Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

Articles regarding using FreeSurfer manual interventions
by Liane Hunter 16 Jul '13

16 Jul '13

Hello, I wanted to inquire if anyone knows of any articles in the literature that quantify the differences between using FreeSurfer with and without manual intervention. Thank you Liane -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine

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subcortical segmentation
by Liane Hunter 16 Jul '13

16 Jul '13

Hello, I noticed that when I am checking the subcortical segmentation the brainmaskdoes not accurately display the subcortical structures ( ie. the putamen is too small). The segmentation appears to be correct when I compare it to the original file. Does anyone know why this is the case? Also, if I make changes to the subcortical segmentation based on the original file will this change accurately edit the brainmask? Thank you. Sincerely, Liane Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine

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Re: [Freesurfer] Xhemi question
by Boratyn, Daria A. 16 Jul '13

16 Jul '13

Couple of quick things in regards to smoothing prior to calculating the LI. I'm just trying to use the fsaverage_sym atlas and improve my xhemi registration, not conduct a thickness asymmetry analysis. Should the smoothing be done before the xhemi registration? If so, do you have a recommendation for the smoothing kernel? Also, how many vertices are there in fsaverage_sym's surface? Thank you, Daria Daria A. Boratyn, Clinical Research Coordinator MS Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531 ---------- Forwarded message ---------- From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Date: Fri, Jun 7, 2013 at 1:31 PM Subject: Re: [Freesurfer] Xhemi question To: Daria Boratyn <boratyn(a)nmr.mgh.harvard.edu<mailto:boratyn@nmr.mgh.harvard.edu>>, "Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>" <Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> Hi Daria, the only way is to map the individual curvature to the group space (fsaverage_sym) and see if the curvatures seem to align. doug ps. Please post questions to the FreeSurfer list. Thanks! On 06/07/2013 11:13 AM, Daria Boratyn wrote: > Hi Doug, > > We are experimenting with adding xhemi to our processing stream. Is there > is a way to QC the results at an individual subject level? > > Best, > Daria > > > Daria A. Boratyn, > Clinical Research Coordinator > MS Imaging Lab > Massachusetts General Hospital > 149 13th Street | Boston, MA 02129 > 617-726-7531<tel:617-726-7531> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358<tel:617-724-2358> Fax: 617-726-7422<tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://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<mailto:Freesurfer@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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rtview.sh & fsig
by Michael Bannert 16 Jul '13

16 Jul '13

Dear Freesurfer experts, I have been using Freesurfer in combination with rtview.sh to visualize my retinotopic mapping results (rotating wedge) and to define masks for individual visual areas. The command that I use for this is something like: rtview.sh --s *subj_id* --lh --polar --real polar/real.nii.gz --imag polar/imag.nii.gz --fsig polar/fsig.nii.gz I was under the impression that by specifying fsig, Freesurfer would internally threshold the resulting polar map according to an F-test to show only significant vertices. Is this true? I actually doubt that this is the case because I noticed in the "configure overlay display" that the maps are seemingly arbitrarily thresholded at a "Min" of 0.4. Is this threshold derived based on statistical principle? How can I do proper statistics with fsig.nii.gz in Freesurfer, i.e. define alpha, correct for multiple comparisons etc.? Thanks, Michael P.S.: Just to provide some context for my question... imho it doesn't matter much if a given vertex is significantly activated if the only purpose is to define boundaries between visual areas. However, an exception would be the definition of such boundaries in the cortical surface near the fovea where boundaries between areas cannot be identified as reliably as in more eccentric regions. I was thinking that by focusing only on significant vertices, I would be able to isolate only those voxels that can clearly be assigned to a single visual area - even if that means that I may have to discard some vertices near the fovea. -- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031

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ROI info in the DK atlas
by Yang, Daniel 16 Jul '13

16 Jul '13

Dear FreeSurfer Expert, I would like to draw the specific ROI of the DK atlas (not specific individual, but this ROI in general). I'm wondering how this ROI can be extracted/created as a mask so that I can draw it on the brain using some software? Could you please advise? Thanks a lot, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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tracula -path option 0 unknown
by Gerit Pfuhl 16 Jul '13

16 Jul '13

Dear Freesurfer experts, for one subject (out of over 80 already processed) I get i nthe last step an error I am unable to locate. The output from the tracula -path command says at the end: option 0 unknown. There are no reported problems in -prep, and -bedp. The script uses default values (I run this subject 3 times, always gets stuck on -path, not before). The subject was processed fine in tracule 5.1.0 with flt. Now in 5.2.0 we use bbr Excerpt of the output ... /igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /fastfs/igis/MRI_fs_rec_dti/64-10-094-1/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt ERROR: Option 0 unknown Thanks for all help to understand this Gerit

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Free surfer license error
by Muhammad Naveed Iqbal Qureshi 15 Jul '13

