated. Thank you!___ 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] TR mismatch between analysis and data analysis
Dear Doug, Thanks for your earlier reply. I have installed fsl on my machine, and have progressed a little further through the retinotopy analysis. However, I now have the following error. ERROR: TR mismatch between analysis and data analysis TR = 2, data TR = 0 I used mri_convert f.nii f.nii -tr 2000 to try to fix the problem, but had no success (below is the output). Your help would be very much appreciated. Thanks in advance Kiley FreeSurfer:/data1/RETINOTOPY selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc Surface data self lh -- selxavg3-sesslogfile is /media/sf_DATA1/RETINOTOPY/log/selxavg3-sess-bold-rtopy.self.lh-120326071335.log -- --- /media/sf_DATA1/RETINOTOPY/IFEE2211 Mon Mar 26 07:13:35 EDT 2012 anadir = /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output M A T L A B (R) Copyright 1984-2012 The MathWorks, Inc. R2012a (7.14.0.739) 32-bit (glnx86) February 9, 2012 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# IFEE2211 ### /media/sf_DATA1/RETINOTOPY/IFEE2211 - $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/virtualuser/freesurfer/matlab/MRIread.m - outtop = /media/sf_DATA1/RETINOTOPY Extension format = nii.gz FreeSurfer Virtual Machine sudo password: freesurfer FreeSurfer Virtual Machine sudo password: freesurfer nruns = 4 autostimdur = outanadir = /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh FreeSurfer Virtual Machine sudo password: Found 111344/120028 (92.8) voxels in mask Creating Design Matrix ... creation time = 0.007 sec DoMCFit = 1 ntptot = 492, nX = 36, DOF = 456 Saving X matrix to /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh/Xtmp.mat XCond = 1.20413 (normalized) Computing contrast matrices FreeSurfer Virtual Machine sudo password: OLS Beta Pass run 1 t= 0.0 : FreeSurfer Virtual Machine sudo password: ERROR: TR mismatch between analysis and data analysis TR = 2, data TR = 0 From: Kiley Seymour kiley_seym...@yahoo.com.au To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Sunday, 25 March 2012 1:05 PM Subject: Re: mkbrainmask-sess Hi again, Could this error be due to the fact that I don't have a full version of fsl installed and configured on my ubuntu virtual machine? i.e. does fsfast require fsl to be installed? Thanks K From: Kiley Seymour kiley_seym...@yahoo.com.au To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Friday, 23 March 2012 3:04 PM Subject: mkbrainmask-sess Dear Freesurfers, I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM). I was unable to run this command as freesurfer could not find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below). Any help with this would be much appreciated. Thanks Kiley FreeSurfer:~/data1/RETINOTOPY mkbrainmask-sess -s IFEE2211 -d ~/data1/RETINOTOPY /media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHSfslmaths.fsl Scratch Dir is /tmp/mkbrainmask_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras = (-0.0536701, 0.992375, 0.110955) k_ras = (0.00114604, -0.111054, 0.993814) writing to /tmp/mkbrainmask_7930/in.nii... # -- Using FSL's BET to Extract Brain-- # /media/sf_DATA1/RETINOTOPY/IFEE2211/bold bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1
Re: [Freesurfer] TR mismatch between analysis and data analysis
You'll have to re-run the preprocessing (or change all the .nii files). doug Kiley Seymour wrote: Dear Doug, Thanks for your earlier reply. I have installed fsl on my machine, and have progressed a little further through the retinotopy analysis. However, I now have the following error. ERROR: TR mismatch between analysis and data analysis TR = 2, data TR = 0 I used mri_convert f.nii f.nii -tr 2000 to try to fix the problem, but had no success (below is the output). Your help would be very much appreciated. Thanks in advance Kiley FreeSurfer:/data1/RETINOTOPY selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc Surface data self lh -- selxavg3-sess logfile is /media/sf_DATA1/RETINOTOPY/log/selxavg3-sess-bold-rtopy.self.lh-120326071335.log -- --- /media/sf_DATA1/RETINOTOPY/IFEE2211 Mon Mar 26 07:13:35 EDT 2012 anadir = /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output M A T L A B (R) Copyright 1984-2012 The MathWorks, Inc. R2012a (7.14.0.739) 32-bit (glnx86) February 9, 2012 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# IFEE2211 ### /media/sf_DATA1/RETINOTOPY/IFEE2211 - $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/virtualuser/freesurfer/matlab/MRIread.m - outtop = /media/sf_DATA1/RETINOTOPY Extension format = nii.gz FreeSurfer Virtual Machine sudo password: freesurfer FreeSurfer Virtual Machine sudo password: freesurfer nruns = 4 autostimdur = outanadir = /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh FreeSurfer Virtual Machine sudo password: Found 111344/120028 (92.8) voxels in mask Creating Design Matrix ... creation time = 0.007 sec DoMCFit = 1 ntptot = 492, nX = 36, DOF = 456 Saving X matrix to /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh/Xtmp.mat XCond = 1.20413 (normalized) Computing contrast matrices FreeSurfer Virtual Machine sudo password: OLS Beta Pass run 1t= 0.0 : FreeSurfer Virtual Machine sudo password: ERROR: TR mismatch between analysis and data analysis TR = 2, data TR = 0 *From:* Kiley Seymour kiley_seym...@yahoo.com.au *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Sunday, 25 March 2012 1:05 PM *Subject:* Re: mkbrainmask-sess Hi again, Could this error be due to the fact that I don't have a full version of fsl installed and configured on my ubuntu virtual machine? i.e. does fsfast require fsl to be installed? Thanks K *From:* Kiley Seymour kiley_seym...@yahoo.com.au *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, 23 March 2012 3:04 PM *Subject:* mkbrainmask-sess Dear Freesurfers, I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM). I was unable to run this command as freesurfer could not find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below). Any help with this would be much appreciated. Thanks Kiley FreeSurfer:~/data1/RETINOTOPY mkbrainmask-sess -s IFEE2211 -d ~/data1/RETINOTOPY /media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras =
