Freesurfer May 2013

freesurfer@nmr.mgh.harvard.edu

174 participants
299 discussions

Re: [Freesurfer] FMRI surface transformation for vertex-wise connectivity analysis
by Thomas Yeo 16 May '13

16 May '13

Hi Ludovico, The mri_vol2surf example I sent you directly resample to fsaverage5, which is around 4mm spacing, resulting in 18715 vertices for both hemispheres combined after excluding the medial wall in the surfaces. I am also including the freesurfer mailing list in the email as suggested by Bruce. --Thomas On Thu, May 16, 2013 at 8:25 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Ludovico > > I wouldn't downsample before calling mri_surf2surf. We have tools for > uniformly parcellating the cortex (mris_make_face_parcellation) that can be > used for this purpose after sampling the timecourses to the cortex. > > > cheers > Bruce > On Thu, 16 May 2013, Ludovico Minati wrote: > >> Hi Bruce, >> >> many thanks. Yes sorry I shall use the list from now on. But let me >> just ask you a clarification as we are already on these questions >> >> For our connectivity analyses, at present we parcellated in 3D volume >> space the cortex into a pre-set number of roughly equal volume >> parcels, ranging in number between around 500 to 10,000. I would need >> to translate this approach to the surface space in Freesurfer, i.e. be >> able to smooth on the cortical surface and undersample it. What is the >> best approach that can be used? >> >> Along this like: you wrote around 150k vertices/hemisphere. For our >> purposes that's an enormous number, much larger than the number of EPI >> voxels. How can we mesh downsample before calling mri_vol2surf? >> >> Again thanks for your kind help and patience >> >> Ludovico >> >> >> On 16 May 2013 14:09, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>> Hi Ludovico >>> >>> can we move this discussion to the FreeSurfer list in the future so >>> others >>> can answer? >>> >>> 1. Hard to say as sometimes one works better than the other, you'll just >>> have to try. The transform should be rigid (6DOF) since the scalings are >>> read from the header, why would you want affine? I think Doug has worked >>> on >>> this and you can specify it in the bbregister command line, but I've >>> never >>> used it. >>> >>> 2. About 150K vertices/hemisphere. They are distributed initially at 1mm >>> spacing (the surface of the voxels), and cannot be tuned. There are some >>> tools around for mesh downsampling if you want, and this is even easier >>> if >>> you go to fsaverage space (with mri_surf2surf) where we have >>> representations >>> based on recursive icosahedral supersamplings. >>> >>> 3. This is due to a bug in the initial nifti format that didn't allow >>> any >>> one dimension greater than 64K. If you output in .mgz it should be >>> nvertices >>> x 1 x 1 x ntimepoints. >>> >>> 4. Search for "coordinate systems" on our wiki. This is documented >>> extensively. >>> >>> there are also matlab i/o functions for reading/writing all our formats >>> (e.g. MRIread.m) >>> >>> cheers >>> Bruce >>> >>> >>> On Thu, 16 May 2013, Ludovico Minati wrote: >>> >>>> Hi Thomas, >>>> >>>> thanks. A few quick questions, which hopefully will take little of >>>> your time but save me a lot of hassle: >>>> >>>> 1) bbregister. Do you advise using FLIRT or SPM for initialization? Is >>>> this a rigid-body transformation, or an affine one? Any way I can >>>> control the DOF? If I use SPM shall I feed the mean realigned volume >>>> here, as I expect? >>>> >>>> 2) recon-all. What is the typical number of vertices for the cortex? >>>> Any way I can control it, i.e. sample more or less finely? This would >>>> be particularly relevant for our task. >>>> >>>> 3) mri_vol2surf. Perhaps naively I was expecting an output file simply >>>> consisting of a list of values, i.e. one per vertex (assuming a single >>>> input volume that is). But the documentation says: "The output will be >>>> a data set with Nv/R colums, 1 row, R slices, and Nf frames..." What >>>> is the reshaping