Freesurfer February 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
199 discussions

Re: [Freesurfer] What does trac-all do on the file 'bvecs'?
by Xiangzhen Kong 07 Feb '12

07 Feb '12

Could you give me something about the transpsition here? I checked the code flip4fsl and found there are two kinds of sign. line 59. set sign = `echo $inorient | sed "s/[LAS]/+\ /g; s/[RPI]/-\ /g"` line 99. set sign = `echo $inorient | sed "s/[RAS]/+\ /g; s/[LPI]/-\ /g"` e.g. When the orientation of DWI is LPS, we have to transform data to RAS. ($fslplipx=1) The first sign = +-+ and the second sign = --+. So I have to multiple the bvecs(extracted from DICOM) by [-1 -1 +1], but NOT [+1 -1 +1]. Why are they different? Thanks! 2012-02-04 Xiangzhen Kong 发件人： Anastasia Yendiki 发送时间： 2012-02-04 00:48:58 收件人： Xiangzhen Kong 抄送： freesurfer 主题： Re: [Freesurfer] What does trac-all do on the file 'bvecs'? When the DWIs are transformed to LAS and processed with eddy_correct, the same transformations are applied to the respective bvecs. On Fri, 3 Feb 2012, Xiangzhen Kong wrote: > Hi, all~ > ? > I use trac-all with .nii data, not dicom. So I have to specify the bvecs and > bvals in the config file. > Trac-all requires a bvecs file in 3 columes, but FSL need that in 3 raws. > I wonder what does trac-all do on the bvecs file that I specify. > And I have check the code 'trac-preproc' and the log, but found nothing, > except copy and Eddy-current "correction". > ? > ps: The orientation of my dicom and .nii fils are both LPS, and the bvecs is > read from the DICOM header via nibabel. > But FSL requires LAS. I thinks trac-all have done the transposition on the > bvecs somewhere. > What orientation of bvecs does trac-all need when run with .nii files? > ? > Thanks! > ? > Xiangzhen > ? > 2012-02-03 > ? > > 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.

3 3

Re: [Freesurfer] Conversion of an mgh file to nii (fwd)
by Bruce Fischl 07 Feb '12

