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Re: [Freesurfer] convert surface label on to functional image
by Douglas N Greve 13 Dec '11

13 Dec '11

The easiest thing is to use mri_label2vol, something like mri_label2vol --label yourlabel.label --temp functemplate.nii --reg register.dat --proj frac 0 1 .1 --hemi lh --subject subject --o yourlabel.nii doug Zhangyuanchao wrote: > Thanks for your response! > > In fact, the label that I want to convert to functional space was > obtained by between-group comparisons, so it does not belong to any > existing parcellation template. > > What should I do in this case? > > Thanks! > > Best, > > --- *11年12月13日，周二, Douglas N Greve > /<greve(a)nmr.mgh.harvard.edu>/* 写道： > > > 发件人: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > 主题: Re: [Freesurfer] convert surface label on to functional image > 收件人: "Zhangyuanchao" <woshizhangyc(a)yahoo.cn> > 抄送: freesurfer(a)nmr.mgh.harvard.edu > 日期: 2011年12月13日,周二,上午5:48 > > Hi Yuanchao, I would recommend that you use the aparc+aseg.mgz > file for this. This file has cortical labels already in the > volume, you just need to map them to your functional space, > something like > > mri_label2vol --aparc+aseg --temp functemplate.nii --reg > register.dat --o aparc+aseg.fmri.nii > > doug > > Zhangyuanchao wrote: > > hi, expert, > > > > By mapping a surface label to a functional template, I want to > extract the corresponding cortical gray matter region in the > functional space. I know I should use the mri_label2vol command. > > In the help page of mri_label2vol, I see some examples of this > command. > > > > 2. Convert a surface label into a binary mask in the functional > space. > > Fill in all the cortical gray matter. Require that a functional > voxel > > be filled at least 30% by the label: > > > > mri_label2vol --label lh-avg_central_sulcus.label --temp > f.nii --reg register.dat --fillthresh .3 --proj frac 0 1 > .1 --subject bert --hemi lh > > --o cent-lh.nii > > > > 3. Convert a surface label into a binary mask in the functional > space. > > Sample a 1mm ribbon 2mm below the gray/white surface. Do not > require a fill threshold: > > > > mri_label2vol --label lh-avg_central_sulcus.label --temp > f.nii --reg register.dat --proj abs -3 -2 .1 --subject bert > --hemi lh > > --o cent-lh.nii > > > > I want to extract the cortical gray matter on the functional > images corresponding to the surface label. I do not know which of > the above commands could obtain the result I want and which > parameters I should use to obtain what I want. > > > > For example 3, I do not quite catch what "Sample a 1mm ribbon > 2mm below the gray/white surface. " this sentence means. > > Thanks for your help! > > > > > > Best > > > > Yuanchao > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > </mc/compose?to=Freesurfer(a)nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu </mc/compose?to=greve(a)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 > > > > 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. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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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Cluster-wise correction for multiple comparisons: customized Zstats data
by Xinian Zuo 13 Dec '11

13 Dec '11

Hi List, I have a question on how to write out the matlab vector containing the Z-statistics and perform subsequent multiple corrections. I already read some functions and know how to write it to a mgh surface file. Here, my question is 'is there any specific things on the header of the surface file, which allows me to do cluster-wise correction (see corrected p-value < 0.025) if there is such a command for that?'. Thanks! -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn) Google Scholar Citations: http://scholar.google.com/citations?user=a3-gVGMAAAAJ&hl=en

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thickness or volume?
by Lindsay Ercole 13 Dec '11

13 Dec '11

What is the current opinion on using cortical volumes rather than reporting on thickness? Sincerest thanks, Lindsay

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problem using an older environment...
by Joe Andreano 12 Dec '11

12 Dec '11

Hello folks, I'm trying to reanalyze some old data that was originially analyzed in freesurfer version 4. Because the code I was using was from 4.0, I set the environment to 4 before starting, then made a new analysis and a few new contrasts. When I tried to run selxavg3-sess with the following command: selxavg3-sess -analysis nmdm_ALL42_V_fix -sf SESSID_ALL_FINAL -df . I got the following error message: /autofs/space/albus_003/users/nmdm_2/nmdm_004 ---------------------------------------- $id:fastselxavg3.m, v 1.88.2.5 2010/11/11 16:55:08 greve Exp $ /usr/local/freesurfer/stable5_0_0/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/stable5_0_0/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/stable5_0_0/matlab/MRIread.m --------------------------------------- outtop = /autofs/space/albus/3/users/nmdm_2 Extension format = nii.gz ??? Reference to non-existent field 'mcstem' Error in ==> fast_ldanaflac at 171 if(isempty(flac.mcstem)) Error in ==> fast_selxavg3 at 55 flac0=fast_ldanaflac(analysis); >>-------------------------------------- ERROR: fast_selxavg3() failed\n Note that I have confirmed that I am indeed running version 4, but the commands called in the error ("/usr/local/freesurfer/stable5_0_0/fsfast/toolbox/fast_selxavg3.m", etc.) are referencing version 5. Note also that the code being used here is adapted directly from an earlier analysis which was run in version 4 and which I know worked without errors. Anybody have any idea what's happening here? Even some information on what 'mcstem', or ldanaflac do would be helpful. (I have attached my analysis.info file) Thanks, Joe Andreano _________________________________ Joseph M. Andreano, PhD Research Fellow Interdisciplinary Affective Science Lab Massachusetts General Hospital _________________________________

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multiple overlay - tksurfer
by vin . 12 Dec '11