Re: [Freesurfer] make_average_subject
It might be failing on the aseg, so try it with --no-aseg doug Bruce Fischl wrote: Hi Sonya did you run out of RAM? How much is on your machine? cheers Bruce On Fri, 23 Mar 2012, sonya kaur wrote: Dear all,I'm getting an error with the make_average_subject command on freesurfer. The error is vm_allocate (size=262144) failed (error code 3). According to the freesurfer helpdesk, it seems to be a problem with creating an average aseg. Is there any solution for this that you know of? Thank you in advance! -- Sonya Kaur Clinical Psychology Graduate Student Department of Psychology The University of Texas, Austin 1 University Station, A8000 Austin, TX 78712 SEA 4.110E sonya_k...@mail.utexas.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] question about FSGD file
Hi ZhiLiangLong, what you have set up probably does not make sense. By
using gender as a covariate (male=1 and female=2), you are saying that
you expect females to be twice as thick as males.
doug
ZhiLiangLong wrote:
Hi, FS experts:
I'm scanning freesurfer pages about FSGD files here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V
and i'm interested in one contrast file(the example of Contrast 5
right-left.intercept.mtx). The original FSGD file is list as follows:
GroupDescriptorFile 1
Title OSGM
Class MaleRight
Class MaleLeft
Class FemaleRight
Class FemaleLeft
Variables Age
Input subject1 MaleRight 30
Input subject2 MaleLeft 40
Input subject3 FemaleRight 50
Input subject4 FemaleLeft 60
The contrast file is : 0.5 -0.5 0.5 -0.5 0 0 0 0, meaning to exame the
difference between Righties and Lefties regressing out the effects of
gender and age.
Now i consider gender as the covariate variable ('1' represents the
Male and '2' represents the Female), and i setup a new FSGD file:
GroupDescriptorFile 2
Title OSGM
Class Right
Class Left
Variables Age gender
Input subject1 Right 30 1
Input subject2 Left 40 2
I also want to exame the difference as suggested above, and I setup
the new contrast file as :1 -1 0 0 0 0.
My question is that : are the new FSGD and contrast files correct to
exame the difference as suggested by original FSGD and contrast files?
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--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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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
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Re: [Freesurfer] question about Cluster-wise Correction for Multiple Comparisions
ZhiLiangLong wrote: Hi all: I'm performing the group analysis on my own data using command line on FS5.1.0 and i'm a little confused about the Clusterwise Correction for Multiple Comparisions. the command is as follows: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 1 4 mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite In this command, does the vertex-wise threshold (here, '4') mean that the vertex whose p value is lower than 0.0001 can be considered to used for the Correction for Multiple Comparisions ? yes likewise, does the sign (here,'neg') mean that only negtive vertexs can be considered? yes Is there a criterion which vertex-wise threshold and sign i should choose? If you have an apriori hypothesis as to the sign that your results will be (eg, malefemale), then you can use that sign. If not then use abs (absolute). I would not choose a vertex-wise threshold less than p=.05. Hope you can give me some suggestions ! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Displaying FSL zstats onto FreeSurfer
Zurcher Nicole wrote: Hi everyone, I have two questions regarding FreeSurfer and FSL interoperation and it would be great if someone could help. 1) When displaying subject-level FSL FEAT data onto the FS volume using the command tkmedit blobby orig.mgz lh.white -overlay ./featdir/stats/zstat1.nii.gz -overlay-reg featdir/reg/freesurfer/anat2exf.register.dat fthresh 1.3 -fmid 2.3 -fslope 1” (mentioned on http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html) What /p/-value does the threshold of 1.3 correspond to? Is it a zscore? It is -log10(p), so p=.01 is 2 2) What would be the best way to display FSL group-level FEAT data (zstats) onto the FreeSurfer surface? As far as I understand, the FSL and FreeSurfer Interoperation website explains how to display subject level-feat on the surface. For the group-level data, it only explains how to run group-level analyses using mri_glmfit based on lower-level FSL FEAT directories. Is there a way to directly map the zstats from FSL group-level analyses onto the FreeSurfer surface? You can use the $FREESURFER_HOME/average/mni152.register.dat. Note that this is for display only. You still have all the shortcomings of doing the analysis in the volume. doug Thanks in advance for the help! Nicole ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Freesurfer coordinate problem
which MNI coordinate system? We don't know anything about surfstat. Can you tell us what you want to do without using the surfstat commands? doug xiaoning wu wrote: Hi all, Recently I have a problem about coordinate of freesurfer. I have reprocessed the MRI data to get the cortical thickness and then I want to get the indexes, coordinate and cortical thickness of a region of interest(ROI). I have use the Surfstat toolbox of matlab to process the data.Now I want to use the function SurfStatROI ( function maskROI = SurfStatROI( centre, radius, surf ) ) to get the ROI, however, I have known the MNI coordinates (x,y,z) only .I want to convert this MNI coordinates to the freesurfer coordinates which can be used by SurfStatROI.center. That is ,if I use the function SurfStatReadSurf to read surf files (surf=SurfStatReadSurf(..)) to get the variable surf, then I can get surf.coord(:,index) by a index. How can the surf.coord() corresponding to the MNI coordinate systems or Talairach systems. I have seen the website of Freesurfer coordinate systems (http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) but I can not solve my problem. Looking forward to your help sincerely. Your sincerely! Xiaoning Wu Mar 20,2012 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] [BUG] epidewarp.fsl