factor R for? How do I deal with this, i.e. how do I >>>> simply get a value per vertex? Or am I missing something here? Is >>>> mri_vol2surf averaging over neighbouring vertices? >>>> >>>> 4) Where do I read the Euclinean co-ordinates of the vertices from? >>>> >>>> Cheers >>>> >>>> Ludovico >>>> >>>> On 16 May 2013 04:30, Thomas Yeo <ythomas(a)csail.mit.edu> wrote: >>>>> >>>>> >>>>> Hi Ludovico, >>>>> >>>>> Just remember that you need to run "recon-all" on your T1 anatomical >>>>> first. >>>>> >>>>> For bbregister, the command goes something like this: bbregister >>>>> --bold --s $anat_s --init-fsl --mov $input --reg $reg. I find the >>>>> bbregister cost function value a good indication of whether the >>>>> registration has good well. Below 0.5 is good. Below 0.6 is probably >>>>> acceptable. >>>>> >>>>> For mri_vol2surf, the command goes something like this: mri_vol2surf >>>>> --mov $f --reg $reg --hemi $hemi --projfrac 0.5 --trgsubject >>>>> fsaverage5 --o $output --reshape --interp trilinear >>>>> >>>>> Cheers, >>>>> Thomas >>>>> >>>>> On Wed, May 15, 2013 at 8:57 PM, Bruce Fischl >>>>> <fischl(a)nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>> >>>>>> Hi Ludovico >>>>>> >>>>>> you can get vertex-level timecourse by using bbregister to register >>>>>> the >>>>>> EPI >>>>>> data to the surface, then mri_vol2surf to sample onto the surface. >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> >>>>>> On Wed, 15 May 2013, Ludovico Minati wrote: >>>>>> >>>>>>> Hello Thomas, >>>>>>> >>>>>>> yes sure. Our area of interest is early dementia diagnosis, and we >>>>>>> are >>>>>>> exploring the predictive value of graph topological indices. As you >>>>>>> know >>>>>>> there are major volume changes in dementia, and from the literature I >>>>>>> have >>>>>>> convinced myself we may be better off resolving this confound through >>>>>>> working on the surface, rather than playing around with ad-hoc >>>>>>> atlases >>>>>>> for >>>>>>> volumetric normalization. >>>>>>> >>>>>>> I have got plenty of signal processing code to perform the analyses >>>>>>> from >>>>>>> BOLD timeseries; what I am looking for now is a way to apply >>>>>>> Freesurfer >>>>>>> normalization to obtain vertex-level time-courses. >>>>>>> >>>>>>> Hence, I am so far only interested in solving the following problem >>>>>>> with >>>>>>> Freesurfer: we have as input an individual T1 scan and a series of >>>>>>> EPI >>>>>>> volumes, we want to preprocess/coregister/normalize them with >>>>>>> Freesurfer and >>>>>>> extract the BOLD timecourses for each vertex. No fMRI analysis in >>>>>>> Freesurfer, no group analysis. >>>>>>> >>>>>>> Hopefully it is not too complex? I am dwarfed by the range of >>>>>>> commands >>>>>>> available! >>>>>>> >>>>>>> Thank you very much in advance >>>>>>> >>>>>>> Ludovico >>>>>>> >>>>>>> -----Original Message----- >>>>>>> From: Thomas Yeo <ythomas(a)csail.mit.edu> >>>>>>> Sender: yeoyeo02(a)gmail.com >>>>>>> Date: Wed, 15 May 2013 10:07:00 >>>>>>> To: Bruce Fischl<fischl(a)nmr.mgh.harvard.edu> >>>>>>> Cc: lminati(a)ieee.org<lminati(a)ieee.org>; Dennis >>>>>>> Chan<D.Chan(a)bsms.ac.uk> >>>>>>> Subject: Re: FMRI surface transformation for vertex-wise connectivity >>>>>>> analysis >>>>>>> >>>>>>> Hi Ludovico, >>>>>>> >>>>>>> Can you give me the context of what you need? >>>>>>> >>>>>>> Cheers, >>>>>>> Thomas >>>>>>> >>>>>>> On Wed, May 15, 2013 at 9:52 AM, Bruce Fischl >>>>>>> <fischl(a)nmr.mgh.harvard.edu> wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Hi Ludovico >>>>>>>> Thomas Yeo (ccd) has a set of scripts for this purpose >>>>>>>> Cheers >>>>>>>> Bruce >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On May 14, 2013, at 8:50 PM, "Ludovico Minati" <lminati(a)ieee.org> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Ludovico >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 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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Re: [Freesurfer] problem with func2roi-sess
by Douglas N Greve 15 May '13

