Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

Reviewer not satisfied
by Jürgen Hänggi 24 Jun '13

24 Jun '13

Dear FS experts In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition. We wrote the following: The thickness maps produced are not limited to the voxel resolution of the image and thus sensitive for sub-millimeter differences between groups (Fischl, Dale 2000). The way in which the resolution of the cortical thickness maps goes beyond the resolution of the original acquisition can be imagined as a (conventional) partial volume correction procedure. The cortex is smooth at the spatial scale of a couple of millimeters, which is imposed as constraint by FreeSurfer to estimate the location of the surface with subvoxel accuracy. For instance, if a given voxel is darker than its neighbouring grey matter it probably contains more CSF and so the surface model is at a slightly different position than if the neighbouring voxels were brighter and therefore contain probably more white matter. Now, the reviewer says that we are to vague in our description. He would like to know what is exactly meant by a "couple of millimeters". Is this 1-3 mm or rather 3-5 mm or any other value? Thanks in advance for any suggestion 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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ribbon label volume mapping
by Colin Reveley 23 Jun '13

23 Jun '13

If one has a volume of integers, each representing a cortical area, can one map that to the surface as a set of labels, in a smart way that e.g. takes the mode of the voxels that lie on the vector between equivalent white and pial nodes (ie uses curvature and thickness information, tacitly or explicitly)? the labels are not exactly on the ribbon. There are many voxels outside the ribbon that are non zero. Like caudate etc. and some voxels that are within the ribbon but are zero because the label data is was/is non-isotropic originally (which is the problem we want to solve in fact). that would be great. Now let's say you already have labels on a mesh. can you generate a ribbon volume of labels, i.e. the opposite operation to what I enquire about above (opposite but not inverse operation)? This is work in rhesus. So my pipeline is very barebones indeed, really just mri_normalize ... mri_tesselate mri_inflate/smooth/sphere mris_fix_topology <-noaseg -noaprc> mris_make_surfaces <-naseg -noaparc> I only have access to what is generated by that sequence or what I can subsequently generate. I can generate a freesurfer like ribbon with mris_fill. My understanding of labels and data mapping in general in freesurfer is very poor. Maybe adapting one of your matlab scripts might be an idea, if there is not another way? many thanks, Colin, Sussex

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Re: [Freesurfer] Cortical statistical maps
by 传玺 23 Jun '13

23 Jun '13

Dear FS expert, I have run recon-all on all my subjects, and how can I get Cortical statistical maps except QDEC? -------- Forwarding messages -------- From: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> Date: 2013-06-23 20:50:43 To: "传玺" <13611360710(a)163.com> Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cortical statistical maps what three steps? Have you run recon-all on all your subjects? If you, check out qdec if your analysis is a simple one? On Sun, 23 Jun 2013, ?? wrote: > Dear FS expert?I have complete those three steps of FS,then how can I get the Cortical statistical > maps? as follows:[IMAGE] > > thank you for your help! > > > > > ?????????????? > >

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Cortical statistical maps
by 传玺 23 Jun '13

23 Jun '13

Dear FS expert： I have complete those three steps of FS,then how can I get the Cortical statistical maps? as follows: thank you for your help!

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TRACULA - tract volume and length
by Fred Sanders 22 Jun '13

22 Jun '13

Dear DTI experts, I am trying to understand how to interpret tract length & volume measurements that TRACULA provides. For example, let’s say a clinical population differs from a control group in mean FA of a particular tract, and tract length & volume are comparable across the 2 groups. I think this would support the notion that the tract’s diffusion properties are indeed different across the two groups and that the FA finding are unlikely to be an artifact of probabilistic tractography. Is this a correct interpretation? Conversely, if group differences in tract volumes were detected, would you recommend comparing mean FA across the two group while covarying for tract volume? Thanks!

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Possible to generate connectivity map using FS and Tracula
by Salil Soman 22 Jun '13

22 Jun '13

Dear Doug, Is there a way to use the Freesurfer and Tracula output to compute connectivity maps? Thanks! Sal

3 2

check orientation
by Brigitte Dahmen 22 Jun '13

22 Jun '13

Dear Freesurfer experts, is there a command in Freesurfer to check for correct orientation (LAS vs. PSR) of T1 images (similar to "fslhd" in FSL)? Thank you very much! Brigitte

5 9

retinotopic mapping selxavg3-sess error
by Bianca van Kemenade 21 Jun '13

21 Jun '13

Dear Freesurfers, I'm setting up freesurfer to do retinotopic mapping. I use a PC with Windows XP, so I installed Freesurfer using the VirtualBox (with Xubuntu). I managed to get through the initial steps for retinotopic mapping, but I get stuck at the actual analysis. The point where I get stuck is: selxavg3-sess -a rtopy.self.lh -s P2_BK It starts the analysis, but runs into problems at the stage "Using FSL's BET to extract brain" and gives the following error output: # ---------- Using FSL's BET to Extract Brain------------------ # /home/virtualuser/freesurfer/ shared/P2_BK/bold bet.fsl /tmp/mkbrainmask_4425/in.nii /tmp/mkbrainmask_4425/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found /bin/rm: cannot remove `_tmp*': Protocol error ERROR: bet failed I tried updating FSL in case that is the problem, but it is only available for Ubuntu 10.04 and up, whereas the Ubuntu system that is provided to install the Freesurfer virtual disk image is 9.04. If anyone has an idea how to proceed let me know, any help is much appreciated. Thanks, Bianca

2 1

use mri_convert to flip A/P labels
by Ray, Siddharth 21 Jun '13

21 Jun '13

Hi, I have niftii files of some subjects where A/P labels are flipped. Is there anyway I can flip those labels using mri_convert, like mri_convert -left-right-reverse for flipping L/R labels. Thanks, -Siddharth

2 1

Fwd: missing surfaces
by Deirdre O Shea 21 Jun '13

21 Jun '13

---------- Forwarded message ---------- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: Fri, Jun 21, 2013 at 11:33 AM Subject: Re: [Freesurfer] missing surfaces To: Deirdre O Shea <deirdreoshea84(a)gmail.com> Hi Deirdre can you cc the list so that others can answer? Bruce On Fri, 21 Jun 2013, Deirdre O Shea wrote: Hi Doug and Bruce, > > I have an error.logs file which shows only this message for one of the > subjects.. > > mrisReadTriangleFile(/share/**users/doshea/WHICAP_PET/** > W32714V2/3DT1/FreeSurfer/surf/**rh.pial): surface > doesn't match /share/users/doshes/WHICAP_**PET/w32714v2/3dt1/ > > > > > On Fri, Jun 21, 2013 at 9:57 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Deirdre > > can you send us the recon-all.log, or at least the last 100 lines of > it? > cheers > Bruce > > On Thu, 20 Jun 2013, Deirdre O Shea wrote: > > Dear FreeSurfers, > > I have been using FreeSurfer for editing for the past year now > and I have > recently come across an > issue that I have not seen before in a new dataset. The pial > surfaces are > missing in the right > hemisphere following the first run of Freesurfer (before any > edits). There > are also some without > white matter surfaces. However, not all my subjects have shown > this and are > just fine. Any > suggestions on how i can fix this? > > Thanks, > Deirdre > > > > > 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<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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Freesurfer June 2013