Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

Re: [Freesurfer] freesurfer question
by Bruce Fischl 10 Jan '13

10 Jan '13

Hi Catherine can you clarify? Are you getting them properly segmented in the aseg? Is this a disease population? There are a bunch of things going on in the images you sent, although it's hard to be sure from a single slice. It looks like your bandwidth is low enough that you are getting a lot of signal pileup in temporal regions. There also appear to be cortical lesions. Bruce On Thu, 10 Jan 2013, Catherine Bois wrote: > Ps. I have attached a few screenshots of the problem we are experiencing, to > clarify. We are also getting large areas of hyper-intensive white matter too. > > > Quoting Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> on Wed, 9 Jan 2013 08:52:08 > -0500 (EST): > >> Hi Catherine >> >> what version are you running? We have a fix in 5.2 that helps this problem. >> It's not quite out yet, but you could download a beta if you want >> >> cheers >> Bruce >> >> On Wed, 9 Jan 2013, Catherine Bois wrote: >> >>> Hi, >>> >>> I am currently editing some scans (ie adding control points etc), >>> however I keep finding that after the editing often the brains look >>> "worse" than they did before; especially the medial temporal lobe >>> area. I have taken care not to put too many control points in/made >>> sure not to place them in partial volume areas, and only in areas that >>> are clearly excluded white matter. This problem has happened >>> repeatedly, yet looking at scans that my colleagues have edited (some >>> with up to 2000 control points) this problem does not occur. Has this >>> happened before, is it the software "malfunctioning" in some way? >>> >>> Thank you very much for your reply, >>> >>> >>> >>> >> >> >> 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] Tracula preprocessing step error
by Allison Gruber 10 Jan '13

10 Jan '13

Hi Anastasia, Thanks so much for your help. I was able to correct this problem in my configuration file. I have now run into another error- "bvecs and bvals don't have the same number of entries." I have read other postings about this error and can see that my bvec file is not formatted correctly when I import into Excel. However, I am not sure how to correctly fix this formatting. I know that I have 28 bval entries and 84 bvec entries, so the overall number is correct. I am just unclear on how to fix the formatting of the bvec file so that it corresponds correctly to the ordering in the bval file (which order the bvec entries should appear in within the three columns). Do you have any resources on this? Thank you again for your help, Allison Quoting Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: > > Hi Allison - The mri_convert command at the top of your log file is > trying to convert the directory /Users/Desktop/Tracula/diffusion_DTI to > a nifti file. From the name of that nifti file, it looks like it's > expecting to find a field map and not finding it. > > Hope this helps, > a.y > > On Tue, 8 Jan 2013, Allison Gruber wrote: > >> Dear Freesurfer experts, >> >> I have encountered the following error while running the tracula >> pre-processing command and was hoping you could help me understand how >> to correct this. >> >> Selection from log: >> >> mri_convert /Users/Desktop/Tracula/diffusion_DTI/ >> /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz >> mri_convert /Users/Desktop/Tracula/diffusion_DTI/ >> /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz >> corRead(): can't open file /Users/Desktop/Tracula/diffusion_DTI/COR-.info >> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> reading from /Users/Desktop/Tracula/diffusion_DTI/... >> Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr >> 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 >> >> trac-preproc exited with ERRORS at Tue Jan 8 14:34:39 EST 2013 >> >> Please let me know if this is not enough information. Thank you for >> your help. >> >> Allison >> _______________________________________________ >> 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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problem with preprocessing
by Maryam Vaziri Pashkam 09 Jan '13

09 Jan '13

Hi Doug, I am running preprocessing on freesurfer 5.1 using this line: preproc-sess -s 121210_xu_Object4catmod_10 -df sessdir -per-run -sliceorder siemens -fsd bold -fwhm 0 -mni305-2mm -surface self lhrh -force and I get a "Segmentation fault " error. Here is part of the output with the error: .... mri_segreg --mov bold/007/tmp.bbregister.28256/template.nii --init-reg bold/007/tmp.bbregister.28256/reg.init.dat --out-reg bold/007/tmp.bbregister.28256/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103 2011/03/02 00:04:24 nicks Exp $ setenv SUBJECTS_DIR /ncf/vcn/Maryam/mri-space/subjects cd /ncf/vcn/Maryam/mri-space/studies/Obj4cat_mod/unpackdata/121210_xu_Object4catmod_10 mri_segreg --mov bold/007/tmp.bbregister.28256/template.nii --init-reg bold/007/tmp.bbregister.28256/reg.init.dat --out-reg bold/007/tmp.bbregister.28256/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname ncfws09.rc.fas.harvard.edu machine x86_64 user mvpashkam movvol bold/007/tmp.bbregister.28256/template.nii regfile bold/007/tmp.bbregister.28256/reg.init.dat subject green_alligator_kcb dof 6 outregfile bold/007/tmp.bbregister.28256/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1358526945 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.007 0.027 -1.374; -0.026 0.032 0.999 -28.956; 0.008 0.999 -0.032 7.006; 0.000 0.000 0.000 1.000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Segmentation fault I have attached the full log file. I am not sure where the problem is. The anatomical data of the subject has been analyzed using recon all on freesurfer 4.5. I have used similar method for 9 other subjects and there was no error on any of them before. Any idea why am I getting a segmentation error? Thanks, Maryam