15 May '13

Hi Jeff, I found the problem. The first line looks something like this: #!ascii label /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label , from subject ontal_LH_CD_R01BTX_pat9_sess1.label vox2ras=TkReg when mri_vol2roi was originallywritten, it was not expecting such long file names. The "DidntWork" label has a length that is a little too long. The "DidWork" is just short enough. You can just edit the label to remove the pathpart of the .label file (ie,"/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label" . That information is not used at all, so it can actually be anything. doug On 05/15/2013 03:01 PM, jwaugh(a)nmr.mgh.harvard.edu wrote: > Thank you Doug. I really appreciate your help. I've attached two label > files from the same subject, one that worked and one that didn't. Both > were created using mri_cor2label and used aparc+aseg.mgz. I have viewed > the non-working labels using tkmedit and they look good. Again, I > appreciate your help - right now a clever idea is held up by this func2roi > problem! > > - Jeff > > > >> Can you put it in a place where I can see it? I tried to look, but I did > not have perms. You can also just email it to me >> On 5/14/13 6:26 PM, jwaugh(a)nmr.mgh.harvard.edu wrote: >>> I have checked the label file directly - it is of comparable size with > others, and has the same structure. I've rerun the mri_cor2label > command >>> and regenerated the labels for all subjects. Most confusing, func2roi > works for some subjects in this cohort and not others. In contrast, > the >>> whole cohort has been used with parallel labels with no problem. If > there is "something wrong with [my] label", what things could it be? > Has anyone else seen this particular error message? >>> Thanks, >>> Jeff >>>> it looks like ther is something wrong with that label >>>> On 05/14/2013 04:34 PM, jwaugh(a)nmr.mgh.harvard.edu wrote: >>>>> Hello Freesurfers, I would appreciate any advice or help you can > provide. >>>>> I am using the following command, run under Stable 3 (to keep the > current >>>>> analysis comparable to prior papers): >>>>> func2roi-sess -roidef MedOrbitofrontal_LH_t6_0_sm5_0thresh -analysis > newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5 -maskcontrast >>>>> newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5_contrast -labelfile > /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label > -maskthresh 6.0 -masktail pos -maskmap t -s CD_R01BTX_pat9_sess1 -df > sessdirfile >>>>> The error message is as follows (it outputs exactly like this, > apparently >>>>> intermingled with another output): >>>>> ras2vox src (tkreg) Qsrc ------------- >>>>> -0.320 -0.000 -0.000 32.000; >>>>> -0.000 -0.00mri_vol2roi: could not scan # of lines from >>>>> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label > No such file or directory >>>>> 0 -0.320 32.000; >>>>> 0.000 0.200 0.000 15.000; >>>>> 0.000 0.000 0.000 1.000; >>>>> I have never seen this error before - any suggestions why I'm getting > it? >>>>> This same command structure ran perfectly on separate ROIs over the last >>>>> few days. I confirmed that the corresponding .label files are > structured >>>>> identically to those for other ROIs that worked. >>>>> Just in case it's helpful, this is the command that I used to > generate >>>>> the >>>>> .label files: >>>>> mri_cor2label --c >>>>> /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aparc+aseg.mgz > --id 1014 --l >>>>> /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/MedOrbitofrontal_LH_${identifier}.label. >>>>> Thank you! >>>>> Jeff >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> 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 >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > _______________________________________________ >>>> Freesurfer mailing list >>>> 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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tracula error
by Skyler Gabriel Shollenbarger 15 May '13

15 May '13

Hi all, We ran tracula prep stage and it exited with errors: 'Selected streamline has fewer than 5 points'. We have attached the log and error files if needed. Thank you in advance! Skyler -- Skyler G. Shollenbarger Graduate Student - UWM Brain Lab Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee

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new version
by stdp82＠virgilio.it 15 May '13

15 May '13

Hi list, I apologize for the trivial question but, how I can be sure that the version that I'm using is effectively updated (version 5.3)? Stefano

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rs-fMRI data on pial surface
by René Besseling 15 May '13

15 May '13

Hi Freesurfers, For this analysis I plan to do, I want to map resting-state data in native (T1) space to the pial surface. The command I use for this is: mri_vol2surf --src fMRI_nat.nii --regheader subjID --hemi lh --projfrac-avg 0 1 0.05 --surf pial --o fMRI_2surf.mgh So the intention is to average the resting state data over the cortex and to map this to the pial surface. However, if I'm not mistaken the --projfrac-avg option projects along the outward pointing surface normal. Therefore, when using the pial surface, I expected that the proper call would be --projfrac-avg 0 -1 -0.05. However, this command does not run, whereas the command given above does, and yields (sensible) output. So is the command given above correct after all? And does this imply that for the pial surface, the volumetric data is actually projected along the inward pointing normals? Best regards, René

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mri_glmfit error with design matix
by Sinead Kelly 15 May '13

