Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Need admin rights to run FS on mac?
by Adityakumar Kasinadhuni 08 Jun '10

08 Jun '10

Hi, This is Kumar. I am a grad student at the Dept of Biomedical Engineering, University of Florida. I would like to bring to your notice a problem that I am facing when I am running FreeSurfer on my mac at the lab. I am testing the freesurfer installation as documented on the Free Surfer Wiki. I was able to run the first few commands without an issue other than it saying "cannot create.xdebug_tkmedit" but it ends up running well. When I try to run the recon-all command, it says I do not have admin rights to make a directory and so I used "sudo" to boost the privileges. This time it says, FREESURFER_HOME: Undefined Variable Can you please help me in this regard? Thank you. -- Aditya Kumar. K Grad Student, Department of BME UF.

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[Fwd: Re: Different slices number for control group]
by Michael Harms 08 Jun '10

08 Jun '10

Sorry, my initial reply went to just to Laura, and not the list. -MH -------- Forwarded Message -------- From: Laura Verga <ildestinodiunombrello(a)gmail.com> To: Michael Harms <mharms(a)conte.wustl.edu> Subject: Re: [Freesurfer] Different slices number for control group Date: Tue, 8 Jun 2010 17:13:14 +0200 Hi MIchael, thanks so much for your answer. Firstly: you're absolutely right about the number of slices. My mistake. I meant 150. I will surely contact my physicist. Thanks again and sorry for being imprecise. 2010/6/8 Michael Harms <mharms(a)conte.wustl.edu> Hi Laura, What do you mean in saying that the images of the control group are taken from a "different acquisition session"? Different subjects are always scanned in a different "session"... Assuming that all subjects were scanned on the same scanner, the differing number of slices in the acquisitions for the two groups could still be a major confound for a group comparison, depending on the sequence used. For example, with an MPRAGE acquisition, many k- space lines are acquired during each "TR", so changing the number of slices will in principle change the contrast and spatial filtering properties of the acquisition, even if all other parameters are identical. In your case, the change in the number of slices is quite dramatic. You probably need to talk to your local MR physicist regarding the sequence that you used, the details of how it is implemented on the Philips scanner, and whether a change in number of slices will affect the contrast and spatial filtering due to the manner in which the Philips sequence loops through k-space. BTW: 128 sagittal slices of 1 mm thickness is only 128 mm, which is not enough to cover the L/R dimension of a human head. Were those really the parameters? cheers, -MH On Tue, 2010-06-08 at 10:50 +0200, pikase(a)tin.it wrote: > Hi freesurfers! > > We want to estimate the differences of cortical thickness between two > groups. The images of the control group are taken from a different > acquisition session. the only differences would be the number of > slices (200 vs 128). > It is still possible to compare the two groups? > > Images were acquired on the sagittal plane on a 3T Phillips scanner, > SENSE coil, voxels 1x1x1, matrix 256x256, T1 MPR. > > Thanks so much for your time > > Laura > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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.

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Different slices number for control group
by pikase＠tin.it 08 Jun '10

08 Jun '10

Hi freesurfers! We want to estimate the differences of cortical thickness between two groups. The images of the control group are taken from a different acquisition session. the only differences would be the number of slices (200 vs 128). It is still possible to compare the two groups? Images were acquired on the sagittal plane on a 3T Phillips scanner, SENSE coil, voxels 1x1x1, matrix 256x256, T1 MPR. Thanks so much for your time Laura

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Label files for the Cortical Ribbon
by Tina Jeon 07 Jun '10

07 Jun '10

Hello all! After creating some labeling files from aparc.a2005s.annot, I noticed that my sulci and gyri volumes generated from the .label files (i.e., after running mri_annotation2label and mri_label2vol) were only representing the outer layer of the white surface. Is there any way to generate .label files that include the entire cortical ribbon? Thanks, any help would be appreciated. Tina

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cannon open .mgh file using MRIread
by corinna bauer 07 Jun '10