07 Feb '12

FYI ---------- Forwarded message ---------- Date: Tue, 7 Feb 2012 09:15:37 -0500 From: Ziad Saad <saadz(a)mail.nih.gov> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Conversion of an mgh file to nii I just realized my post got rejected from the message list since I I am not a subscriber. Could you throw it up there for me? thanks z On Feb 7, 2012, at 9:10 AM, Bruce Fischl wrote: > thanks Ziad > Bruce > On Tue, 7 Feb 2012, Ziad Saad wrote: > >> Greetings, >> >> I am not sure what is causing the problem but if you are trying to create a volume where you have a non zero value at some coordinate you can use: 3dUndump with options -xyz and -master . This will create a mask volume with a non-zero value at specified xyz locations, or around these locations depending on the options you use. The -xyz option is used to specify the coordinate which you get from your seed location in FreeSurfer and the master option specifies the dataset grid that your output should match - the time series for regression analysis. >> This assumes, that the X Y Z of the dipole location corresponds to the same anatomical location as the X Y Z in your volumes. Note that AFNI uses RAI for axis orientation, so you'll likely need to negate the 1st two dimensions of the X Y Z you have at hand. >> You could also create volumetric masks with more complicated routes, such as 3dSurf2Vol but I don't see the reason for that. >> >> cheers, >> Ziad >> >> On Feb 6, 2012, at 7:16 PM, Bruce Fischl wrote: >> >>> you could do the same if you sampled your test.nii into the volume. At >>> the moment it's a surface overlay, so as Doug points out no volume loader >>> will know what to do with it. You need the surface geometry/topology to >>> properly display it. If you want to sample it into the volume I think you >>> want mri_surf2vol. >>> >>> cheers >>> Bruce >>> >>> On Mon, 6 Feb 2012, Omer Tal wrote: >>> >>>> Hey Bruce, >>>> >>>> Maybe I can give more background information to help explain what I am >>>> trying to do here. >>>> >>>> I have a subject which I have both MEG and fMRI data on. When I >>>> reconstructed my subject, I chose a dipole as a seed location and used it >>>> for my MEG analysis. Now I want to use the same location as a seed for my >>>> fMRI analysis, so I created an mgh file which had the value of 1 only in >>>> the FS vertex/dipole corresponding to my seed. I can view all versions of >>>> it, mgh, mgz and nii w/ no problem on tksurfer. On FSL though, I can't. >>>> >>>> The reason I went this approach is when I wanted to use the same >>>> aparc_aseg parcellations in my fMRI data, all i had to do is use >>>> mri_convert on the aprac+aseg.mgz and I had a nice nii file I could view >>>> in FSL or AFNI overlaying my fMRI data and use the same ROIs in both >>>> modalities for analysis. Therefore, I thought it would make sense to do >>>> the same here, and create a mgh/mgz file and convert to an nii to get my >>>> mask that I could use in AFNI. >>>> >>>> Do you believe my approach is impractical? >>>> >>>> For loading in AFNI, all I did was afni test.nii. >>>> >>>> Thank you, >>>> Omer >>>> >>>>> Ziad: any idea why Omer can open this file in tksurfer but not afni? Omer: >>>>> I don't think you'll be able to load it in FSL since it's essentially a >>>>> surface. Can you give us details about how you are trying to load it in >>>>> AFNI? Are you using SUMA? >>>>> >>>>> On Mon, >>>>> 6 Feb 2012, Omer Tal wrote: >>>>> >>>>>> Sorry, that was the wrong error description (for the AFNI portion). >>>>>> >>>>>> It just says cannot open dataset test.nii >>>>>> >>>>>> Well, if it doesn't work on FSL or AFNI, I would guess it is the >>>>>> conversion process from FreeSurfer. I don't think anyone on AFNI knows >>>>>> mri_convert or mri_sruf2surf. >>>>>> >>>>>> Honestly just trying to get support for your product for a very simple >>>>>> task, not sure where else I could find someone who would know how to use >>>>>> FS outputs. >>>>>> >>>>>> Omer >>>>>> >>>>>> >>>>>>> It sounds like it is doing the right thing. The geometry is going to be >>>>>>> bogus because it is a surface. You should post to the AFNI list. >>>>>>> doug >>>>>>> >>>>>>> Omer Tal wrote: >>>>>>>> Hey Bruce, >>>>>>>> >>>>>>>> So the mgh file loads fine in tksurfer (shows proper map) for the >>>>>>>> given >>>>>>>> subject, and so does its corresponding mgz (created from mri_convert). >>>>>>>> >>>>>>>> In FSL there is no physical error, but when loading in the nii file, >>>>>>>> the >>>>>>>> X >>>>>>>> location is in ~786XX instead of the typical -128 to 128 or something >>>>>>>> close, Y has no slices to go through at all, and Z seems for the most >>>>>>>> part >>>>>>>> normal (240 slices centered at 0). >>>>>>>> >>>>>>>> When I was trying to load those in AFNI, it simply said "ncols 157373 >>>>>>>> in >>>>>>>> volumes exceeds 32768" even though the reshape has been done. >>>>>>>> >>>>>>>> Thank you, >>>>>>>> Omer Tal >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> does it load ok in freesurfer (in tksurfer)? What error do you get in >>>>>>>>> AFNI/FSL? If it >>>>>>>>> >>>>>>>>> On Mon, 6 Feb 2012, Omer Tal wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>>> Hey Doug, >>>>>>>>>> >>>>>>>>>> Here is what I type it the terminal and what pops back at me. The >>>>>>>>>> error >>>>>>>>>> shows up later when trying to load (either though AFNI or FSL). >>>>>>>>>> >>>>>>>>>> mri_surf2surf --sval test.mgh --tval test.nii --reshape-factor 241 >>>>>>>>>> --s >>>>>>>>>> 111123 --hemi lh >>>>>>>>>> >>>>>>>>>> srcsubject = 111123 >>>>>>>>>> srcval = test.mgh >>>>>>>>>> srctype = >>>>>>>>>> trgsubject = 111123 >>>>>>>>>> trgval = test.nii >>>>>>>>>> trgtype = >>>>>>>>>> srcsurfreg = sphere.reg >>>>>>>>>> trgsurfreg = sphere.reg >>>>>>>>>> srchemi = lh >>>>>>>>>> trghemi = lh >>>>>>>>>> frame = 0 >>>>>>>>>> fwhm-in = 0 >>>>>>>>>> fwhm-out = 0 >>>>>>>>>> label-src = (null) >>>>>>>>>> label-trg = (null) >>>>>>>>>> OKToRevFaceOrder = 1 >>>>>>>>>> Reading source surface reg >>>>>>>>>> /home/otal/raweegmeg/structuralDB//111123/surf/lh.sphere.reg >>>>>>>>>> Loading source data >>>>>>>>>> INFO: trgsubject = srcsubject >>>>>>>>>> Saving target data >>>>>>>>>> Reshaping 241 (nvertices = 157373) >>>>>>>>>> Saving to test.nii >>>>>>>>>> >>>>>>>>>> Thank you, >>>>>>>>>> Omer Tal >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> what's your command line and terminal output? >>>>>>>>>>> >>>>>>>>>>> Omer Tal wrote: >>>>>>>>>>> >>>>>>>>>>>> Tried both, but neither gave a proper nii image. >>>>>>>>>>>> >>>>>>>>>>>> Any other ideas? >>>>>>>>>>>> >>>>>>>>>>>> Omer Tal >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>>> That particular number factors to 241 and 653, so use one of >>>>>>>>>>>>> those >>>>>>>>>>>>> as >>>>>>>>>>>>> the reshape factor to surf2surf. >>>>>>>>>>>>> doug >>>>>>>>>>>>> >>>>>>>>>>>>> Omer Tal wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> Hey Doug, >>>>>>>>>>>>>> >>>>>>>>>>>>>> I believe for this patient/hemisphere the number of vertices is >>>>>>>>>>>>>> 157373. >>>>>>>>>>>>>> >>>>>>>>>>>>>> What is the workaround in the case my number of vertices is >>>>>>>>>>>>>> unluckily >>>>>>>>>>>>>> a >>>>>>>>>>>>>> prime? >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>> Omer Tal >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Omar, how many vertices? The reshape only works if the >>>>>>>>>>>>>>> number >>>>>>>>>>>>>>> is >>>>>>>>>>>>>>> not >>>>>>>>>>>>>>> prime (actually the largest prime factor has to be less than >>>>>>>>>>>>>>> 2^15. >>>>>>>>>>>>>>> doug >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Omer Tal wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hey Bruce, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thank you for the prompt response. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The line is as follows: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> mri_convert -it mgh -ot nii test.mgh test.nii. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Since I do agree that the issue is arising from the NIFTI bit >>>>>>>>>>>>>>>> limit, >>>>>>>>>>>>>>>> i >>>>>>>>>>>>>>>> tried doug's suggestion of >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> mri_surf2surf --sval test.mgh --tval test.nii --reshape-factor >>>>>>>>>>>>>>>> 6 >>>>>>>>>>>>>>>> --s >>>>>>>>>>>>>>>> subject_name --hemi lh >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> But it doesn't seem to solve the problem. even though now i >>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>> load >>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>> through FSL without it failing and quitting, the image is >>>>>>>>>>>>>>>> faulty >>>>>>>>>>>>>>>> w/ >>>>>>>>>>>>>>>> over >>>>>>>>>>>>>>>> 78,000 data points in the X direction, none in Y, and 240 in >>>>>>>>>>>>>>>> Z. >>>>>>>>>>>>>>>> At >>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>> point, Doug told him to send the file in and no more follow-up >>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>> shown... >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Please advise. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thank you very much, >>>>>>>>>>>>>>>> Omer Tal >>>>>>>>>>>>>>>> UCSD Keck Center for Functional MRI >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Omer >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> what file are you trying to convert? What is your entire >>>>>>>>>>>>>>>>> command >>>>>>>>>>>>>>>>> line >>>>>>>>>>>>>>>>> with output and what problems do you have? Nifti >>>>>>>>>>>>>>>>> unfortunately >>>>>>>>>>>>>>>>> only >>>>>>>>>>>>>>>>> allows >>>>>>>>>>>>>>>>> 16 bits for the width/height/depth/nframes, so surface >>>>>>>>>>>>>>>>> overlays >>>>>>>>>>>>>>>>> can't >>>>>>>>>>>>>>>>> usually fit as nvertices x 1 x 1 x nframes since nvertices > >>>>>>>>>>>>>>>>> 2^16 >>>>>>>>>>>>>>>>> (or >>>>>>>>>>>>>>>>> 2^15 >>>>>>>>>>>>>>>>> signed). >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> cheers >>>>>>>>>>>>>>>>> Bruce >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Mon, 6 Feb 2012, Omer >>>>>>>>>>>>>>>>> Tal wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hey there, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I am trying to convert an mgh file I created into an nii >>>>>>>>>>>>>>>>>> volume >>>>>>>>>>>>>>>>>> so >>>>>>>>>>>>>>>>>> I >>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>> load it in AFNI. I was trying to use mri_convert, which I >>>>>>>>>>>>>>>>>> have >>>>>>>>>>>>>>>>>> used >>>>>>>>>>>>>>>>>> previously to make nii volumes from my aparc+aseg and it >>>>>>>>>>>>>>>>>> worked >>>>>>>>>>>>>>>>>> great, >>>>>>>>>>>>>>>>>> but >>>>>>>>>>>>>>>>>> this time the resulting file is faulty. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I've noticed a previous thread where someone ran into a >>>>>>>>>>>>>>>>>> similar >>>>>>>>>>>>>>>>>> problem, >>>>>>>>>>>>>>>>>> and it had to do w/ too many vertices existing for NIFTI, >>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>> Doug >>>>>>>>>>>>>>>>>> suggested using mri_surf2surf, but it didn't work for that >>>>>>>>>>>>>>>>>> guy >>>>>>>>>>>>>>>>>> or >>>>>>>>>>>>>>>>>> me >>>>>>>>>>>>>>>>>> (at >>>>>>>>>>>>>>>>>> which point I think he was sending you files). >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Seems like it should be something common and trivial, but I >>>>>>>>>>>>>>>>>> can't >>>>>>>>>>>>>>>>>> get >>>>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>>>> too work, any suggestions? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thank you, >>>>>>>>>>>>>>>>>> Omer Tal >>>>>>>>>>>>>>>>>> UCSD Keck Center for Functional MRI >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> 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. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> 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 >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>> >>>> >>>> >> >> >> >>

