Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

Subcortical volume stream
by Gabor Perlaki 21 Jan '14

21 Jan '14

Dear all, Is there any commands in Freesurfer, which segment only the subcortical structures for me? The -autorecon2 calculates also the surfaces which seems unnecessary. However, I don't know whether the final surfaces have an effectt on subcortical volumes. There was a question about it on the Freesurfer's mailing list, but no answer ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/031576.html) Which is the most time-efficient way to get subcortical segmentation with Freesurfer? Thanks, Gabor

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Problem with the Monte Carlo simulation
by Sophie Maingault 21 Jan '14

21 Jan '14

Dear FreeSurfer experts, We are running group analyses in 430 young healthy volunteers using Qdec interface and FreeSurfer 5.3. FDR correction seems to be not enough restrictive and on the contrary use a Bonferroni correction with the total number of vertices would be too much restrictive. In this context we would like to use the Monte Carlo simulation but we built our specific template and as you may know this is not possible in this case, this error message being displayed: " Erreur in Monte Carlo simulation: This function only works when using fsaverage as the common-space subject ". Thus I have two questions: 1) is it possible to adapt the Monte Carlo simulation to our template using some command line or something else? 2) If not what advice can you give to us? Thanks a lot, Best regards, Sophie Maingault

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Changing primary slice direction
by Arash Jalalian 20 Jan '14

20 Jan '14

Hi Freesurfer Community, I am using matlab to do a histogram segmentation on a FLAIR volume. The algorithm I am using best works with axial direction. Is there any way to change the primary slice direction from sagittal to axial? I have tried mri_convert with --out_orientation set to LIA but that produces coronal. Regards, Arash

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Join my network on LinkedIn
by Rosalia Dacosta Aguayo via LinkedIn 19 Jan '14

19 Jan '14

LinkedIn ------------ Rosalia Dacosta Aguayo requested to add you as a connection on LinkedIn: ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accept invitation from Rosalia Dacosta Aguayo http://www.linkedin.com/e/-qq80um-hqm8yw3z-1f/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… View profile of Rosalia Dacosta Aguayo http://www.linkedin.com/e/-qq80um-hqm8yw3z-1f/rso/112324517/IcZz/name/66471… ------------------------------------------ You are receiving Invitation emails. This email was intended for Freesurfer List. Learn why this is included: http://www.linkedin.com/e/-qq80um-hqm8yw3z-1f/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Fwd: Control point failure - CA Normalize
by Mark Plantz 17 Jan '14

17 Jan '14

Hi Bruce, The nu.mgz file looks OK to me (I also attached a picture). When I opened the talairach with "tkregister2" everything looked ok, except I couldn't get the green lines from the original surface to show (even after pressing 's' in the viewing window). Anyways, since these two files seem to be OK, do you think it is an atlas issue? Thank you! - MP On Thu, Jan 16, 2014 at 7:36 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Mark > > does the input to mri_ca_normalize look ok (the nu.mgz)? Is the > talairach.xfm ok? > > Bruce > > On Thu, 16 Jan 2014, Mark Plantz wrote: > > Hello freesurfers, >> >> I am running into a problem during the "CA Normalize" sequence of >> autorecon-2. It looks like freesurfer is having a hard time creating >> control >> points based off the atlas I am using. The output is as follows: >> >> "finding control points in <Left_Cerebral_White_Matter>...found 0 >> control >> points" >> >> This repeated for the other various regions included in the atlas. >> The >> only control points found were "168 control points" in the >> "Right_Cerebral_White_Matter". Could this possibly be an alignment issue? >> If >> so, is there an easy way to check the alignment? >> >> Thank you, >> >> >> Mark >> >> >> >> >> >> >> > > 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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BEM Surfaces
by obregon＠nmr.mgh.harvard.edu 17 Jan '14

17 Jan '14

Hi, Happy New Year everyone! I'm having issues creating the BEM meshes for one of my subjects using mne_watershed_bem: the outer skull surface is crossing the inner skull surface and cutting into the brain (image attached). I know this program employs Freesurfer's watershed algorithm, though I'm not entirely sure how it does so. Could someone please advise me on how to fix this issue? Thanks! --G

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Desikan atlas in MNI space (in a nii file)?
by Fred Sampedro 17 Jan '14

17 Jan '14

Dear FreeSurfer users, I am searching for the Desikan atlas (which I have in the tailarach space) in the MNI space, as a file (Desikan_mni.nii). I am aware that transforming from one space to the other is not a very good idea but nevertheless I would like to test some computations. Anyone can attach/send a link/know of if exists such a file? Thanks a lot Fred Sampedro Hospital de Sant Pau (Barcelona)

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xhemi correct for multiple comparisons
by krista kelly 17 Jan '14

17 Jan '14

Hello, I'm analysing interhemispheric differences using xhemi. I have followed the instructions on the webpage with no problems. I do have a few questions though. 1) When viewing the results in tksurfer, which color represents "left hemisphere is larger" and which represents "right hemisphere is larger"? 2) I have no idea how to view the results in tksurfer AFTER performing the step of correcting for multiple comparisons. Any suggestions? 3) I've noticed from the archives that some people are performing laterality indices. How would I calculate laterality indices? Thanks! Krista

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V1.thresh
by krista kelly 17 Jan '14

17 Jan '14

Hi all, Can anyone provide information regarding how v1.thresh.label and v2.thresh.label that are automatically implemented in FreeSurfer are thresholded? Thanks! Krista

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xyztrans error
by Tessa Vuper 17 Jan '14

17 Jan '14

Hi all, I receive the following error when I run the selxavg3 -sess command: ERROR: cannot find /usr/local/freesurfer/stable5/bin/fsl. 5.0.2.xyztrans.sch Any thoughts on how to fix this? Thank you so much for your help, tessa Tessa Vuper Clinical Research Coordinator, Manoach Lab Psychiatric Neuroimaging, MGH Martinos Center for Biomedical Imaging 617-726-1908

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Freesurfer January 2014