what does it do? What is the terminal output? Satrajit Ghosh wrote: epidewarp.fsl does not take non-integer smoothing kernel sizes. cheers, satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] [BUG] epidewarp.fsl
hi doug, here is the error, it told me there was a problem in an if statement somewhere. if you use smooth = 2.0 instead of 2 you will get the error. cheers, satra --- [snip] fslmerge -t /mindhive/gablab/users/keshavan/scripts/BrainImagingPipeline s/utils/test/fmunwarp/temp/ph.nii.gz /mindhive/gablab/users/keshava n/scripts/BrainImagingPipelines/utils/test/fmunwarp/temp/ph.zeros.nii.gz /mindhive/gablab/users/keshavan/scripts/BrainImagingPipelines/utils/test/fm unwarp/temp/dph Masking with /mindhive/gablab/users/keshavan/scripts/BrainImagingPipeline s/utils/test/fmunwarp/temp/brain.nii.gz Standard error: if: Badly formed number. Return code: 1 Interface EPIDeWarp failed to run. --- On Mon, Mar 26, 2012 at 10:39 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what does it do? What is the terminal output? Satrajit Ghosh wrote: epidewarp.fsl does not take non-integer smoothing kernel sizes. cheers, satra --**--** __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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/**compliancelinehttp://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] about QAtools
Hi Chunhui, The wm-anat-snr missing step is misleading. That file gets created when QAtools generates the SNR/WM measures using the wm-anat-snr command. It is not part of the recon-all stream. If you specify the default status log file included with the scripts you should not get that error (using the -completeStatusFile flag). This is a slight bug which I need to fix. I'm not sure about the X error, I'll investigate that. The gawk command is a dependency issue (http://www.gnu.org/software/gawk/). -Louis On Mon, 26 Mar 2012, chenchunhuichina wrote: Hi Louis and Freesurfers Last time you helped me fixed the convert command problem, and then QATools can run on my computer smoothly. But I just realized that this error message is still there, Received X error! error code : 1 request code : 148 minor code : 179 Error text: 'BadRequest (invalid request code or no such operation)' there is also an error message says: gawk: commond not found Is this also a dependecy problem? However, I do get the summary log and the html file with snapshots. In the log file, it says: ERROR: Recon-all steps missing in subject sub2 status file wm-anat-snr I thouhg recon-all run all steps automaticly, what should I do with this missing step? Thanks for your help! 2012-03-26 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 ·¢¼þÈË£º Louis Nicholas Vinke ·¢ËÍʱ¼ä£º 2012-03-06 23:50:05 ÊÕ¼þÈË£º chenchunhuichina ³ËÍ£º freesurfer Ö÷Ì⣺ Re: [Freesurfer] about QAtools Hi Chunhui, I believe this is a dependency issue, since the convert command is part of the ImageMagick Studio. You'll need to download and install the binaries (http://www.imagemagick.org/). I'll make of note of this on the wiki page. -Louis On Tue, 6 Mar 2012, chenchunhuichina wrote: Dear Freesurfer experts, I installed the QAtools and tried a subject with this commond: $QA_TOOLS/recon_checker -s sub13 -snaps-detailed -gen-asegLUT aseglut.txt but I encountered the following Error message, can someone help me figure it out? Any help is appreciated, thanks! Error message 1: Received X error! error code : 1 request code : 148 minor code : 179 Error text: 'BadRequest (invalid request code or no such operation)' Error message 2: /opt/fmritools/QAtools/takesnapshotpreset.sh : line 89: convert: command not found both of the above two error messages shown in the screen many times, and there was no figures in the 'QA_check.html' By the way, I do not have solid anatomical background, is it acceptable that I only use QAtools for quality control, without manual editing? I am thinking manual editing by non-experts will induce incorrect data. Any suggestion? Thanks a lot! 2012-03-06 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 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] normal vector projection
You don't need to do that registration. Instead, use --identity xDS with mri_surf2vol. doug Seok Lew wrote: Hi, After freesurfer reconstruction, I tried to project surface normal vectors on the ribbon. I used the following scripts, but the projected vectors were out of the ribbon when I visualized it freeview. The vectors were placed outside of the ribbon. Anyone knows any idea ? fslregister --mov mri/orig.mgz --s xDS --reg rrr.dat --dof 12 --tmp ./tmp/ mri_surf2surf --s xDS --hemi lh --sval-nxyz pial --tval ./pl_100.mgz mri_surf2vol --surfval pl_100.mgz --hemi lh --surf pial --volreg rrr.dat --outvol pln_pribbon.mgz --fillribbon --template mri/orig.mgz Thank in advance, Seok Lew, Ph.D. MEG Core Laboratory Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School s...@nmr.mgh.harvard.edu mailto:s...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] volume mapping
Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer. a.y On Mon, 26 Mar 2012, Johnson wrote: Hi FS expert I need to know the transformation matrix itself since I will do the transformation in matlab. I successfully transformed white matter fibers coordinates to T1 using AIR 5.0 from LONI lab. They provide a transformation matrix. Now I want to transform the coordinates from T1 to Freesurfer space, so my question is: what is the transformation matrix that relates the T1 which FS have used for parcellation and segmentation with the aparc+aseg.mgz file? I searched the logs but couldn't find such matrix. I don't want to do a registration step since it will be less accurate than the one that was generated during the segmentation process. Also is it just one transformation or a combination of transformations? 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.