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Problems in testing out newly installed Freesurfer with autorecon-1 option
by Susan Kuo 09 Jan '13

09 Jan '13

Hi, I'm currently in the process of verifying that my install of Freesurfer works. I have an Ubuntu 12.04.1 LTS box. I encountered what appeared to be 4 errors after running *recon-all -s bert -autorecon1.* The last line I included here states that the command completed without error, so I'm not sure if I should be concerned that*nu_correct* wasn't found, or that there were loading errors, and a *mincREAD()* error. Could you help me identify what I need to do to correct these issues? I've included the standard output for this command as a text file here. There appear to be 4 issues: ***ISSUE 1: cannot find *nu_correct* ************************* nu_correct: Command not found. INFO: current FREESURFER_HOME does not match that of previous processing. ***ISSUE 2: No such file or directory error******************** cp: cannot stat `./tmp.mri_nu_correct.mni.25253/nu2.mnc': No such file or directory mri_binarize --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25253/ones.mgz mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc ***ISSUE 3: Loading error****************************** Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25253/ones.mgz --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25253/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25253/output.mean.dat mghRead(./tmp.mri_nu_correct.mni.25253/ones.mgz, -1): could not open file ***ISSUE 4: Loading error****************************** Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz (standard_in) 1: syntax error mris_calc -o ./tmp.mri_nu_correct.mni.25253/nu2.mnc ./tmp.mri_nu_correct.mni.25253/nu2.mnc mul mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc ****This is the last line to standard output, and it seems reassuring********************** recon-all -s bert finished without error at Tue Jan 8 17:49:19 EST 2013 I appreciate whatever help you can give me, and thank you very much for your time! The attached is a text file. Best, S Kuo

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Re: [Freesurfer] longitudinal processing
by Martin Reuter 09 Jan '13