1 0

problem defining mrs voxel using mri_volsynth
by Todd Jolly 07 Feb '12

07 Feb '12

Hi all, Recently I have been trying to reconstruct a mrs voxel using mri_volsynth using the VOIpositions given in the .rda file. The VOI co-ordinates are as follows: VOIPositionSag 31.6911 VOIPositionCor -25.1448 VOIPositionTra 24.5879 When I input these co-ordinates into mri_volsynth the voxel is in the wrong location. However when I reverse the sign for the Sag and Cor positions then the voxel is very close to right position. After a lot of trial and error I found that after inverting the sign for the X and Y co-ordinates, I have to then +1 on all 3 positions in order for the synthesised volume to be in the correct position. So using the three positions shown above I have to use the following command: mri_volsynth --dim 18 18 18 1 --pdf const --c_ras -30.6911 26.1448 25.5879 --o filename Can anyone explain why I have to reverse the sign and add 1 in order for the voxel to be in the correct location? Is it something to do with using the dcm2nii converter? Also is it normal for the .rda to give the co-ordinates for the centre of the voxel rather than the top corner of the voxel? Thanks Todd

1 0

Conversion of an mgh file to nii
by Omer Tal 07 Feb '12

07 Feb '12

Hey there, I am trying to convert an mgh file I created into an nii volume so I can load it in AFNI. I was trying to use mri_convert, which I have used previously to make nii volumes from my aparc+aseg and it worked great, but this time the resulting file is faulty. I've noticed a previous thread where someone ran into a similar problem, and it had to do w/ too many vertices existing for NIFTI, and Doug suggested using mri_surf2surf, but it didn't work for that guy or me (at which point I think he was sending you files). Seems like it should be something common and trivial, but I can't get it too work, any suggestions? Thank you, Omer Tal UCSD Keck Center for Functional MRI

3 21

applying new cortical parcellations
by David Grayson 06 Feb '12

06 Feb '12

Hi Freesurfer experts, I would like to apply a novel cortical parcellation from an average surface (http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011) to subjects that I have previously ran through recon-all. I have found a number of tools that seem related to this – can anyone tell me the precise steps that need to be taken? Thank you very much, David

2 1

question regarding my contrast
by Jacobs H (NP) 06 Feb '12

06 Feb '12

Dear FreeSurfers, I have been doing some basic cortical thickness analyses, which all went good. Now I want to analyze some additional things, and I want to make sure that my contrast files are ok. Could you help me out or give me advice? So, I have three groups (control - MCI - Alzheimer) and I want to examine the effect of blood pressure on each group separately (corrected for age centered). Thus, I would make three different fsgd files with this contrast: 0_1_0 Then I want to compare how blood pressure effects the group differences (controls vs MCI / MCI vs AD/ controls vs AD) when controlling for age: would that be: 0.5 -0.5 -0.5 0.5 0 0 ? Every help is greatly appreciated1 Thank you Best Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