Re: [Freesurfer] volume mapping
Hi I found it in a 256x256x256 space while the T1 we use is in different space, I found this page on the registration step: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat I wish to know how this script work? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz what is the transformation used ? JG On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer. a.y On Mon, 26 Mar 2012, Johnson wrote: Hi FS expert I need to know the transformation matrix itself since I will do the transformation in matlab. I successfully transformed white matter fibers coordinates to T1 using AIR 5.0 from LONI lab. They provide a transformation matrix. Now I want to transform the coordinates from T1 to Freesurfer space, so my question is: what is the transformation matrix that relates the T1 which FS have used for parcellation and segmentation with the aparc+aseg.mgz file? I searched the logs but couldn't find such matrix. I don't want to do a registration step since it will be less accurate than the one that was generated during the segmentation process. Also is it just one transformation or a combination of transformations? thanks 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. -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgad...@uic.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] volume mapping
If you want to register your DWI to T1, you should register to mri/brain.mgz. You can do this with bbregister, or with any affine registration tool of your choice. On Mon, 26 Mar 2012, Johnson wrote: Hi I found it in a 256x256x256 space while the T1 we use is in different space, I found this page on the registration step: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat I wish to know how this script work? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz what is the transformation used ? JG On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer. a.y On Mon, 26 Mar 2012, Johnson wrote: Hi FS expert I need to know the transformation matrix itself since I will do the transformation in matlab. I successfully transformed white matter fibers coordinates to T1 using AIR 5.0 from LONI lab. They provide a transformation matrix. Now I want to transform the coordinates from T1 to Freesurfer space, so my question is: what is the transformation matrix that relates the T1 which FS have used for parcellation and segmentation with the aparc+aseg.mgz file? I searched the logs but couldn't find such matrix. I don't want to do a registration step since it will be less accurate than the one that was generated during the segmentation process. Also is it just one transformation or a combination of transformations? thanks 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
Re: [Freesurfer] volume mapping
Hi Let me re-phrase my question: I already did registration from DWI to T1, this step is OK. Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not the aparc+aseg-in-rawavg file). I know I have two choices: 1) do registration using bbregister 2) since Freesurfer during processing have already done this step, the transformation matrix is there somewhere, the question is where to find it? which log or which file? this choice is better since it is more accurate. Thanks JG On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: If you want to register your DWI to T1, you should register to mri/brain.mgz. You can do this with bbregister, or with any affine registration tool of your choice. On Mon, 26 Mar 2012, Johnson wrote: Hi I found it in a 256x256x256 space while the T1 we use is in different space, I found this page on the registration step: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat I wish to know how this script work? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz what is the transformation used ? JG On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer. a.y On Mon, 26 Mar 2012, Johnson wrote: Hi FS expert I need to know the transformation matrix itself since I will do the transformation in matlab. I successfully transformed white matter fibers coordinates to T1 using AIR 5.0 from LONI lab. They provide a transformation matrix. Now I want to transform the coordinates from T1 to Freesurfer space, so my question is: what is the transformation matrix that relates the T1 which FS have used for parcellation and segmentation with the aparc+aseg.mgz file? I searched the logs but couldn't find such matrix. I don't want to do a registration step since it will be less accurate than the one that was generated during the segmentation process. Also is it just one transformation or a combination of transformations? thanks 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. -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgad...@uic.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical Normalization Questions
Hi Jeff and all, For normalization (i.e., divide the measurement under study by some global measurement), I would not argue favourably, as this procedure can bias the results in the opposite direction if a global effect is present. Instead, include it as a covariate is not as harmful. My suggestion is, when there is no clear approach about using or not a global measurement as a nuisance, the relationships between the measurement under study, the independent variable, and the putative nuisance should be calculated, and models with and without the nuisance should be analysed and presented. The discussion should consider both analyses together, and enough information should be presented so that the final interpretation is left to the reader. Specifically for area, I suggest analysing and presenting two models: (1) without any global measurement and (2) with global area as nuisance. If brain volume (whichever way it is measured) is to be considered a potential nuisance for the disorder you are analysing, it can be included in the model #2 above, even given that they are not orthogonal to each other, and are related to global area. Non-orthogonality between the nuisance variables is not a problem as it is when effects of interest are involved. Hope this helps! All the best, Anderson On 23/03/12 11:29, Michael Harms wrote: Our reply to that is here http://bjp.rcpsych.org/content/196/5/414.2.long which reminded me of other papers that have also used a global thickness measure to covary for mean cortical thickness and thereby address whether any regional thickness differences were in excess of global cortical thickness differences between groups -- see references [1,4] in our Reply. cheers, -MH Hi Michael and others, maybe it's this one: http://bjp.rcpsych.org/content/196/5/414.1.long best, -joost On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms mha...