Freesurfer

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30132 discussions

blood hyper-intensity
by Colin Reveley 24 Oct '13

24 Oct '13

Hi - I wonder if anyone has experience in dealing with T1 images where there is hyperintenisty of blood vessels? the data involved is MDEFT scans where only a head coil is used. I read it is a long solved problem for acquisition, but these scans do not correct it and nor will future scans. the difficulty is getting 3 classes (CSF,WM,GM) for nu_correct,mri_normalise or FSL Fast or whatever. It's quite a big obstacle for data that is otherwise quite excellent. One would think one could just threshold it out after brain extraction and to an extent one can but it's very imperfect. segmenting 4 classes doesn't especially work either (so far) if anyone has experience segmenting this stuff (especially getting mri_normalise to work) I'd be grateful for advice. e.g. attached Colin Reveley

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freeview "invalid drawable"
by Elissa McIntosh 24 Oct '13

24 Oct '13

Hi, When trying freeview command (see below) from the “Testing your freesurfer installation” page using my own data, freesurfer opened, but I am concerned about the “invalid drawable” lines. The message happened when I ran this command on the "bert" data too. What does invalid drawable mean? [CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% freeview -v $SUBJECTS_DIR/ABU/mri/norm.mgz -v $SUBJECTS_DIR/ABU/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/ABU/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/ABU/surf/rh.pial:annot=aparc:edgecolor=red 2013-10-22 12:47:02.811 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.812 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.839 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.840 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Thank you, Elissa

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mri_surf2surf error - 'could not determine type of...'
by Paul Beach 23 Oct '13

23 Oct '13

Hello FS experts, I'm attempting to transform the Yeo2011 annotations (lh & rh) from fsaverage to individual subjects so as to then sample the cortical maps to subject surfaces using mri_label2vol. However, I'm getting the error in the subject line when I put in the following commands: *mri_surf2surf --srcsubject fsaverage \* *--srcsurfval lh.Yeo2011_17Networks_N1000.annot \* *--trgsubject HS_001 --trgsurfval lh.Yeo_17Network_native.annot --hemi lh* I suspected that I have to put a src_type and trg_type in there, but I wasn't sure what type of types would be appropriate for use in mri_label2vol. For the latter command I was planning on utilizing something similar to a previous e-mailer's command (below): *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot \* *--o outfile.nii.gz --hemi lh --subject HS_001 \* *--temp $SUBJECTS_DIR/HS_001/mri/orig.mgz --identity* Any suggestions for getting past this error? Thanks for your help, Paul -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology

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Re: [Freesurfer] Subject processing difference between computers
by Ed Gronenschild 23 Oct '13

23 Oct '13

see http://dx.plos.org/10.1371/journal.pone.0038234 On 22 Oct 2013, at 18:18, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Tue, 22 Oct 2013 16:15:44 +0000 > From: "West, John D." <jdwest(a)iupui.edu> > Subject: [Freesurfer] Subject processing difference between computers > To: "freesurfer " <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <793D43FE7976404CB5E172709AB1F4081123FECA(a)IU-MSSG-MBX102.ads.iu.edu> > Content-Type: text/plain; charset="us-ascii" > > Hello. > > We are moving our processing from an older super computer to a new > one here at Indiana University. Preliminary testing is showing a > significant difference between final summary stats results between > subjects processed on the old system versus the new. The version > of freesurfer on both systems is identical. Comparing the logs of > the same subject run on both systems, I've found that the > differences seem to start with the mri_watershed function > specifically the main basin size. For the same subject we find: > > Old computer: > main basin size=22667431830 voxels, voxel volume =1.000 > = 22667431830 mmm3 = 22667431.936 cm3 > > New computer: > main basin size=22208239350 voxels, voxel volume =1.000 > = 22208239350 mmm3 = 22208239.616 cm3 > > As you can see they are very different. My theory is this is > propagating through the rest of the process and giving us different > summary stats at the end. I should note that both aseg and aparc > stats are affected. > > I am also enclosing the logs for both runs as well as the > differences found through the diff command (this is a lot parse > through as even time stamp differences are picked up). Essentially > what I am trying to find out is if these differences we are > noticing are typical when changing computers and if not what could > be causing these differences that I may not be picking up on. > > Thanks for the help. > -John >

