Freesurfer

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30096 discussions

T or Z values in QDEC
by Kelly, Philip 17 May '13

17 May '13

Dear Freesurfer list members, Within QDEC I have found a number of clusters that show significantly different cortical thickness and local gyrification between two groups. The cluster summary exhibits the p value, coordinates and other information regarding the cluster, however I wanted to report the t or z values and was unsure in finding or computing this from QDEC. The p-value must be computed from one of these scores but I could not find it to be reported in any of the output. Searching on the mailing list and tutorials, I could not find an easy solution to this. Thanks for your time and I look forward to hearing back. All the best, Philip Kelly

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Freesurfer hemisphere surface flipping
by Hamza Alshuft 16 May '13

16 May '13

Dear Freesurfers and experts Does anyone know how to flip hemisphere surfaces (cortical thickness) for with-in group analysis? I am analysing a cohort of unilateral chronic knee OA patients and want to within-group correlate the cortical thickness changes with the mechanical pain threshold. (A perfect study would be having only Rt. or Lt. knee pain and then the hypothesis would be a contra-lateral brain cortical thickness changes) but since I have a mixed patients of Rt and Lt knee pain, I want to flip only one group to match the other and make them all as they were having same laterality, and then do a correlation analysis using QDEC! Any help will be much appreciated Thanks Hamza This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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F Problem running : mri_cc -aseg.auto_
by Ray, Siddharth 16 May '13

16 May '13

Hi, I am new to freesurfer and was trying to run it on couple of my subjects but I am stuck (for last 40 hrs) at stage "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/sray2/Desktop/combirx/cr052_ip_output/mri/transforms/cc_up.lta cr052_ip_output" it seems. The last few lines of the log file were: searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.1 global minimum found at slice 122.0, rotations (-3.99, 3.36) final transformation (x=122.0, yr=-3.992, zr=3.355): 0.996 -0.059 -0.069 25.704; 0.058 0.998 -0.004 -3.212; 0.070 0.000 0.998 -51.078; 0.000 0.000 0.000 1.000; Have anyone came across this error before ? and know how to fix this. Please let me know. Thanks in advance. ~Siddharth Ray P.S. I have attached the log file here.

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5.3 mri_convert bug?
by Chris Steward 16 May '13

16 May '13

Hi, Tried running recon-all on two different linux systems and same error occurs in the mri_nu_correct.mni.log when running mri_convert on the nu1.mnc ie.. . . . Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 64 CV of field change: 0.000946853 Outputting Volume: ............................................................ mri_convert ./tmp.mri_nu_correct.mni.24934/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.24934/nu1.mnc orig_nu.mgz --like orig.mgz --conform ncopen: filename "./tmp.mri_nu_correct.mni.24934/nu1.mnc": Not a netCDF file miopen: MINC package entry point Error opening ./tmp.mri_nu_correct.mni.24934/nu1.mnc mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.24934/nu1.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.24934/nu1.mnc... Any help appreciated. Thanks, Chris

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Differences between FLIRT & bbregister-TRACULA outputs out of expected range
by Ali Ezzati 16 May '13

16 May '13

Hello FreeSurfers and TRACULA expert, I would be grateful if anyone could help me with my problem: I was able to run all the steps of TRACULA on several subjects without any error message. My problem is that the average FA/MD/RD/AD outputs are not in the same range as previous studies. For example, the average FA values for all the tracts are between 0.6 and 0.8, which I think is too high - especially since my population are elderly adults. I wonder if anyone else had the same issue and if anyone can help me what might be the source of the problem. While I was trying to narrow down the possible sources of error, I reran a couple of subjects registering with both "FLIRT" & "bbregister". I think in the latest version of tutorial "bbregister" is the preferred method. The results show very large differences between the 2 methods! Is this expected &/ normal? Although these are different from each other, both of them still are out of range (i.e. average FA value 20% more than literature), so registration method -alone- is not the source of my 1st problem. Thank you so much, Ali

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Fsaverage b0
by Fotiadis, Panagiotis 16 May '13

16 May '13

Hi FreeSurfer experts, I was wondering whether there is an average b0 scan in the fsaverage space or in the MNI space? Thank you, Panagiotis.

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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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