07 Jun '10

When I load the file directly to load_mgh I still get the error ERROR: could not open /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac35.mgh for reading ??? Attempt to reference field of non-structure array. Error in ==> gwratiotest at 5 gray2=gray.vol; here is my matlab file: function gwratiotest gray=load_mgh('/home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac35.mgh'); white=load_mgh('/home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/lh.white.projdist.neg1.mgh'); gray2=gray.vol; white2=white.vol; gwratio.vol = gray2 / white2; MRIwrite(gwratio, '/home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/lh.gwratio.mgh'); end On Fri, Jun 4, 2010 at 12:20 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Corinna, > > sorry, I'm not sure what's going wrong. Can you try loading that volume > calling load_mgh directly? Make sure the filename is exactly right. It's > hard to tell with all the carriage returns in your email. > > cheers > Bruce > > > > On Fri, 4 Jun 2010, corinna bauer wrote: > > When I run mri_info I get: >> >> Volume information for >> >> /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac.35.mgh >> type: MGH >> dimensions: 23334 x 1 x 5 >> voxel sizes: 1.0000, 1.0000, 1.0000 >> type: FLOAT (3) >> fov: 23334.000 >> dof: 0 >> xstart: -11667.0, xend: 11667.0 >> ystart: -0.5, yend: 0.5 >> zstart: -2.5, zend: 2.5 >> TR: 3000.00 msec, TE: 3.61 msec, TI: 1000.00 msec, flip angle: >> 8.00 degrees >> nframes: 1 >> ras xform present >> xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = >> 5.5017 >> : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = >> 11.5254 >> : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = >> 0.0000 >> >> talairach xfm : >> >> /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/transforms/talairach.xfm >> Orientation : LIA >> Primary Slice Direction: coronal >> >> voxel to ras transform: >> -1.0000 0.0000 0.0000 11672.5020 >> 0.0000 0.0000 1.0000 9.0254 >> 0.0000 -1.0000 0.0000 0.5000 >> 0.0000 0.0000 0.0000 1.0000 >> >> voxel-to-ras determinant -1 >> >> ras to voxel transform: >> -1.0000 0.0000 0.0000 11672.5020 >> -0.0000 -0.0000 -1.0000 0.5000 >> -0.0000 1.0000 -0.0000 -9.0254 >> 0.0000 0.0000 0.0000 1.0000 >> >> >> >> On Fri, Jun 4, 2010 at 9:58 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> >wrote: >> >> if you run mri_info on the .mgh file does it return reasonable looking >>> values? >>> >>> On Fri, 4 Jun 2010, corinna bauer wrote: >>> >>> Hi Bruce, >>> >>>> I am having trouble getting my .mgh files to open in MRIread. I get the >>>> following error message. >>>> >>>> ERROR: could not open /home/freesurfer4.4.0/ >>>> subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac35.mgh for reading >>>> ERROR: loading >>>> >>>> >>>> /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac35.mgh >>>> as MGH >>>> ??? Attempt to reference field of non-structure array. >>>> >>>> Error in ==> gwRatio at 24 >>>> gwratio.vol = gray.vol / white.vol; >>>> >>>> >>>> here's my .m file >>>> >>>> function gwRatio >>>> >>>> rootdir = '/home/freesurfer4.4.0/subjects/corinna/ADNI'; >>>> paths=dir([rootdir,'/*']); >>>> >>>> numel(paths) >>>> num = numel(paths); >>>> >>>> for ii = 1:num >>>> if(paths(ii).isdir && ~strcmp(paths(ii).name,'.') && >>>> ~strcmp(paths(ii).name,'..')) >>>> >>>> graypath= >>>> fullfile(rootdir,paths(ii).name,'mri/lh.white.projfrac35.mgh'); >>>> whitepath = >>>> fullfile(rootdir,paths(ii).name,'mri/lh.white.projdist.neg1.mgh'); >>>> outpath = fullfile(rootdir,paths(ii).name,'mri/lh.gwratio.mgh'); >>>> >>>> fprintf('----- Processing %i of %i -----\n', ii, num); >>>> fprintf('gray: %s\n', graypath); >>>> fprintf('white: %s\n', whitepath); >>>> fprintf('out: %s\n', outpath); >>>> >>>> gray = MRIread(graypath); >>>> white = MRIread(whitepath); >>>> gwratio = gray; >>>> gwratio.vol = gray.vol / white.vol; >>>> MRIwrite(gwratio, outpath); >>>> end >>>> end >>>> >>>> corinna >>>> >>>> >>>> >>> 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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skull stripping of IBSR using freesurfer
by Jinyoung Hwang 06 Jun '10

06 Jun '10

Hi all, I'm trying to obtain skull stripped images using freesurfer. Unfortunately, I couldn't perform the skull stripping function for 7_8 data within IBSR dataset (http://www.cma.mgh.harvard.edu/ibsr/) I used following command. > mri_watershed -T1 7_8.img f7_8.img The error message was --- mri_watershed error: w=White Matter =Intensity too high (>240)... valid input? --- How can I deal with this kind of error? regards, Jinyoung

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FDR correction in FS vs. SPM
by Jürgen Hänggi 04 Jun '10

