Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

template replacement
by Ilwoo Lyu 17 Jul '14

17 Jul '14

Dear FS experts, I am trying to adapt a macaque template (dim: 250 by 300 by 300, voxel size: 0.8202 mm). I changed voxel spacing and dimensions to be the same as the MNI305 template in freesurfer, but it seems not to work correctly for the affine transformation in the Talairach space. Here are my questions: 1) Should I change the voxel size and dimensions of the macaque template? 2) Should I change the original coordinate system of the macaque template into the Talairach space? If so, how can I do that (eg, roughly aligned to (or registration) the MNI template)? Thank you! Ilwoo

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Re: [Freesurfer] Temporal lobe reconstruction problem
by james pardon 17 Jul '14

17 Jul '14

Hi Louis, I would appreciate if I could get your feedback on this specific subject we are experiencing problems with. Thanks James On Tue, Jul 15, 2014 at 8:20 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi James > > I did, and one of our RAs here is going to be looking into it. Louis (ccd) > can give you more information > > cheers > Bruce > > On Tue, 15 Jul 2014, james pardon wrote: > > Hi Bruce, >> I was wondering whether you have seen my email below? >> >> Thanks so much >> >> Cheers, >> James >> >> >> On Sat, Jul 12, 2014 at 9:18 AM, james pardon <james.pardon15(a)gmail.com> >> wrote: >> Hi Bruce, >> I have sent the link for a problem subject via a private >> message. Please note since MS causes hypointense lesions in white >> matter I have used an algorithm that fills hypointense lesions in WM >> with median intensity of normal appearing WM. >> >> Thanks >> James >> >> >> On Fri, Jul 11, 2014 at 11:19 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi James >> >> if you upload a problem subject we will take a look (the >> whole subject dir please) >> cheers >> Bruce >> On Fri, 11 Jul 2014, james pardon wrote: >> >> Hi all, >> On a few subjects with a specific pathology >> (MS) I cannot easily reconstruct temporal >> lobes. >> I think this issue comes up quite regularly on >> the mailing list, and I have tried to trouble >> shoot using control points, WM edits, even >> getting back to orig/001.mgz to correct areas >> that >> may seem the culprit for breaking surface >> reconstruction. Some subjects have gone >> through 7-8 >> runs of recon-all with different edits but >> still the problem persists in a few subjects >> in my >> study. >> >> I have also tried to use -mprage and -3T flags >> along the way to allow more liberal control >> point growing, despite an improvement in my >> results some of subjects still have very bad >> surface constructions. I have attached two >> snapshots to this email and I am happy to >> upload >> the complete subject folder if you need to >> take a look at them. >> >> As far as the SNR is concerned, I have >> designed my study based on recommended >> Freesurfer >> parameters a couple of years ago on 3T Siemens >> Trio with 32-channel receiver coil. >> >> A huge thank you for your previous helps, and >> thanks in advance for helping me with this new >> issue. >> >> James >> >> >> _______________________________________________ >> 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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why the size become larger after fdr correction
by wang kangcheng 17 Jul '14

17 Jul '14

Dear experts I use the following command and the Size(mm^2) was28.65. mri_surfcluster --in leg.volume.lh.20/g2v2/sig.mgh --thmin 3.7190 --no-adjust --sign abs --subject fsaverage --hemi lh --annot aparc.a2009s --mask leg.volume.lh.20/mask.mgh --sum leg.volume.lh.20/g2v2/sig.z3.7190.txt # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs Annot 1 4.068 160031 28.65 -7.5 -42.6 9.2 87 G_cingul-Post-ventral However, When I used the FDR correction and found that size become larger (76467.08). mri_surfcluster --in leg.volume.lh.20/g2v2/sig.mgh --fdr 2.3 --no-adjust --sign abs --subject fsaverage --hemi lh --annot aparc.a2009s --mask leg.volume.lh.20/mask.mgh --cwsig 5 --sum fdr.2.3.txt # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs Annot 1 4.068 160031 76467.08 -7.5 -42.6 9.2 149953 G_cingul-Post-ventral Why the size become larger ? Or is there some problem? Thank you

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Polar angle wedge default position
by Jackie Lam 17 Jul '14

17 Jul '14

Thanks Doug. I assume that Freesurfer begins with 0 and proceeds to positive values if one specifies “counterclockwise” in the rtopy.par file, and if one chooses “clockwise” I assume Freesurfer starts with 0 and proceeds to negative values. Is that right? >On 07/16/2014 04:29 PM, Jackie Lam wrote: >> Hello all, >> >> In Freesurfer’s analysis of retinotopy data, what is the phase assigned by freesurfer to the very beginning of the > stimulation paradigm? >> I would assume that it should be 0, but it would be good to verify. > Yes, 0. > Then, how do the phases proceed after the beginning? To negative values or positive values? > positive >> >> In general, which phase values are assigned to a full cycle of the stimulation paradigm (start, 1/4cycle, 1/2 cycle and 3/4 cycle)? > I don't understand what you mean > doug >> >> Thanks >> > _______________________________________________ >> > Freesurfer mailing list >> Freesurfer at nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > > greve at nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > Fax: 617-726-7422