15 Jul '13

Hello,I have successfully installed freeon my mac pro server.but when i try to run the tkmedit it is giving the following error message, although I have copied the license information in freesurfer home directory.[Geodesics:~] EGI% tkmedit bert orig.mgz--------------------------------------------------------------------------ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.Kindly reply me as soon as possible.Thank you Best Regards, Muhammad Naveed Iqbal Qureshi BK21 Student Graduate Research Assistant Computer Vision and Multimedia Lab Department of Computer Engineering Chosun University 375, Seosuk-dong, Dong-gu, Gwangju, 501-759, South Korea Tel: (+82) 62-230-7756 Email: mniqureshi(a)hotmail.com URL: http://cvm.chosun.ac.kr/ P please don't print this e-mail unless you really need to

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Do I need to edit wm.mgz after deleting extra dura?
by ye tian 15 Jul '13

15 Jul '13

Dear Freesurfers, I deleted some extra dura that was included in the pial surface. I recompiled using recon-all -autorecon-pial -subjid <subject_name>. The wm.mgz file, however, was still wrong. Do you think I should edit it as well? The wm.mgz before and after manual editing are shown on the left and right panels of the attachment. Thank you very much! Sincerely, Ye

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Re: [Freesurfer] Working with MEMPRAGE
by Kayle Sawyer 15 Jul '13

15 Jul '13

Hi all, Can the MEMPRAGE be specified in recon-all with the -i flag? We have been using the MEMPRAGE RMS scans and discarding the multiecho scans. If we instead specify the multiecho scans for recon-all, do we need to give any additional parameters (e.g. the number of echoes) for it to utilize the 4 echoes to detect dura and refine pial surfaces in mris_make_surfaces, as described below? Or would we have to run recon-all with the RMS, then after it finishes re-run mris_make_surfaces manually with the -dura flag to refine the pial surface? Also, I'd like to make sure we are using dcmunpack properly. We take the scan.info file and parse it like this: "-run [MEMPRAGE_4e_p2_1mm_iso run number] 3danat mgz 001.mgz" so the multi echo scan gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 35 > Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Working with MEMPRAGE > To: Jonathan Holt <whatsdac(a)umich.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <alpine.LRH.2.02.1305091043500.13418(a)gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII > > it needs to be: > > mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh > > note the "4" which tells it how many echoes to read > > On Thu, 9 May 2013, Jonathan Holt wrote: > >> I input: >> >> mris_make_surfaces -dura memprage_echo%d.mgz subjid lh >> >> it returns: >> >> detecting dura using 0 echos from memprage_echo%d.mgz >> >> >> Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. >> >> >> On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: >> >>> can you send me the full command line? It should say 4 echoes, not 0 >>> On Thu, 9 May 2013, Jonathan Holt wrote: >>> >>>> Thanks Bruce, >>>> >>>> should the hemisphere's be processed separately, or how do I signify lh and rh simultaneously? >>>> >>>> Also, should the fact that after running mris_make_surfaces, it says "detecting dura using 0 echos from memprage_echo%d.mgz" be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. >>>> >>>> jon >>>> On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: >>>> >>>>> Hi Jon >>>>> >>>>> yes, the subject and hemi need to be defined (they are required parameters) >>>>> Bruce >>>>> On Wed, 8 May 2013, Jonathan Holt wrote: >>>>> >>>>>> Hi all, >>>>>> combed through the mail archives to figure out how to work with multi echo >>>>>> mprage, found what I need but I wanted to confirm which of these two >>>>>> commands is the appropriate >>>>>> mris_make_surfaces -dura memprage_echo%d.mgz 4 subjid lh/rh >>>>>> mris_make_surfaces -dura memprage_echo%d.mgz do the subjid and hemispheres need to be specified as per the 1st line? >>>>>> jon >>>>>>

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Post-hoc anonymizing subject: binary files
by Andrew Ward 15 Jul '13

15 Jul '13

Hi folks, I am wondering if anyone has run into this problem before, and has a solution. We are trying to post-hoc anonymize FreeSurfer reconstructions. It's a simple matter to move the reconstruction directory, as well as to replace any instances of the old subject ID in text files (e.g. stats or log files). However, when I open any of the binary files (e.g. lh.pial) in a text editor, the last line includes the mris_make_surfaces command called to make the surface. This includes the old, pre-anonymized subject ID. I am worried about reading & writing these files using an ASCII editor, because I don't want to corrupt the binary encoding. Additionally, because the binary format is not public, there appear to be no tools to read & write to these ASCII tails in the binary data. Is there a way to either strip these lines, or to replace the reference to the old subject ID with the anonymized ID (this option is preferable)? Ideally, we don't want to have to reconstruct every binary file using the updated subject ID. Thanks for the help! Andrew Ward Brigham and Women's Hospital (BBNG) Massachusetts General Hospital (GRU) Athinoula A. Martinos Center for Biomedical Imaging 149 13th St., Rm 10.008 Charlestown, MA 02129 Phone: 617-726-6213 Fax: 617-726-5760

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Freesurfer July 2013