Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Re: [Freesurfer] question regarding control point edits
by Adam Mezher 23 Jul '14

23 Jul '14

Hi Bruce, Yeah that was my thinking as well. So, if after running 500 subjects through FS and 100 need similar edits in the anterior temporal lobes, we will have no choice but to perform manual edits for each case individually? Thanks for clarifying! Adam Mezher > > Hi Adam I don't think so as how would we don't know where the anterior temporal lobe at that stage in the process. Bruce On Tue, 22 Jul 2014, Adam Mezher wrote: > Hi FreeSurfer group, > I was wondering if there is a way to include control points in my command > line when I run recon-all. We are working with a large dataset and many of > the subjects have underestimations in the anterior temporal lobes so it > would be beneficial to expand the WM surface slightly on numerous cases > rather than doing control point edits on each case individually. > > Thank you, > Adam Mezher >

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Mapping stats into volume with mri_label2vol
by Jackie Lam 23 Jul '14

23 Jul '14

Hello all, I am trying to map polar angle and eccentricity into the voxels underneath a particular label. For each vertex in the label file, I’ve put in the respective angle in the stats column. I then used mri_label2vol with the --label-stat flag to map the angle values into the volume. Comparing the angle values for each individual voxel and each vertex, I’ve noticed that some values that are in the voxels are not present in the vertices (ie a particular voxel might have a value of 0.5 but none of the vertices have that exact value). What happens when the values are mapped from the vertex into the volume? Is there some averaging or weighting process or something? Many thanks, jack

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wm/pial surfaces from manually created surfaces
by Itamar Kahn 23 Jul '14

23 Jul '14

Greetings, I would like to use two surfaces that I created manually on the same anatomy and to create a single subject with the surfaces such that one is the pial and the other is the wm surface. Any leads on how to achieve this will be greatly appreciated. Thanks, Itamar

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qcache number of vertices error
by O'Shea,Andrew 23 Jul '14

23 Jul '14

Hello, I am running into an error when using qcache. Subjects that have had manual edits are exited with errors, while subjects that have not had edits run fine. All subjects have had –make all ran after edits and finished without errors. I have read about this problem and tried some of the solutions but am still getting errors. When I first tried running –qcache I received this error: Reading curvature file /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.volume ERROR: number of vertices in /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.volume does not match surface (128222,130849) ERROR: reading curvature file Linux c2a-s21.ufhpc 2.6.32-358.23.2.el6.x86_64 #1 SMP Sat Sep 14 05:32:37 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1492 exited with ERRORS at Wed Jul 23 10:32:24 EDT 2014 To make sure everything was ran I re-ran –make all and got make: Nothing to be done for `all’. I then ran –vno_match_check and it said everything was fine: Pass: all surfaces and surface data for subject 1492 for hemi lh have the same number of vertices. Pass: all surfaces and surface data for subject 1492 for hemi rh have the same number of vertices. I saw Doug gave this suggestion ( using –surf volume –qcache) to someone who was having the same problem this resulted in qcache getting past the volume stage but failing lh.w-g.pct.mgh Reading curvature file /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.w-g.pct.mgh ERROR: number of vertices in /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.w-g.pct.mgh does not match surface (128222,130849) ERROR: reading curvature file Linux c1a-s11.ufhpc 2.6.32-358.23.2.el6.x86_64 #1 SMP Sat Sep 14 05:32:37 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1492 exited with ERRORS at Wed Jul 23 11:07:01 EDT 2014 Any suggestions on how to address this? Any idea of the cause? I assuming it has something to do with the manual edits since unedited ppl run fine. -Andrew

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Re: [Freesurfer] recon-all error
by Cheng Peng 23 Jul '14

