Freesurfer April 2013

freesurfer@nmr.mgh.harvard.edu

131 participants
220 discussions

QDEC questions
by Tudor Popescu 21 Apr '13

21 Apr '13

Dear experts, Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from misbehaving, and so after running a first whole-brain group cortical thickness analysis on my structural data, I have some questions: 1. After running recon-all with the –qcache flag (i.e. presmoothing), files of the type lh.thickness.*.mgh were created for all 38 subjects (19 in each group), however files of the type *rh*.thickness.*.mgh were not created for 5 out of the 19 subjects of the first group. Log files *recon-all-status.log * and *recon-all.log* (attached, for one of those 5 subjects) both mention that the process ran on Mar22nd ended with errors, although I can't quite see what that was 2. When I take age as a continuous factor (covariate), the list of clusters in my results look dramatically different from the clusters that I get for the same contrast ran without the covariate. Why is that, given that normally adding a covariate very rarely changes the results by a great deal? Also in my case, I had quite a narrow (and well-balanced between the groups) age range! 3. I know that discrete factors cannot be taken as nuisance factors, but it seems they also can't be taken as covariates. How does one, then, control for the effects of e.g. gender in a group comparison? 4. When should values other than 10 be used for the FWHM parameter of the smoothing? 5. How come QDEC allows you to set the FWHM parameter, when in fact it is also set in the qcache stage of recon-all, which precedes QDEC? Many thanks in advance!! Tudor

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Re: [Freesurfer] Hippo-subfields
by Marcos Martins da Silva 20 Apr '13

20 Apr '13

Thank you for your answer, Juan. Yes, I want a surface of the whole hippocampus and I thought I had just obtained that using freeview and adding all hippo-subfield files. That resulted in the screenshot I previously attached. I just do not know how I can save the resultant surface. After I checked "show as isosurface in 3D view" the low and high threshold controls appeared. The default threshold values on Freeview for low was 127.5 and high was 255. When I played with these controls, the size of the surfaces changed on 3D view. That is why I made the second question. I was trying to select the correct values for low and high threshoulds so I get an image consistent with the volume values we get after running kvlQuantifyPosteriorProbabilityImages. After setting the correct values I would like to save the work as a surface so I could load the whole surface instead of loading each individual subfield file. But I did not find a "save as surface" option. So I used the screenshot tool to "save" the work. This way I could at least show you what I got but I thought it was not the best way to do it. Relating to the last question about generating a new segmentation (anterior, body and posterior), you said I could use simple geometric rules to get it. Could you tell me where I can find instructions about how to do it? Sorry, I am afraid I am a novice here and my questions are the best proof of this, so I would like to thank you for all your patience. Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu: Dear Marcos, > > > 1- How do I save the combined 3D view I got as a surface? > > Do you want a surface of the whole hippocampus? In that case I would > suggest adding up the probability volumes from all the subfields and > thresholding the resulting volume. > > > > 2-I know the hippo-subifields .mgz files are probability maps and if I > > guess right kvlQuantifyPosteriorProbabilityImages read these files to > > count how many voxels you have in each subfield. I also guess it count > > only the voxels with reasonable high probability to be part of each > > subfield. If so, what is the minimum value between 1 and 255 the > > program use to decide if a particular voxel is valid? > > The estimates of the volumes are based on soft probabilities, so all > voxels with non-zero probability contribute towards the estimate. For > instance, a voxel with value 255 contributes to the volume 255 times as > much as a voxel with a value of 1. > > > > 3- Is it possible to merge hippo-subfield .mgz files data and to > > generate a different segmentation like anterior (anterior quarter), > > body (the2 intermediate quarters) and posterior (posterior quarter). > > There are currently no scripts in FreeSurfer to generate such a > partition. But you could always take a mask of the whole hippocampus > (either from aseg.mgz of from the combination of all the subfields, like > I mentioned in 1) and define some simple geometric rules to create it. > > Kind regards, > > Eugenio > > > > > > > > TY in advance > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Technical Assistant Position Available at MIT
by Satrajit Ghosh 19 Apr '13

19 Apr '13

For details of the position and for applying see: http://sh.webhire.com/servlet/av/jd?ai=631&ji=2681168&sn=I

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autorecon2-cp error
by Claudia Dacquino 19 Apr '13