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Can't Remove WM
by Weber, Wade (weberw) 17 Jul '14

17 Jul '14

Hi Surfers, I am running recon-all on some subjects and have run into a strange problem. When we go back to look at the WM voxels for editing, the wm.mgz layer has a light blue tint over the whole layer. When we try to edit the WM voxels, we can add , but we cannot delete any WM voxels. Also, all the WM voxels show up as yellow instead of red as we have set them to show up as red. We tried deleting all the FS files and re-doing the recon-all, but it still shows up like this. This has only happened on 3 or 4 subjects out of about 50. I've attached a picture of our problem Thanks in advance! Wade Weber, MS Clinical Research Manager Division of Bipolar Disorder Research Department of Psychiatry and Behavioral Neuroscience University of Cincinnati

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qdec error
by Anna Jonsson 17 Jul '14

17 Jul '14

Dear group, I now have error loading my qdec table into qdec, for this error fsid column: 1 Number of factors: 8 Number of subjects: 168 ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: age_demeaned for subject XXX However those 5 of those "factors" are continious, and Im assuming the problem is that for some reason qdec thinks they are categorical, and should have a file with levels corresponding to them. How I make freesurfer know they are continuous? Kind Wishes, Linn

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Re: [Freesurfer] How to extract significant result for each subject
by wang kangcheng 17 Jul '14

17 Jul '14

Dear Douglas I try the analysis of volume and other indexes, not just thickness. I was confused that why the data of volume for each subject was so small (data in the file of cache.th13.pos.y.ocn.dat, e.g 1.39463 1.50616 2.53250) after using the command of mri_glmfit-sim (mri_glmfit-sim --glmdir aaa.thickness(or volume, sulc).lh.10 --cache 1.3 pos --cwp 1 --2spaces). Could you tell me the unit for each index (e.g thickness, volume, sulc,pial_lgi)? Thank you

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?Sequence for Hippo_subfields
by Kev 17 Jul '14

17 Jul '14

Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev

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Re: [Freesurfer] trac-all -prep error field map error
by Eileen Moore 17 Jul '14

17 Jul '14

Hi Anastasia, OK - our imaging physicists had developed a wrapper script around epidewarp which takes our dicom images and converts them into the phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). It looks like the tracula script requires dicom images. Is there a way for me to do epidewarp manually and then follow through with the remaining steps using trac-all? Thanks, Eileen. Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <alpine.LRH.2.03.1407141119560.23459(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > > Hi Eileen - That step is run with the program epidewarp.fsl, which you can > run on the command line to see the available options. The input phase map > volume is expected to have either 2 frames (2 separate phase maps) or 1 > frame (the difference phase map). This error from trac-all means that it > found that your input phase map has something other than 1 or 2 frames, so > it doesn't know how to handle it. > > Hope this helps, > a.y > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring > to > > run tracula on some? images acquired from a GE scanner. I am running into > > problems when I try to perform the registration-based B0-inhomogeneity > > compensation, getting an error in the terminal output: "ERROR: > Unrecognized > > format of phase map". However, trac-all -prep runs fine when I skip the > > B0-inhomogeneity compensation step. Is there something else I need to do > to > > use field map correction? > > > > I've attached the trac-all.log and a copy of the terminal output. > > > > Thanks, > > Eileen. > > > > > > > > >

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Error in pre-processing
by 渡辺杏里 16 Jul '14

16 Jul '14

Dear TRACULA experts I am writing to ask about an error in pre-processing in TRACULA. After making FSL radiological header of dwi_orig_flip.nii.gz, an error occurs. When the name of file is changed from dwi_orig_flip.mghdti.bvals to bvals, I can't find the file dwi_orig_flip.mghdti.bvecs. So an error is mv: rename /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals: No such file or directory caused. The content of bvals is not overwritten. I attached my configuration file, the error log and bvals. -error log- fslorient -forceradiological /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.nii.gz INFO: found /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvecs /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvecs mv -f /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals mv: rename /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/dwi_orig_flip.mghdti.bvals to /volumes/mybook/Anri/diffusion_tutorial/HC_025/dmri/bvals: No such file or directory Many thanks for your help. Best Wishes, Anri WATANABE ********************************************************************** 京都府立医科大学附属病院精神科・心療内科渡辺杏里 ********************************************************************** WATANABE ANRI Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine **********************************************************************

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Freesurfer