23 Jul '14

Hi, Bruce: I attached the file with an email and sent it to you an hour ago and received an automatic reply saying it's pending for approval due to the size of the email. Is there another way to upload my image or it's getting processed? I don't want to spam you guys since i already sent it twice and got the same result. Thanks! Cheng Peng On Wednesday, July 23, 2014 9:39 AM, Cheng Peng <pcdulaney(a)yahoo.com> wrote: Hi, Bruce, I attached the nu.mgz file with this email, i'm at home right now and would upload T1.mgz later if need to. As far as i know individual recon-all runs were completed without error (two scans on one subject, two hours apart), really appreciate the help! Cheng Peng Maryland Neuroimaging Center On Wednesday, July 23, 2014 9:32 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Cheng do the cross-sectional runs look okay? The base? If so, does the first intensity normalized images look ok (the T1.mgz and the nu.mgz)? If you can't track it down, upload the subject and we will take a look cheers Bruce On Wed, 23 Jul 2014, Cheng Peng wrote: > Hi, Freesurfer experts: > > > > I encountered an error message while i was attempting to run a longitudinal > study (following the instructions from > https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, step 2 > under workflow summary) > > egister_mri: find_optimal_transform > find_optimal_transform: nsamples 2185, passno 0, spacing 8 > GCAhistoScaleImageIntensities: could not find wm peak > resetting wm mean[0]: 102 --> 107 > resetting gm mean[0]: 64 --> 64 > input volume #1 is the most T1-like > using real data threshold=0.0 > skull bounding box = (0, 0, 0) --> (255, 255, 255) > using (85, 85, 128) as brain centroid... > mean wm in atlas = 107, using box (53,53,96) --> (116, 116,159) to find MRI > wm > WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1 > before smoothing, mri peak at 0 > WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1 > after smoothing, mri peak at 0, scaling input intensities by inf > > It appears that the skull strip step has failed as brainmask.mgz is > completely blank. I tried to look up the error message online but found > little help there. I would really appreciate it if someone can explain the > problem or where to look for an explaination. I attached the recon-all error > log with this email, i would also include nu.mgz but the last email attached > with that was blocked due to the size of the image. > > Thanks! > > Best Regards, > > Cheng Peng > > Maryland Neuroimaging Center > > > > > > > > _______________________________________________ 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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lgi for longitudinal scans
by Anna Jonsson 23 Jul '14

23 Jul '14

Dear group, If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the "normal" baseline command on the .long data? thank you, kind wishes Anna

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recon-all error
by Cheng Peng 23 Jul '14

23 Jul '14

Hi, Freesurfer experts: I encountered an error message while i was attempting to run a longitudinal study (following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, step 2 under workflow summary) egister_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=0.0 skull bounding box = (0, 0, 0) --> (255, 255, 255) using (85, 85, 128) as brain centroid... mean wm in atlas = 107, using box (53,53,96) --> (116, 116,159) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf It appears that the skull strip step has failed as brainmask.mgz is completely blank. I tried to look up the error message online but found little help there. I would really appreciate it if someone can explain the problem or where to look for an explaination. I attached the recon-all error log with this email, i would also include nu.mgz but the last email attached with that was blocked due to the size of the image. Thanks! Best Regards, Cheng Peng Maryland Neuroimaging Center

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running freesurfer subcortical segmentation on a T2 weighted image only ?
by Vincent Noblet 23 Jul '14

23 Jul '14

Dear all, I was wondering if there is a way to use the segmentation of freesurfer on a T2 weighted image only (without a T1 weighted image). Sincerely Vincent Noblet

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bad freesurfer segmentation
by Doety Prins 23 Jul '14

23 Jul '14

> Dear freesurfer experts, > > I experienced some problems with the segmentation of my T1 scans, as both the white surface and the pial surface are placed incorrectly (see attached images). This seems to me to be a too big difference with what it should look like, that I think could not be fixed with the standard troubleshooting strategies. > > Do you have any solutions for this? Is it for instance possible to make changes to the recon-all script to shift the surfaces? > > Thanks in advance, > > Doety

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Pathstat.byvoxel.txt question
by Sarina Sacco 23 Jul '14

23 Jul '14

Hi all freesurfer experts , I have a question about the command trac-all-stat-c ,what is the interpolation that uses?

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