@conte.wustl.eduwrote: Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in whole brain thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was... cheers, -MH On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: Hi Jeff yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have said normalize by the 2/3 root of ICV (maybe David can comment on this as well) cheers Bruce On Thu, 22 Mar 2012, Jeff Sadino wrote: Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations? Thank you, Jeff ___ 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 ___ 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
Re: [Freesurfer] volume mapping
Actually, (1) should be more accurate, because bbregister uses the surface reconstruction obtained from the T1 to optimize the contrast across the gray/white boundary in the registered DWI. However if you want to convert to the 1mm, 256^3 voxel size that was used as input to freesurfer, see mri_convert --conform. On Mon, 26 Mar 2012, Johnson wrote: Hi Let me re-phrase my question: I already did registration from DWI to T1, this step is OK. Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not the aparc+aseg-in-rawavg file). I know I have two choices: 1) do registration using bbregister 2) since Freesurfer during processing have already done this step, the transformation matrix is there somewhere, the question is where to find it? which log or which file? this choice is better since it is more accurate. Thanks JG On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: If you want to register your DWI to T1, you should register to mri/brain.mgz. You can do this with bbregister, or with any affine registration tool of your choice. On Mon, 26 Mar 2012, Johnson wrote: Hi I found it in a 256x256x256 space while the T1 we use is in different space, I found this page on the registration step: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat I wish to know how this script work? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz what is the transformation used ? JG On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer. a.y On Mon, 26 Mar 2012, Johnson wrote: Hi FS expert I need to know the transformation matrix itself since I will do thetransformation in matlab. I successfully transformed white matter fibers coordinates to T1 usingAIR 5.0 from LONI lab. They provide a transformation matrix. Now I want to transform the coordinates from T1 to Freesurfer space, so my question is: what is the transformation matrix that relates the T1 which FS have used for parcellation and segmentation with the aparc+aseg.mgz file? I searched the logs but couldn't find such matrix. I don't want to do a registration step since it will be less accurate than the one that was generated during the segmentation process. Also is it just one transformation or a combination of transformations? thanks 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
Re: [Freesurfer] calculating DLPFC or frontal lobe grey and white matter volumes
Try this cd $SUBJECTS_DIR/subject mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz mri_segstats --seg mri/wmparc.a2009s.mgz --sum stats/wmparc.a2009s.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject --surf-wm-vol --ctab $FREESURFER_HOME/WMParcStatsLUT.txt --etiv doug On 03/22/2012 12:57 PM, sam bedford wrote: Dear All We want to find frontal lobe grey and white matter volumes in a patient group to compare it with control group. In particular, we want to see the grey and white matter volumes in the dorsolateral prefrontal cortex (DLPFC). However we seem to be having problems finding this region on the processed data for white matter volume (after recon-all command). It was previously suggested in this mailing list that we can get grey matter volume for the DLPFC by combining the following volumes: $hemi.G_frontal_middle.label $hemi.S_frontal_inferior.label $hemi.S_frontal_middle.label We are wondering how to get white matter volumes in the same region... If getting the DLPFC volume is difficult then can we just use the frontal grey and white matter volumes to make between group comparisons. From aseg and aparc files in the stats folder, adding all the following values below would give us frontal white and grey matter volumes. Or is there a simpler and less time consuming way to calculate grey and white matter volume in the frontal lobe? Frontal lobes - White Matter volume caudalmiddlefrontal lateralorbitofrontal medialorbitofrontal paracentral parsopercularis parsorbitalis parstriangularis precentral rostralmiddlefrontal superiorfrontal frontalpole Frontal lobes - Grey Matter volumes G_and_S_frontomargin G_and_S_paracentral G_and_S_subcentral QQQ??? G_and_S_transv_frontopol G_front_inf-Opercular G_front_inf-Orbital G_front_inf-Triangul G_front_middle G_front_sup G_precentral S_front_inf S_front_middle S_front_sup Thanks in advance Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] mri_vol2surf failed, segmentation error