09 Jan '13

Hi Catherine, with edits I think it is best to re-use the 5.0 cross data for the longitudinal processing. Also conceptually there is a difference between longitudinal processing and longitudinal statistical analysis. The image processing will reduce variability of your measures and even if you are interested in cross sectional differences between groups (e.g. thickness differences at baseline), it would be a good idea to run everything through the longitudinal stream. If there is longitudinal image data, I think it will always be advantageous to process it with the longitudinal stream as opposed to the cross sectional. Different scanners are usually not problematic if each subject stays on their scanner and scanners are randomly assigned across groups. If scanners get switched in a longitudinal study, many bad things can happen: - one group switches on average earlier than the other -> bias - only a single or very few time points are on one side of the switch -> cannot model the scanner effect well, as there is no reliable slope on that side of the switch. Anyway it may be a good idea to model the scanner as a covariate and test for a scanner effect. We have seen effects even in software updates on the scanner (e.g. growing brains) and certainly a hardware switch will drastically change the images. Linear mixed effects models are the right mechanism to analyze longitudinal data. Best, Martin On Wed, 2013-01-09 at 19:22 +0000, Catherine Bois wrote: > Thank you for your reply. I am currently trying to decide which method > would be the best to analyze the data we have...We have ca 500 scans > of individuals with differing number of time points for different > individuals and certain clinical measures we wish to relate to > particularly cortical thickness and different cortical regions. > However, the problem is that the scans were not all collected with the > same scanner; would longitudinal still prove to be advantageous over > cross-sectional analysis. As all the manual edits have been conducted > in version 5.0 it would be preferable to keep these and use version > 5.1 for -base -long (unless of course this could be done with better > consistency if using version 5.1?). I was also planning to analyze the > data with linear mixed effect models, does this sound reasonable? > > Thanks very much for your help > > > > > Quoting Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> on Wed, 09 Jan > 2013 13:46:35 -0500: > > > Hi Catherine, > > > > yes, the first step is independent (cross sectional) processing of all > > time points (normal recon-all). > > > > We usually do not recommend to mix versions. But the 5.1 longitudinal > > stream has been designed in a way that it can take the cross sectional > > data from 5.0. So it is possible. Just make sure that if you add time > > points and subjects you still use 5.0 for the cross sectional recons and > > 5.1 for base and long to be consistent. > > > > Alternatively wait a little longer and re-run everything from scratch > > with the new 5.2 version that will come out hopefully this month. > > > > Best, Martin > > > > On Wed, 2013-01-09 at 14:22 +0000, Catherine Bois wrote: > >> Sorry, another question about longitudinal processing; just realized > >> that my institution has been using version 5.0, so all the cross > >> sectional processing has been done with this version, is it ok to go > >> ahead and do base and long with version 5.1 once I have managed to get > >> this installed? > >> > >> Thanks, > >> > >> ----- Forwarded message from C.Bois(a)sms.ed.ac.uk ----- > >> Date: Wed, 09 Jan 2013 13:35:12 +0000 > >> From: Catherine Bois <C.Bois(a)sms.ed.ac.uk> > >> Subject: longitudinal processing > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> > >> Hi, just to clarify, > >> > >> When beginning longitudinal analysis, the first step is the same as > >> cross-sectional processing, eg just the "normal" recon-all command, > >> for each subject, and each individual time point? Then the norm.mgz > >> files are used? > >> > >> Thanks > >> > >> -- > >> The University of Edinburgh is a charitable body, registered in > >> Scotland, with registration number SC005336. > >> > >> > >> > >> ----- End forwarded message ----- > >> > >> > > > > > > > > > > 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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longitudinal processing
by Catherine Bois 09 Jan '13

09 Jan '13

Sorry, another question about longitudinal processing; just realized that my institution has been using version 5.0, so all the cross sectional processing has been done with this version, is it ok to go ahead and do base and long with version 5.1 once I have managed to get this installed? Thanks, ----- Forwarded message from C.Bois(a)sms.ed.ac.uk ----- Date: Wed, 09 Jan 2013 13:35:12 +0000 From: Catherine Bois <C.Bois(a)sms.ed.ac.uk> Subject: longitudinal processing To: freesurfer(a)nmr.mgh.harvard.edu Hi, just to clarify, When beginning longitudinal analysis, the first step is the same as cross-sectional processing, eg just the "normal" recon-all command, for each subject, and each individual time point? Then the norm.mgz files are used? Thanks -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ----- End forwarded message ----- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Postdoctoral Position at Harvard Medical School/Boston Children's Hospital
by Gaab, Nadine 09 Jan '13

09 Jan '13

The Gaab Labhttp://www.childrenshospital.org/research/gaablab and (www.babymri.org<http://www.babymri.org>)) at the Laboratories of Cognitive Neuroscience at Children's Hospital Boston (Developmental Medicine Center) invites applications for a NIH funded post-doctoral associate in the area of developmental cognitive neuroscience/pediatric fMRI. Available resources include a 3.0T MRI scanner, a child-friendly Mock scanner and analysis platforms based in MATLAB/UNIX. The candidate will be expected to design, organize and conduct pediatric and infant (f)MRI experiments, analyze behavioral and fMRI data, prepare manuscripts for publication, and participate in conferences. The NIH and foundation funded projects will focus on neural and behavioral pre-markers of developmental dyslexia in infants and pre-reading children as well as typical reading and language development. The successful applicant should have a doctoral degree in a field related to developmental cognitive neuroscience (e.g., cognitive neuroscience, neuroscience, developmental psychology, medicine or psychology). Individuals with a background in electrical engineering, biomedical engineering or computer science will also be considered, as appropriate. The successful applicant must possess excellent English verbal and written communication skills. Applicants are expected to have a very strong research background in the design and statistical analysis of functional brain-imaging experiments. Experience with SPM, FSL, Freesurfer, UNIX/LINUX/ and/or programming skills (MATLAB, C++; Python) are desirable and experience with MVPA or connectivity analyses a plus. Experience with pediatric functional neuroimaging and language and reading research are useful. Approximate start date is Spring/Summer 2013 (the earlier the better). Successful applicants will be appointed at Children's Hospital Boston and Harvard Medical School. For consideration please send a statement of interest, a CV and a list of three potential referees via email to Nadine Gaab, PhD (nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu>). The search will continue until the position is filled. -- "If we knew what it was we were doing, it would not be called research, would it?" A. Einstein (1879-1955) Nadine Gaab, PhD Assistant Professor of Pediatrics Harvard Medical School Faculty Affiliate Program in Neuroscience, Harvard Medical School Member of the Faculty of Education Harvard Graduate School of Education Children's Hospital Boston Department of Medicine/Division of Developmental Medicine Laboratories of Cognitive Neuroscience 1 Autumn Street (Office 643) Boston, MA 02115 nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu> phone: (857)-218-3021 Main Lab: 617-355-0400 fax: 617-730-0518 http://www.childrenshospital.org/research/gaablab www.babymri.org<http://www.babymri.org/>