1 0

ribbon.mgz Without aseg.mgz
by Clark Fisher 06 Feb '12

06 Feb '12

Hello, I'm working with primate data, and I'm wondering: is there any way to create a ribbon.mgz file from surfaces since I don't have aseg.mgz? I can't seem to run mris_volmask without it, and running reconall -autorecon3 -noaseg did not output ribbon.mgz. Thanks for the help, Clark

2 2

Gyrus tracing
by Jordan Poppenk 06 Feb '12

06 Feb '12

Dear Freesurfer experts, While the recon-all stream makes it easy to map gyri onto specific voxels via the label files that are produced, I'm interested in tracing a gyrus from beginning to end to gather info along that gyrus. I can't do this based on just aparc voxel maps because of the way that gyri fold -- I can't tell if a gyrus has suddenly become very fat or has simply folded back and forth. The best thing would be to access the line that Freesurfer thinks marks the middle of the gyrus as well as the lines delimiting its sulcal boundaries. I get the impression that Freesurfer computes this during the normal recon-all stream on an inflated sphere. My question is: is it possible to access this information? If so, where might I look? Thank you in advance for any advice you might be able to offer. Cheers, Jordan ____________________ Jordan Poppenk, Ph.D. Post-doctoral Research Fellow Princeton Neuroscience Institute jpoppenk(a)princeton.edu

2 5

Re: [Freesurfer] persistent bvecs error
by Alexander Lebedev 04 Feb '12

04 Feb '12

Hello Anastasia! Thank you very much for your response! My bvecs and bvals were created by saving excel spreadsheet as a tab delimited file on mac. I reformated my bvecs manually using "nano" and reran the preprocessing. Unfortunately, it exited with the same error. I'm providing you my reformated bvecs... I believe that the problem is not in reading of decimals, because running this step with "fake" bvecs of 1s and 0s (test_bvecs.txt) produces the same output with zeros, and everything seems to be ok with the tutorial dataset... What would you suggest? --- Best Regards, Alex

1 1

Re: [Freesurfer] vertex extraction
by Douglas N Greve 04 Feb '12

04 Feb '12

Hi Alex, we don't have an elegant solution to this, but you can do it in matlab easily enough. If your data D are in a N-by-327684 matrix (I assume that this is left and right hemis), then a.vol = permute(D(:,1:163842),[2 3 4 1]); MRIwrite(a,'lh.yourdata.mgh'); b.vol = permute(D(:,163843:end),[2 3 4 1]); MRIwrite(b,'rh.yourdata.mgh'); doug Alexander Lebedev wrote: > Excuse me for disturbing Douglas, > > The matter is that I have the coefficients for each vertex and I would > like to find the easiest way to display them into the brain space, > showing their importance for the classification. My original ascii > file contains N-by-327684 matrix (N subjects, 327 684 vertices - 163 > 842 for each hemisphere). But I can easily change it if necessary... > I'm just wondering if there is a way to do this... I'm asking because > it seems like "y.mgh -> y.asc" (mri_convert y.mgh y.ascii --ascii) > conversion is available only one-way. > --- > Regards, > Alex > > > * Alexander Lebedev <awlman(a)rambler.ru> [Fri, 27 Jan 2012 10:07:11 > +0400]: >> Yes, sorry... >> --- >> Alex >> >> > Hi Alex, I'm not sure I understand what you mean. Do you mean that > you >> > have a coefficient for each vertex and you want to display your >> results >> > on a surface and need to get them into a format that FS can read? >> > doug >> > >> > Alexander Lebedev wrote: >> > > Yes, thanks a lot Douglas! That's what I was looking for. And it's >> > > much easier than my approach... I needed to extract the vertices > in >> > > order to perform a multivariate analysis in R. May I also ask >> another >> > > question then? I have performed pls-regression and would like to > map >> > > the coefficients into the brain space... Is there such an >> opportunity >> > > (at least theoretically speaking) ? >> > > --- >> > > Regards, >> > > Alex >> > > >> > > > > -- 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

2 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer February 2012