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skull striping error question
by Subhabrata Chaudhury 23 Oct '13

23 Oct '13

Hi Everyone, I have some data where the skull striping hasnt worked properly and there are some skull remaining. However, upon looking at the white and pial surfaces, those look perfectly fine. My question is will the erroneous skullstriping affect the supratentorial volume estimation ? I will be highly obliged if someone can address this concern. Regards Subha

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Re: [Freesurfer] Projecting voxel intensities to a surface file
by Arash Nazeri 23 Oct '13

23 Oct '13

Sorry. I meant to do that. ---- Original Message ---- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Arash Nazeri <arashnazeri(a)aol.com> Sent: Wed, Oct 23, 2013 8:25 am Subject: Re: [Freesurfer] Projecting voxel intensities to a surface file Hi Arash can you cc the list on this type of email so that others can answer? Particularly Matt Glasser! I suspect that they have already run bbregister, but I'm not sure. cheers Bruce On Wed, 23 Oct 2013, Arash Nazeri wrote: > Hi Bruce, > Thanks for your response. I think this will do the trick generally, is it > also possible to apply mri_vol2surf to the Human Connectome Project > preprocessed files, or should I rerun the recon-all? In the HCP dataset, the > surface files are in the gifti format and the diffusion images are already > registered to the structural volumes. Based on the documentations it seems > that mri_vol2surf is hard-wired for outputs generated from recon-all. > > Cheers, > Arash > > > > -----Original Message----- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Arash Nazeri <arashnazeri(a)aol.com> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Tue, Oct 22, 2013 10:17 pm > Subject: Re: [Freesurfer] Projecting voxel intensities to a surface file > > Hi Arash > Yes. Register the surface to the volume with bbregister, then use > mri_vol2surf to do the sampling > Cheers > Bruce > > > > On Oct 22, 2013, at 12:13 PM, Arash Nazeri <arashnazeri(a)aol.com> wrote: > > Dear all, > I'm new to the freesurfer. I want to project surrounding cortical > voxel values (intensities) from a given map (e.g. mean diffusivity map > in a nifti format) to a surface file (e.g. mid-cortical surface in a > gifti fromat) to generate scalar maps like ?h.thickness for group-wise > statistics. Can this be carried out using freesurfer commands? > > Cheers, > Arash > > _______________________________________________ > 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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Re: [Freesurfer] missing eTIV in asegstats2table
by Daniel Ferreira 23 Oct '13

23 Oct '13

Dear Douglas, Please, find attached aseg.stats files for subj1 and subj2. Thanks Daniel

2 1

Extremely intense grey matter being omitted
by Jonathan Holt 23 Oct '13

23 Oct '13

FS experts, Freesurfer has been omitting extremely bright/intense white and grey matter voxels (avg intensity ~150). Mostly this happens in areas that should be encompassed by the surfaces. Is there a way to tell recon-all to include these areas? I fear it may believe they are dura because of the similar intensity values. jon

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reconall error
by Rashmi Singh 23 Oct '13

23 Oct '13

Hello FreeSurfer experts, I am trying to run recon all on my data set, but I got following error message. Please help me understand the message and suggest solution. Thanks, Rashmi #@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013 /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/ANAL2013/CombT1T2Practice/FreeSurfer/AA470-2prac/mri mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (130, 148, 130) --> (130, 148, 130) using (130, 148, 130) as brain centroid... mean wm in atlas = 126, using box (130,148,130) --> (129, 147,129) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux enders 2.6.32-52-server #114-Ubuntu SMP Wed Sep 11 19:06:34 UTC 2013 x86_64 GNU/Linux recon-all -s AA470-2prac exited with ERRORS at Tue Oct 22 13:57:26 CDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 1

Projecting voxel intensities to a surface file
by Arash Nazeri 22 Oct '13

22 Oct '13

Dear all, I'm new to the freesurfer. I want to project surrounding cortical voxel values (intensities) from a given map (e.g. mean diffusivity map in a nifti format) to a surface file (e.g. mid-cortical surface in a gifti fromat) to generate scalar maps like ?h.thickness for group-wise statistics. Can this be carried out using freesurfer commands? Cheers, Arash

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