Can you run it outside of the pipeline to assure that it is not a pipeline issue? doug On 03/18/2012 08:54 AM, Qingyang Li wrote: Hi all, I am new to the freesurfer world. I was running a pipeline where I met an error. Here is the command I run and the error message: Command: mri_vol2surf --hemi lh --noreshape --o /working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz --reg /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat --projfrac 0.500 --mov /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz Standard output: srcvol = /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz srcreg = /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /NKI_recon_subjects/sub/surf/lh.white Done reading source surface Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Standard error: Segmentation fault Return code: 139 Interface SampleToSurface failed to run. Thank you all in advance! Yang -- Qingyang Li Balance and focus. On Sun, Mar 18, 2012 at 8:28 AM, freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu wrote: Mailing list subscription confirmation notice for mailing list Freesurfer We have received a request from 67.244.70.75 for subscription of your email address, con...@gmail.com mailto:con...@gmail.com, to the freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailing list. To confirm that you want to be added to this mailing list, simply reply to this message, keeping the Subject: header intact. Or visit this web page: https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/8f8fcc67483bbcee3ff0f76888c79e7704b4a03a Or include the following line -- and only the following line -- in a message to freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu: confirm 8f8fcc67483bbcee3ff0f76888c79e7704b4a03a Note that simply sending a `reply' to this message should work from most mail readers, since that usually leaves the Subject: line in the right form (additional Re: text in the Subject: is okay). If you do not wish to be subscribed to this list, please simply disregard this message. If you think you are being maliciously subscribed to the list, or have any other questions, send them to freesurfer-ow...@nmr.mgh.harvard.edu mailto:freesurfer-ow...@nmr.mgh.harvard.edu. 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] volume mapping
OK T1 space is the space acquired from the machine, original anatomical space regards JG On 03/26/2012 2:25 PM, Bruce Fischl wrote: can you post to the list so others can answer? And can you clarify what you mean by T1 space? On Mon, 26 Mar 2012, Johnson wrote: Hi well, I had to transfer the fiber tracts coordinates from DWI space to T1 space, I used the b0 and the T1 for the registration process, I got the transformation matrix and applied it onto the tracts and they fit very well. Now I want to transform the tracts from T1 space to the freesurfer space, I need to know the transformation matrix that was used during the processing if it was saved in any of the logs thanks Johnson On 03/26/2012 2:09 PM, Bruce Fischl wrote: Hi Johnson what T1 did you register to? Most of the ones we generate (T1.mgz, brainmask.mgz, ...) are in a common coordinate system and you shouldn't have to transform from one to another. cheers Bruce On Mon, 26 Mar 2012, Johnson wrote: Hi Let me re-phrase my question: I already did registration from DWI to T1, this step is OK. Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not the aparc+aseg-in-rawavg file). I know I have two choices: 1) do registration using bbregister 2) since Freesurfer during processing have already done this step, the transformation matrix is there somewhere, the question is where to find it? which log or which file? this choice is better since it is more accurate. Thanks JG On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: If you want to register your DWI to T1, you should register to mri/brain.mgz. You can do this with bbregister, or with any affine registration tool of your choice. On Mon, 26 Mar 2012, Johnson wrote: Hi I found it in a 256x256x256 space while the T1 we use is in different space, I found this page on the registration step: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat I wish to know how this script work? mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz what is the transformation used ? JG On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer. a.y On Mon, 26 Mar 2012, Johnson wrote: Hi FS expert I need to know the transformation matrix itself since I will do the transformation in matlab. I successfully transformed white matter fibers coordinates to T1 using AIR 5.0 from LONI lab. They provide a transformation matrix. Now I want to transform the coordinates from T1 to Freesurfer space, so my question is: what is the transformation matrix that relates the T1 which FS have used for parcellation and segmentation with the aparc+aseg.mgz file? I searched the logs but couldn't find such matrix. I don't want to do a registration step since it will be less accurate than the one that was generated during the segmentation process. Also is it just one transformation or a combination of transformations? thanks 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 -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgad...@uic.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_vol2surf failed, segmentation error
hi Qingyang, you can simply copy and paste the command line into the shell. cheers, satra On Mon, Mar 26, 2012 at 3:12 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Can you run it outside of the pipeline to assure that it is not a pipeline issue? doug On 03/18/2012 08:54 AM, Qingyang Li wrote: Hi all, I am new to the freesurfer world. I was running a pipeline where I met an error. Here is the command I run and the error message: Command: mri_vol2surf --hemi lh --noreshape --o /working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz --reg /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat --projfrac 0.500 --mov /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz Standard output: srcvol = /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz srcreg = /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /NKI_recon_subjects/sub/surf/lh.white Done reading source surface Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Standard error: Segmentation fault Return code: 139 Interface SampleToSurface failed to run. Thank you all in advance! Yang -- Qingyang Li Balance and focus. On Sun, Mar 18, 2012 at 8:28 AM, freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu wrote: Mailing list subscription confirmation notice for mailing list Freesurfer We have received a request from 67.244.70.75 for subscription of your email address, con...@gmail.com mailto:con...