Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

using T2 or flair images
by will brown 08 Nov '14

08 Nov '14

Hi there, I have completed recon-all on a subject but the output is terrible. I have since found multiple series on the CD that was supplied for the subject's scan using "dcmunpack" the output was: Found 7 unique series: 1 4 5 6 7 8 9 Subject XXXXX Date 20120114 Time 082517 Institution Hagley Radiology 1 loc 1.372 5.032 30 0.9375 ROW 244.141 /home/will/Dropbox/BrainformLtd/Freesurfer/November2014/NB/NBScan1/Z01 4 T2AXIALPROP 91.82775 4500.0 90.0 0.429688 ROW 325.39062 /<path to dicoms>/Z15 5 SAGT1FLAIR 7.64 2657.82 90 0.4688 ROW 195.312 /<path to dicoms>/Z53 6 SAGT2FRFSE 88.272 1900 90 0.4297 ROW 122.07 /<path to dicoms>/Z82 7 CORT2FLAIR 167.7 9502 90 0.4102 ROW 162.773 /<path to dicoms>/Z99 8 DWIASSET 88.5 7750 90 0.8594 COL 1953.12 /<path to dicoms>/Z141 9 Ax3DSWAN 22.876 38.2 15 0.4102 ROW 162.773 /<path to dicoms>/Z203 I'm wondering if an expert could advise me on the best next step of progress to improve the output. I only need the pial surfaces and stats. Presumably series 1 is the T1 series? Should I use T2 also? if so which one and how? Please excuse my ignorance. Thanks, Will Brown

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07 Nov '14

So I am trying to use TKregister2 and I keep having this error pop up. I tried looking online for a solution. I tried adding export LIBGL_ALWAYS_INDIRECT=y to my .cshrc file but it did not help. I saw the question asked several times but never any answer to the significance of it, but I am accessing the computer remotely. Any help that could be offered would be greatly appreciated. Nicholas

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Re: [Freesurfer] applying manual freesurfer edits to warped brain image
by David Grayson 06 Nov '14

06 Nov '14

Thanks Bruce, So I just need a warp field in .m3z format. Cool. As this distortion correction is proprietary, we don't actually get the warp fields, which is silly. But I was thinking since scanner distortions are subtle and coarse, it should be sufficient to nonlinearly register the two unsegmented images using a simple intensity-based volumetric registration at a coarse warp resolution. Would the mri_cvs_register tool be suitable for this if I supply the --step3 flag? Otherwise I am stuck with trying to go between Freesurfer and another set of tools. Thanks! -David Date: Sun, 2 Nov 2014 21:44:23 -0500 > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu <javascript:;>> > Subject: Re: [Freesurfer] applying manual freesurfer edits to warped > brain image > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu <javascript:;> > > > Message-ID: <35417931-CE03-4CB8-A30E-C1F34C174B71(a)nmr.mgh.harvard.edu > <javascript:;>> > Content-Type: text/plain; charset="us-ascii" > > What format is the distortion field stored in? If you can get it into .m3z > I believe we have tools to do what you want > > > > > On Nov 2, 2014, at 9:37 PM, David Grayson <dgrayson(a)ucdavis.edu > <javascript:;>> wrote: > > > > Hi freesurfer experts, > > > > I have two T1 images from the same subject acquired at the same time > point. One of the images is distortion corrected using a calibration > phantom, put through the full freesurfer pipeline and then extensively > manually edited. The uncorrected image has had zero processing. What I > would like now is to have the freesurfer segmentations on the uncorrected > image and preserve as much as possible the manual edits. In other words, I > would like to warp the surface meshes already obtained on the distortion > corrected image to the uncorrected image. Is there already a suggested > method that is optimal for this purpose? > > > > Thanks in advance for any advice! > > > > -David > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <javascript:;> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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White matter volume
by Alshikho, Mohamad J. 06 Nov '14

06 Nov '14

Dear Bruce, My questions is just to learn and to improve my understanding. The commands recon-all and dt-recon are routinely generating the statistics at the end of there running and we can check the results in aseg.stats (the output of recon-all) and fa.stats (the output of dt-recon for FA). In those files we have the white matter volume for many different parts of the brain like the right and left cerebral white matter. If we check the volumes in those files we can see that we have differences between the numbers and I can explain that by the following: in aseg.stats the white matter volume is derived from the T1 segmentation in the structural space and in fa.stats the white matter volume is derived from the FA map in diffusion space and the difference between the volumes is the difference between the accuracy of the images in different spaces. Now: 1. If we want to study the relationship between the FA and the right hemispheric white matter volume for example, we should not care about the volumes in fa.stasts because it is not accurate?! in this case what is the optimal and correct method in freeSurfer to do such like this comparison, is it by moving the FA map to the structural space by registering the FA map to T1 or by using the volumes in aseg.stats and the metrics values from fa.stats? or we can use the fa values and the volumes from fa.stats? 2.What is the exact usage for the volumes mentioned in FA.stats 3. What is the meaning and the exact usage of min-max intensity range (intensity of what) in aseg.stats and fa.stats So Sorry for this long email but as always I am looking forward to learn from you Thanks Mohamad