12 Dec '11

Dear FreeSurfer list, Greetings! a newbie to freesurfer. -- would like to overlay tracking group results (Sum from all subjects)-(from FSL ) in the inflated lh & rh. -- - it works with one region (hope it's correct), with following command, where, -fthresh ?? means it shows 50 % threshold based on intensity / only voxels which are overlaid by atleast half of the subjects ?? >tksurfer #Sub_ID lh inflated -annot aparc.annot -ov 1.nii -ovreg register.dat -fthresh 0.3 -fmid 0.3 -fslope 1 - How I can overlay multiple regions, in specific colours, with 50% thr. ? , Thank you :) Vin

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convert surface label on to functional image
by Zhangyuanchao 12 Dec '11

12 Dec '11

hi, expert, By mapping a surface label to a functional template, I want to extract the corresponding cortical gray matter region in the functional space. I know I should use the mri_label2vol command. In the help page of mri_label2vol, I see some examples of this command. 2. Convert a surface label into a binary mask in the functional space.Fill in all the cortical gray matter. Require that a functional voxelbe filled at least 30% by the label: mri_label2vol --label lh-avg_central_sulcus.label --temp f.nii --reg register.dat --fillthresh .3 --proj frac 0 1 .1 --subject bert --hemi lh --o cent-lh.nii 3. Convert a surface label into a binary mask in the functional space.Sample a 1mm ribbon 2mm below the gray/white surface. Do not require a fill threshold: mri_label2vol --label lh-avg_central_sulcus.label --temp f.nii --reg register.dat --proj abs -3 -2 .1 --subject bert --hemi lh --o cent-lh.nii I want to extract the cortical gray matter on the functional images corresponding to the surface label. I do not know which of the above commands could obtain the result I want and which parameters I should use to obtain what I want. For example 3, I do not quite catch what "Sample a 1mm ribbon 2mm below the gray/white surface. " this sentence means. Thanks for your help! Best Yuanchao

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Converting thickness maps to vtk
by Navid Shiee 12 Dec '11

12 Dec '11

Hello, I was wondering if there is a command like mris_convert to create a thickness map in vtk format (either on the white or pial surface) ? Thanks, -- Navid Shiee Ph.D. Candidate Laboratory of MEDical Image Computing (MEDIC) Image Analysis and Communication Laboratory (IACL) Johns Hopkins University

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tracula failed to find header file for -t
by Scott Hayes 12 Dec '11

12 Dec '11

Hi, I have received the following error message (copied from trac-all.log file). fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k /Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt ** ERROR (nifti_image_read): failed to find header file for '-t' ** ERROR: nifti_image_open(-t): bad header info Error: failed to open file -t ERROR: Could not open image -t Image Exception : #22 :: Failed to read volume -t terminate called after throwing an instance of 'RBD_COMMON::BaseException' The file (dwi.nii.gz) exists in the correct location, and appears to have the correct number of frames (60 directions + 10 b0). We scan on a Siemens 3T tim trio. I unpack the data using unpacksdcmdir and I specify the resulting .mgz file in the tracula config file. Running locally on mac os 10.6.8. Any suggestions would be appreciated. Thanks, Scott

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Re: [Freesurfer] tracula and snow leopard: can't allocate region / memory error
by Anastasia Yendiki 12 Dec '11

12 Dec '11

Hi Scott - Sending to the list is always good so that others can find it in the archives when they have similar problems. Do you specify the .dcm or .mgz file in your dmrirc? Does dwi.nii.gz have the right dimensions/frames? a.y On Mon, 12 Dec 2011, Scott Hayes wrote: > Thanks for the prompt response Anastasia--I ran it over the weekend > and it worked. > > I've subsequently encountered a new issue (copied below from the > trac-all.log). The file (dwi.nii.gz) exists in the correct location > (it was written there by tracula). I use unpacksdcmdir for unpacking > the dicoms, and then point the config file to the appropriate .mgz > file, so I'm not doing anything particularly unusual in terms of > unpacking or messing w/ the headers (We scan on a Siemens 3T tim > trio.) I can send this to the listserv if you prefer. > Best, > Scott > > fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k > /Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz > -m -s | awk '{print $1/$2}' > > /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt > ** ERROR (nifti_image_read): failed to find header file for '-t' > ** ERROR: nifti_image_open(-t): bad header info > Error: failed to open file -t > ERROR: Could not open image -t > Image Exception : #22 :: Failed to read volume -t > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > > > > On Fri, Dec 9, 2011 at 12:44 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: >> >> Hi Scott - Here are the tracula executables for snow leopard that we posted >> in response to that thread: >> >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopar… >> >> Let me know if this solves the memory errors. >> >> a.y >> >> >> On Fri, 9 Dec 2011, Scott Hayes wrote: >> >>> Hi Anastasia, >>> I've encountered an error using tracula w/ snow leopard OS that was >>> previously reported on the FS listserv: >>> >>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18829.html >>> >>> I'm wondering if there is a documented solution available? >>> Recompiling from source code would be beyond my expertise. >>> >>> David: I'm cc'ing you just as a heads up--all of the workstations in >>> the imaging center run snow leopard OS. >>> >>> Best, >>> Scott >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > >

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mri_ca_register from virtual box
by Lorenzo Busti 12 Dec '11

12 Dec '11

*Hi everyone * *I got this error while running one of my subjects* * * mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Thu Nov 24 05:15:42 EST 2011 /home/virtualuser/freesurfer/subjects/Petrollini2/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s Petrollini2 exited with ERRORS at Thu Nov 24 05:15:43 EST 2011 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting *I'm working with a virtual machine on a 32 bit computer with 4GB of RAM(2-core Intel processor 2.00 GHz). I raised the ram dedicated to the virtual machine to 1,5 GB: this is the max value permitted before the selecting bar of the virtual box changes from green to red (is it sufficent?)* *I have free space for data. * *Can you help me in solving this problem?* *Thanks* *Lorenzo Busti* * *

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