15 May '13

Dear Members, I am using mri_glmfit for the first time with the .fsgd file below, however, I am receiving the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. I have also pasted the design matrix below as I cannot figure out what is wrong with it. I would really appreciate if anyone could help me this issue. Also note that I am running this for just a subset of my total data set as a test before I run it on my full data set. Thank you very much for your help, Sinead GroupDescriptorFile 1 Title MIR137 Class TGFemale Class TGMale Class TTFemale Class TTMale Variables Age Input CON3140/001 TGFemale 37 Input CON3891/001 TTFemale 33 Input CON4664/001 TTFemale 40 Input CON5591/001 TTMale 41 Input CON7009/001 TGMale 21 Input CON7024/001 TTMale 59 Input CON7038/001 TTMale 56 Input CON7050/001 TTMale 30 Input CON7054/001 TTMale 43 Input CON7055/001 TTMale 43 Input CON7072/001 TTFemale 41 Input CON7082/001 TTFemale 29 Input CON7087/001 TTFemale 23 Input CON7090/001 TGFemale 59 Input CON7092/001 TTFemale 21 Input CON9004/001 TGFemale 28 Input CON9009/001 TTMale 42 Input CON9040/001 TTMale 56 Input CON9064/001 TTMale 55 Input CON9069/001 TGFemale 54 Input CON9070/001 TTFemale 55 Input CON9081/001 TTFemale 50 Input CON9091/001 TTMale 27 Input CON9093/001 TTMale 54 DefaultVariable Age Normalized matrix condition is 1e+08 Design matrix ------------------ 1.000 0.000 0.000 0.000 37.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 33.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 40.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 41.000; 0.000 1.000 0.000 0.000 0.000 21.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 59.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 56.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 30.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 43.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 43.000; 0.000 0.000 1.000 0.000 0.000 0.000 41.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 29.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 23.000 0.000; 1.000 0.000 0.000 0.000 59.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 21.000 0.000; 1.000 0.000 0.000 0.000 28.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 42.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 56.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 55.000; 1.000 0.000 0.000 0.000 54.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 55.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 50.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 27.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 54.000; -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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Recon-all error
by Borzello, Mia 15 May '13

15 May '13

Hi freesurfers, I recently ran a reconstruction, but it's errored. I'm not sure why thought, but I've attached the recon log. Thanks, Mia

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beta v5.3 for fedora 18 and ubuntu 13
by Nick Schmansky 15 May '13

15 May '13

Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-… this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick

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problem with func2roi-sess
by jwaugh＠nmr.mgh.harvard.edu 14 May '13

14 May '13

Hello Freesurfers, I would appreciate any advice or help you can provide. I am using the following command, run under Stable 3 (to keep the current analysis comparable to prior papers): func2roi-sess -roidef MedOrbitofrontal_LH_t6_0_sm5_0thresh -analysis newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5 -maskcontrast newROIs_tap_lh_long_CD_R01BTX_pat9_sess1_sm5_contrast -labelfile /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label -maskthresh 6.0 -masktail pos -maskmap t -s CD_R01BTX_pat9_sess1 -df sessdirfile The error message is as follows (it outputs exactly like this, apparently intermingled with another output): ras2vox src (tkreg) Qsrc ------------- -0.320 -0.000 -0.000 32.000; -0.000 -0.00mri_vol2roi: could not scan # of lines from /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_pat9_sess1_recon/label/MedOrbitofrontal_LH_CD_R01BTX_pat9_sess1.label No such file or directory 0 -0.320 32.000; 0.000 0.200 0.000 15.000; 0.000 0.000 0.000 1.000; I have never seen this error before - any suggestions why I'm getting it? This same command structure ran perfectly on separate ROIs over the last few days. I confirmed that the corresponding .label files are structured identically to those for other ROIs that worked. Just in case it's helpful, this is the command that I used to generate the .label files: mri_cor2label --c /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aparc+aseg.mgz --id 1014 --l /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/label/MedOrbitofrontal_LH_${identifier}.label. Thank you! Jeff

2 2

averaging lh and rh thickness maps on fsaverage_sym surface
by Subhabrata Chaudhury 14 May '13

14 May '13

Hi, I want to create an average thickness map of lh and rh. I have run surfreg steps to map lh to lh sym and rh to rh sym. Can you advise what to do next to mke average thickness maps between two hemispheres ? Will either mris_calc or mri_average work to make the average map ? Thank you Subha

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Freesurfer May 2013