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Re: [Freesurfer] adding insula voxels
by Adam Mezher 06 Nov '14

06 Nov '14

Hi Ani, I actually did end up fixing the insula mis-segmentation using either control points or WM edits for many subjects (I think the one I sent you too, not sure). However, I did notice that in some subjects, the edits will push the wm line out a little too much such that minor part of the medial insula will be labeled as WM instead of insula. It is pretty minor though so don’t think it is a big deal anyway. -Adam

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Re: [Freesurfer] adding insula voxels
by Adam Mezher 06 Nov '14

06 Nov '14

I uploaded one when I sent the first email, did you receive it? Uploaded to: ftp.nmr.mgh.harvard.edu ; cd transfer/incoming The file was titled ‘mezher_insula_fail.tar.gz’ which contains the entire FS folder for one subject. Should I go ahead and resend it? Thanks!

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notal-check/pial edits
by Octavian Lie 06 Nov '14

06 Nov '14

Dear All, this is very basic. I have Analyze volumes, and I was suggested to use -notal-check to bypass the 3rd recon step. I wanted to make sure skipping the T registration step would not have the potential to mess up the spherical registration in autorecon3 in any way on a case by case basis. I do not want to spend time in tkregister2 unless is necessary for the spherical registration step. Also, I anticipate losts of pial edits (let's exclude the wm edits/cp), and I wanted to make sure different command scenarios are correct: 1. recon-all -autorecon1 -subjid edit pia, save brainmask.mgz recon-all -autorecon2 -autorecon3 -subjid 2. recon-all -autorecon1 -autorecon2 -subjid edit pia, save brainmask.mgz recon-all -autorecon2-pial -autorecon3 -subjid (preferred) 3. recon-all -subjid edit pia, save brainmask.mgz recon-all -autorecon-pial -subjid Please comment, thank you, Octavian

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Generating T1 + Aseg views without Tkmedit and Freeview
by Pedro Paulo de Magalhães Oliveira Junior 06 Nov '14

06 Nov '14

I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

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Crash on recon-all on Macbook Pro (Mavericks and Yosemite)
by Matthew Riddle 06 Nov '14

06 Nov '14

Dear Freesurfer Team, I recently installed Freesurfer on a new Macbook pro, which was upgraded to Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing an issue with freesurfer that I’m hoping you might have some idea about. Just to test the install and see what my total time was to run a recon-all on this machine, I ran the normal recon-all on bert with the command from an X11 terminal: sudo –E recon-all –s bert –all The processes crashes in a minute or two at the same place each time, and this is the last bit of output. MRIchangeType: Building histogram writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm /Applications/freesurfer/subjects/bert/mri/orig.mgz /Applications/freesurfer/subjects/bert/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Oct 23 07:32:53 EDT 2014 /Applications/freesurfer/subjects/bert/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014 I tried this on an almost identical machine running Mavericks, and got the exact same problem. >From my bugr output: FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 The recon-all.log file doesn’t provide any additional information, it just mirrors the output from the terminal. Thanks, -Matt

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mris_preproc error
by Cooke, Gillian 05 Nov '14

05 Nov '14

Hi All, I am getting a consistent error when I try to run mris_preproc - I'm baffled as I've used all of my scripts and fsgd files before. There are 2 groups with 3 covariates but I keep getting this error: mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out mris_preproc/lh.HRR60.thickness.10.mgh ERROR: no subjects specified But my fsgd file lists all subject numbers: GroupDescriptorFile 1 Title ACCE HRR60 Class Control Class Cancer Variables Age_demeaned Ed_demeaned HRR60 Input 505_1 Cancer -5.63 1.5 43 Input 506_1 Cancer 7.37 3.5 53 Input 509_1 Cancer 4.37 -0.5 44 Input 517_1 Cancer -20.63 -1.5 38 Input 518_1 Cancer -4.63 -2.5 35 Input 520_1 Cancer 0.37 1.5 37 Input 521_1 Control 3.37 1.5 49 Input 524_1 Cancer 3.37 -0.5 32 Input 525_1 Control -12.63 -2.5 51 #Input 528_1 Cancer 10.37 3.5 Input 529_1 Control -28.63 4.5 32 Input 530_1 Cancer 1.37 1.5 24 Input 531_1 Cancer 6.37 7.5 55 Input 532_1 Cancer -1.63 1.5 14 Input 533_1 Cancer -10.63 3.5 36 Input 534_1 Control -3.63 1.5 25 Input 536_1 Control -11.63 0 47 Input 547_1 Control 10.37 1.5 25 Input 548_1 Control -18.63 -0.5 46 Input 549_1 Cancer -21.63 -0.5 38 Input 554_1 Control -21.63 -0.5 38 Input 558_1 Cancer 9.37 -1.5 24 Input 563_1 Control 0.37 0.5 30 Input 564_1 Control 7.37 1.5 14 Any help is greatly appreciated! Gill _____________________ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain & Cognition Lab Decision Neuroscience Lab Beckman Institute University of Illinois, Urbana

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