@gmail.com, to the freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailing list. To confirm that you want to be added to this mailing list, simply reply to this message, keeping the Subject: header intact. Or visit this web page: https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/8f8fcc67483bbcee3ff0f76888c79e7704b4a03a Or include the following line -- and only the following line -- in a message to freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu: confirm 8f8fcc67483bbcee3ff0f76888c79e7704b4a03a Note that simply sending a `reply' to this message should work from most mail readers, since that usually leaves the Subject: line in the right form (additional Re: text in the Subject: is okay). If you do not wish to be subscribed to this list, please simply disregard this message. If you think you are being maliciously subscribed to the list, or have any other questions, send them to freesurfer-ow...@nmr.mgh.harvard.edu mailto:freesurfer-ow...@nmr.mgh.harvard.edu. 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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
Re: [Freesurfer] mri_vol2surf failed, segmentation error
Thank you Doug and Satra, I ran the same pipeline on another machine after I post the question and it went through with no problem... On the machine which the pipeline failed, I have freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. And on the machine that the pipeline went through, I have freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 on. This might be a version issue? To rule out this possibility, we are testing the ver 5.0.0 of Freesurfer on the machine that failed this step... Will keep you posted when we finish testing ... Also, we did tried to run the script outside the pipeline and received the same error... Yang -- Qingyang Li Balance and focus. On Mon, Mar 26, 2012 at 3:36 PM, Satrajit Ghosh sa...@mit.edu wrote: hi Qingyang, you can simply copy and paste the command line into the shell. cheers, satra On Mon, Mar 26, 2012 at 3:12 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Can you run it outside of the pipeline to assure that it is not a pipeline issue? doug On 03/18/2012 08:54 AM, Qingyang Li wrote: Hi all, I am new to the freesurfer world. I was running a pipeline where I met an error. Here is the command I run and the error message: Command: mri_vol2surf --hemi lh --noreshape --o /working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz --reg /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat --projfrac 0.500 --mov /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz Standard output: srcvol = /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz srcreg = /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /NKI_recon_subjects/sub/surf/lh.white Done reading source surface Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Standard error: Segmentation fault Return code: 139 Interface SampleToSurface failed to run. Thank you all in advance! Yang -- Qingyang Li Balance and focus. On Sun, Mar 18, 2012 at 8:28 AM, freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu wrote: Mailing list subscription confirmation notice for mailing list Freesurfer We have received a request from 67.244.70.75 for subscription of your email address, con...@gmail.com mailto:con...@gmail.com, to the freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailing list. To confirm that you want to be added to this mailing list, simply reply to this message, keeping the Subject: header intact. Or visit this web page: https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/8f8fcc67483bbcee3ff0f76888c79e7704b4a03a Or include the following line -- and only the following line -- in a message to freesurfer-requ...@nmr.mgh.harvard.edu mailto:freesurfer-requ...@nmr.mgh.harvard.edu: confirm 8f8fcc67483bbcee3ff0f76888c79e7704b4a03a Note that simply sending a `reply' to this message should work from most mail readers, since that usually leaves the Subject: line in the right form (additional Re: text in the Subject: is okay). If you do not wish to be subscribed to this list, please simply disregard this message. If you think you are being maliciously subscribed to the list, or have any other questions, send them to freesurfer-ow...@nmr.mgh.harvard.edu mailto:freesurfer-ow...@nmr.mgh.harvard.edu. 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358
[Freesurfer] segmentation of the dural sinuses
Are there any tools associated with freesurfer to aid in segmentation of the dural sinuses (e.g., superior sagittal sinus, transverse sinus, straight sinus, etc) from a T1-weighted anatomical scan? Many thanks, Jon *** Jonathan Winawer Stanford University Department of Psychology Jordan Hall, Building 01-420 450 Serra Mall Stanford, CA 94305 Phone: 650-725-1255 wina...@stanford.edu http://www-psych.stanford.edu/~winawer/ ___ 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] segmentation of the dural sinuses
not that I know of, sorry On Mon, 26 Mar 2012, Jonathan A Winawer wrote: Are there any tools associated with freesurfer to aid in segmentation of the dural sinuses (e.g., superior sagittal sinus, transverse sinus, straight sinus, etc) from a T1-weighted anatomical scan? Many thanks, Jon *** Jonathan Winawer Stanford University Department of Psychology Jordan Hall, Building 01-420 450 Serra Mall Stanford, CA 94305 Phone: 650-725-1255 wina...@stanford.edu http://www-psych.stanford.edu/~winawer/ ___ 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] Cortical Normalization Questions