04 Jun '10

Dear FS experts One of our reviewers would like to know whether the FDR procedures as implemented in FS on one hand and as implemented in SPM on the other hand are comparable. In FS, I think FDR is based on the height threshold (FDRp) and it is outside of the random Gaussian field theory framework, isn't it? For SPM, it has been shown that the FDR procedure based on height threshold (FDRp) is not appropriate in the random Gaussian field theory framework (Chumbley et al., 2010; Chumbley and Friston, 2009, both published in NeuroImage). Therefore, in SPM8 FDRc (based on the cluster volume) was implemented and should be preferred over FDRp, isn't it? Therefore, we conclude that it is not possible to use a comparable parametric multiple comparisons correction procedure in FS and SPM. Do the nonparametric procedures (SnPM for SPM and Monte Carlo simulations in FS) are comparable? Or is it impossible to get any comparable procedure due to the fact that a voxel is in 3D (as in SPM), whereas a vertex is on a 2D manifold (as in FS)? Thanks in advance Regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Alignment problem
by Dankner, Nathan (NIH/NIMH) [F] 04 Jun '10

04 Jun '10

Hello all, I just ran a scan through autorecons 1 and 2, and the surface came out rotated approximately 45 degrees upwards from the front. Will this be a problem when I go to analyze, and if so, how do I go about correcting it? Thanks, Nathan

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subsampling Error with mri_convert of 4D .nii ?
by caspari＠clipper.ens.fr 04 Jun '10

04 Jun '10

HI! I need to subsample my original 4D .nii files (the f.nii or the fmc.nii after motion correction) from 2.5 2.5 2.75 to 2 2 2 mm, in each orignial 4D nii are 200 volumes: After subsampling with mri_convert -vs 2 2 2 001/fmc.nii 001/fmc.nii -oi -ii the output info tells me that the inputstructure changed from nframe 200 to nframe 1 (in outputstructure) as a consequence my subsequent analysis of the estimation of the statistics (-selxavg3-sess, not important I guess) cannot be performed. if I do the same for the f.nii files, the same happens, and -preproc-sess enters with an ERROR ('cannot perform mc') How can I keep my 200 frames in the 4D nii and subsample my voxels at the same time, to then continue my statistics? I would be extremely greatful I someone can help! Natalie xxx

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Re: [Freesurfer] cannon open .mgh file using MRIread
by corinna bauer 04 Jun '10

04 Jun '10

When I run mri_info I get: Volume information for /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac.35.mgh type: MGH dimensions: 23334 x 1 x 5 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 23334.000 dof: 0 xstart: -11667.0, xend: 11667.0 ystart: -0.5, yend: 0.5 zstart: -2.5, zend: 2.5 TR: 3000.00 msec, TE: 3.61 msec, TI: 1000.00 msec, flip angle: 8.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 5.5017 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 11.5254 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 11672.5020 0.0000 0.0000 1.0000 9.0254 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 11672.5020 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 -9.0254 0.0000 0.0000 0.0000 1.0000 On Fri, Jun 4, 2010 at 9:58 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > if you run mri_info on the .mgh file does it return reasonable looking > values? > > On Fri, 4 Jun 2010, corinna bauer wrote: > > Hi Bruce, >> I am having trouble getting my .mgh files to open in MRIread. I get the >> following error message. >> >> ERROR: could not open /home/freesurfer4.4.0/ >> subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac35.mgh for reading >> ERROR: loading >> >> /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac35.mgh >> as MGH >> ??? Attempt to reference field of non-structure array. >> >> Error in ==> gwRatio at 24 >> gwratio.vol = gray.vol / white.vol; >> >> >> here's my .m file >> >> function gwRatio >> >> rootdir = '/home/freesurfer4.4.0/subjects/corinna/ADNI'; >> paths=dir([rootdir,'/*']); >> >> numel(paths) >> num = numel(paths); >> >> for ii = 1:num >> if(paths(ii).isdir && ~strcmp(paths(ii).name,'.') && >> ~strcmp(paths(ii).name,'..')) >> >> graypath= >> fullfile(rootdir,paths(ii).name,'mri/lh.white.projfrac35.mgh'); >> whitepath = >> fullfile(rootdir,paths(ii).name,'mri/lh.white.projdist.neg1.mgh'); >> outpath = fullfile(rootdir,paths(ii).name,'mri/lh.gwratio.mgh'); >> >> fprintf('----- Processing %i of %i -----\n', ii, num); >> fprintf('gray: %s\n', graypath); >> fprintf('white: %s\n', whitepath); >> fprintf('out: %s\n', outpath); >> >> gray = MRIread(graypath); >> white = MRIread(whitepath); >> gwratio = gray; >> gwratio.vol = gray.vol / white.vol; >> MRIwrite(gwratio, outpath); >> end >> end >> >> corinna >> >> > > 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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