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freesurfer question
by Catherine Bois 09 Jan '13

09 Jan '13

Hi, I am currently editing some scans (ie adding control points etc), however I keep finding that after the editing often the brains look "worse" than they did before; especially the medial temporal lobe area. I have taken care not to put too many control points in/made sure not to place them in partial volume areas, and only in areas that are clearly excluded white matter. This problem has happened repeatedly, yet looking at scans that my colleagues have edited (some with up to 2000 control points) this problem does not occur. Has this happened before, is it the software "malfunctioning" in some way? Thank you very much for your reply, -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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unable to download updated mri_segstats
by Salil Soman 09 Jan '13

09 Jan '13

Hi, The link ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.… from the release notes for freesurfer 5.1 ( http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) appears broken. I also checked the anonymous ftp site and found only the directories bbr-papers and growth-curves within the /transfer/outgoing/flat/greve directory. Could someone please direct me to the correct download link for the updated file? Also, is there an updated version of mri_segstats for mac? Thank you. Salil Soman, MD, MS

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Re: [Freesurfer] QA Tools Snaps Scrambled - Clairification
by Irwin, William 09 Jan '13

09 Jan '13

Hi Louis- I was speaking cryptically and/or imprecisely. Of course there are dependencies for IM-- in fact about 8 libraries which are uniquely required by IM. I was thinking about a higher (or lower) level of dependency. This would suggest a more system-level problem, but I'm not having problems with any of the other apps running on my system. Obviously I'm not asking you to help diagnose the health of my system, but though you might have some thoughts/suggestions. Regards, Wil -----Original Message----- From: Irwin, William Sent: Wednesday, January 09, 2013 5:37 AM To: Louis Nicholas Vinke Cc: freesurfer(a)nmr.mgh.harvard.edu; Irwin, William Subject: RE: [Freesurfer] QA Tools Snaps Scrambled Hi Louis- No problem doing command line conversion of an rgb to either jpg or gif in terms of error messages. However, the converted files are scrambled. Might there be a dependency on which ImageMagick relies which still in place, but corrupted? I was under the impression ImageMagick was self-contained. This is a real mystery -Wil -----Original Message----- From: Louis Nicholas Vinke [mailto:vinke@nmr.mgh.harvard.edu] Sent: Tuesday, January 08, 2013 6:29 PM To: Irwin, William Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QA Tools Snaps Scrambled Hi Irwin, It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit are not being generated properly. It may be this peculiar bug where ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 'convert file.rgb file.jpg'. You may get the error 'Improper image header'. The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, which may explain why some images are fine. -Louis On Tue, 8 Jan 2013, Irwin, William wrote: > > Hi- > > > > I’ve come across a peculiar behavior with recon_checker, and am hoping > someone can shed some light on this. > > > > I have used it 100’s of times in the past, but not for about 2 months. > I recently processed a large set of cases I wanted to QC. When I ran > it, some, but not all, of the snaps were corrupted. Specifically the > talairach, aseg, surfs, and all the ‘detailed snaps’, which are > basically additional instances of the aforementioned types. The > inflated, curv, and parc are all just fine. As the process runs, all > images are being displayed in the pop-up windows, and the html page is created. > > > > While there have been no system changes which should affect this, I > upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the > problem. The problem remains. And the problem remains w/ or w/o the > flag for detailed snaps. > > > > If all of the images were corrupted, I would have certainly concluded > something has gone awry with my system. The fact that only some of the > images are corrupted makes me scratch my head. > > > > Thoughts? Suggestions? > > > > Thanks, > > Wil > > > 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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