I think we must be careful about including noisy large scale measurements as global nuisance covariates in the General Linear Model (GLM). The GLM assumes that the independent variables are measured almost without error (eg. see http://en.wikipedia.org/wiki/Errors-in-variables_models). For instance, mean cortical thickness or mean global activity in fMRI (as the mean of many values) should not be as noisy as Intracranial Volume estimates (or the estimated volume of any neuroanatomical structure). -Jorge De: Anderson Winkler andersonwink...@hotmail.com Para: freesurfer@nmr.mgh.harvard.edu Enviado: Lunes 26 de marzo de 2012 13:56 Asunto: Re: [Freesurfer] Cortical Normalization Questions Hi Jeff and all, For normalization (i.e., divide the measurement under study by some global measurement), I would not argue favourably, as this procedure can bias the results in the opposite direction if a global effect is present. Instead, include it as a covariate is not as harmful. My suggestion is, when there is no clear approach about using or not a global measurement as a nuisance, the relationships between the measurement under study, the independent variable, and the putative nuisance should be calculated, and models with and without the nuisance should be analysed and presented. The discussion should consider both analyses together, and enough information should be presented so that the final interpretation is left to the reader. Specifically for area, I suggest analysing and presenting two models: (1) without any global measurement and (2) with global area as nuisance. If brain volume (whichever way it is measured) is to be considered a potential nuisance for the disorder you are analysing, it can be included in the model #2 above, even given that they are not orthogonal to each other, and are related to global area. Non-orthogonality between the nuisance variables is not a problem as it is when effects of interest are involved. Hope this helps! All the best, Anderson On 23/03/12 11:29, Michael Harms wrote: Our reply to that is here http://bjp.rcpsych.org/content/196/5/414.2.long which reminded me of other papers that have also used a global thickness measure to covary for mean cortical thickness and thereby address whether any regional thickness differences were in excess of global cortical thickness differences between groups -- see references [1,4] in our Reply. cheers, -MH Hi Michael and others, maybe it's this one: http://bjp.rcpsych.org/content/196/5/414.1.long best, -joost On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms mha...@conte.wustl.eduwrote: Hi Jeff, I personally like the idea of using average thickness as a covariate to control for a reduction in whole brain thickness, and have used that approach in a paper. If the Abstract that you mentioned indicated that this is flawed, I'd be curious to know what the reason was... cheers, -MH On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: Hi Jeff yes, I think this is still our recommendation for thickness, although perhaps David Salat can verify. As far as surface area, you might get Anderson Winkler to send you a preprint of his newly accepted paper on surface area comparisons and how to do them properly. I would have said normalize by the 2/3 root of ICV (maybe David can comment on this as well) cheers Bruce On Thu, 22 Mar 2012, Jeff Sadino wrote: Hello, For cortical thickness normalizations, Bruce said not to normalize based on a HBM abstract ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). Is this still the consensus? For cortical volume, it is pretty standard to normalize to eTIV. For cortical surface area (jacobian), I couldn't find any information on the wiki. Does anyone have any recommendations? Thank you, Jeff ___ 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 ___ 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
Re: [Freesurfer] about QAtools
Got it. Thanks Louis! 2012-03-27 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 发件人： Louis Nicholas Vinke 发送时间： 2012-03-26 23:27:09 收件人： chenchunhuichina 抄送： freesurfer 主题： Re: Re: [Freesurfer] about QAtools Hi Chunhui, The wm-anat-snr missing step is misleading. That file gets created when QAtools generates the SNR/WM measures using the wm-anat-snr command. It is not part of the recon-all stream. If you specify the default status log file included with the scripts you should not get that error (using the -completeStatusFile flag). This is a slight bug which I need to fix. I'm not sure about the X error, I'll investigate that. The gawk command is a dependency issue (http://www.gnu.org/software/gawk/). -Louis On Mon, 26 Mar 2012, chenchunhuichina wrote: Hi Louis and Freesurfers Last time you helped me fixed the convert command problem, and then QATools can run on my computer smoothly. But I just realized that this error message is still there, Received X error! error code : 1 request code : 148 minor code : 179 Error text: 'BadRequest (invalid request code or no such operation)' there is also an error message says: gawk: commond not found Is this also a dependecy problem? However, I do get the summary log and the html file with snapshots. In the log file, it says: ERROR: Recon-all steps missing in subject sub2 status file wm-anat-snr I thouhg recon-all run all steps automaticly, what should I do with this missing step? Thanks for your help! 2012-03-26 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 ·¢¼þÈË£º Louis Nicholas Vinke ·¢ËÍʱ¼ä£º 2012-03-06 23:50:05 ÊÕ¼þÈË£º chenchunhuichina ³ËÍ£º freesurfer Ö÷Ì⣺ Re: [Freesurfer] about QAtools Hi Chunhui, I believe this is a dependency issue, since the convert command is part of the ImageMagick Studio. You'll need to download and install the binaries (http://www.imagemagick.org/). I'll make of note of this on the wiki page. -Louis On Tue, 6 Mar 2012, chenchunhuichina wrote: Dear Freesurfer experts, I installed the QAtools and tried a subject with this commond: $QA_TOOLS/recon_checker -s sub13 -snaps-detailed -gen-asegLUT aseglut.txt but I encountered the following Error message, can someone help me figure it out? Any help is appreciated, thanks! Error message 1: Received X error! error code : 1 request code : 148 minor code : 179 Error text: 'BadRequest (invalid request code or no such operation)' Error message 2: /opt/fmritools/QAtools/takesnapshotpreset.sh : line 89: convert: command not found both of the above two error messages shown in the screen many times, and there was no figures in the 'QA_check.html' By the way, I do not have solid anatomical background, is it acceptable that I only use QAtools for quality control, without manual editing? I am thinking manual editing by non-experts will induce incorrect data. Any suggestion? Thanks a lot! 2012-03-06 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 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.