19 Apr '13

Hi freesurfer, my autorecon2-cp after ctrl pts edits exited with this error message: CORRECTING DEFECT 0 (vertices=176788, convex hull=8149) Excessive topologic defect encountered: could not allocate -776253752 edges for retessellation Cannot allocate memory Could anyone help me with this, please? Thanks to all. Cheers Claudia

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Re: [Freesurfer] How to calcutate Brain volume?
by Anupa AV 19 Apr '13

19 Apr '13

Dear Cedric, Thanks a bunch. I'll try with mri_label2label. ________________________________ From: "Koolschijn, Cédric" <P.C.M.P.Koolschijn(a)uva.nl> To: Anupa AV <av.anupa(a)yahoo.com> Sent: Monday, April 15, 2013 1:07 PM Subject: Re: [Freesurfer] How to calcutate Brain volume? Dear Anupa, The DLPFC is not a standard label in FS. So you need to create it yourself by merging the following labels: DLPFC: middle frontal gyrus, and inferior and middle frontal sulci See also: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009600.… Best, Cédric ---------------------------------------------------------------- P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain and Cognition Weesperplein 4; Room 3.07 1018 XA Amsterdam The Netherlands E P.C.M.P.Koolschijn(a)uva.nl W http://www.dutcharc.nl// On 4/15/13 7:34 AM, "Anupa AV" <av.anupa(a)yahoo.com> wrote: Dear FreeSurfer Experts, > > >I'd like to know how to measure the volume of a brain region using freesurfer. >I know to obtain the volumes after runnin recon-all command. But I don't find the brain volume of my interest which is DLPFC. >How can I get the brain volume of my interest.? > > > > >Thanks for your response in advance. > > > > >

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How to set the -retinotopy number in mkanalysis-sess due to different cycle time in the eccen and polar
by yufeng huang 18 Apr '13

18 Apr '13

Dear Doug, I want you could give me some guidances with my retinotopic analysis. Eccen run: TR 2 Ncycles 6, 64 sec per cycle, all scan 384 sec. Polar run: TR 2, then follow Ncycles 10, 32 sec per cycle, all scan 320 sec. I write the rtopy.par: stimtype polar diretion neg ncycles 10 and stimtype eccen diretion pos ncycles 6 My question is: How to set the value of -retinotopy in the mkanalysis as the eccen value should be -retinotopic 64 while the polar value should be -retinotopic 32 in the mkanalysis-sess Thanks a lot! Yours Yufeng

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error while performing recon-all for multiple datasets
by Anupa AV 18 Apr '13

18 Apr '13

Dear All, I want to run recon-all for multiple subjects. I named my sbjects as SZ01.nii, SZ02.nii etc. After setting the cd and environmanet variable, I ran using following for loop: >for x in * > do >recon-all -i SZ*.nii -s $x -all >done I got the following error: WHAT MIGHT BE THE REASON FOR THE ERROR??? WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ01.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 19 11:43:24 IST 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ02.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 19 11:43:24 IST 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ03.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 19 11:43:24 IST 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ04.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 19 11:43:24 IST 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Thank you
by Valtina Pouegue 18 Apr '13

18 Apr '13

Hi everyone, I would just say you thank you for the help you give to Freesurfer users. I use Freesurfer for my school project and I ended yesterday. I didn't know anything about Linux before and before segmentation software of cortical surface. I don't think I would did an so great job without your help. Again, Thank you! And Good Luck !!! VP

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Autoreg-sess and mri_surf2vol
by Lucille Deroche 18 Apr '13

18 Apr '13

Hi, My name is Lucille and I'm really new with Freesurfer : My questions are very basic, sorry. I just start a project in segmentation of cerebrum. For converting a surface in volume. I would like to use mri_surf2vol but for that I need a volume registration file . For creating that file, I would use autoreg-sess. In documentation, it is said that : 'The volume registration file contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume' My question is : what here, represent the anatomical reference ? The functionnal volume ? Secondly, for autoreg-sess, the arguments are the subject name and the subject directory. I think the registration I need to create must be between my 2 volumes, so should I use the subject name and subject directory for my 2 subjects ? Sorry,I am really messed... Cheers Lucille

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mri_segstats SNR calculation
by Jordi Delgado 18 Apr '13

18 Apr '13

Dear Freesurfers, After running the first tests of freesurfer 5.2, I found a file named $hemi.w-g.pct.stats on the stats folder. The last column of the file is a SNR calculation, i found on the help manual, that is required to add --snr to perform this calculation. I'm interested to know how this SNR is calculated. Is there any method or paper related? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

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Freesurfer April 2013