Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Data check
by Charlotte Bernard 02 Mar '12

02 Mar '12

Dear Freesurfer users, I would like to know what is the procedure to check the quality of the Freesurfer process on my subjects. I have more than 500 subjects. 1/ Have I to check each segmented region on by one for each subject? 2/ How can we check the quality of the surf process? Thanks a lot for your help, Charlotte

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Recommended reconstruction wiki
by Martijn Steenwijk 02 Mar '12

02 Mar '12

Dear all, On http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction it is indicated that -autorecon-cp should be added if control points are added. Shouldn't this be -autorecon2-cp? Furthermore, suppose control points are added and -autorecon2-cp has been runned. If I then correct the skull strip (as indicated in the wiki) and want to rerun, do I have to call -autorecon2-cp then, or can I just run -autorecon2 -autorecon3? Best, Martijn

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Tracula preproc failure
by Martijn Steenwijk 01 Mar '12

01 Mar '12

Dear all, I'm running Tracula on a brain with some pathology. During the preproc phase it fails with the following error: INFO: Rejected 843 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction INFO: Rejected 10 streamlines as length outliers INFO: Have 2748 total streamlines (min/mean/max length: 38/70/105) Processing pathway 3 of 18... Matching streamline ends INFO: Have 0 non-truncated streamlines (min/mean/max length: 0/0/0) INFO: Center of mass of start points: (nan+/-nan, nan+/-nan, nan+/-nan) INFO: Center of mass of midpoints: (nan+/-nan, nan+/-nan, nan+/-nan) INFO: Center of mass of end points: (nan+/-nan, nan+/-nan, nan+/-nan) Segmentation fault (core dumped) Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Feb 27 19:41:00 CET 2012 I understand that no streamlines are available for initialization. Is that correct? Best, Martijn

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Probabilistic white matter mask
by Palzes, Vanessa 01 Mar '12

01 Mar '12

I found a couple older threads about creating a probabilistic mask in Freesurfer: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11790.html https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-July/014953. html I have modified mri_ca_label with the flag -write-probs and instead of norm.mgz I use aseg.mgz: mri_ca_label -align -nobigventricles -write-probs aseg.mgz transforms/talairach.m3z /Applications/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz Freesurfer then tells me: "writing label probabilities to aseg.mgz" - so I assume that is a success. Now in order to extract a white matter mask, I have tried both mri_extract_label and mri_binarize (although the point of this one is to binarize) to extract these probability values of the white matter areas from aseg.mgz. Unfortunately, I am not getting any probability values in the mask, neither in the form of 0-255 nor 0-1. I've tried searching for another command I can use to create masks, such as mri_wmfilter but I think that one is outdated since it looks to a specific directory called "brain" within the subject folder. Is there another command I can use to extract masks with probability values? Or do I need to run the remaining pipeline of commands after mri_ca_label in order to achieve this? Your help is greatly appreciated. Thanks, Vanessa Palzes Staff Research Associate Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155 -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Thursday, March 01, 2012 9:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 97, Issue 1 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."

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Qdec Error: MatrixMultiply: ml is null!
by Laura Tully 01 Mar '12

01 Mar '12

Hi, I am trying to run a between group analysis in QDEC whilst controlling for intrancranial volume. The design has one dichotomous variable (group2, group2), one continuous (performance on behavioral task), and one nuisance variable (intracranial volume). each time I run it qec crashes with the following error: MatrixMultiply: ml null! What does this error mean and how can I fix it? What is odd is that this error does not seem to be consistently reproducible - after successfully running the analyses without controlling for ICV, I was then able to run it with ICV as a nuisance factor. Thank you! Laura. -- Laura Tully Social Neuroscience & Psychopathology Harvard University 806 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully(a)fas.harvard.edu

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strangely low lhCorticalWhiteMatterVol estimate
by Michael Harms 01 Mar '12

01 Mar '12

Hi guys, We have a subject processed with FS v5.1 in which lhCorticalWhiteMatterVol in aseg.stats is much too low -- only 33781 mm^3. From what I see, the aseg.mgz looks fine. 'mris_volume lh.white' returns 287261 and running mri_segstats without the --excl-ctxgmwm option returns a Left-Cerebral-White-Matter volume of 245169. 'mris_euler_number' indicates no problems with lh.white. Running 'mris_wm_volume' on its own generates the same value of 33781. I also tried running 'mris_wm_volume' with the -v option to see if any interesting messages popped up, but got the message "unknown option -v". Any idea what is going wrong here? So you can see for yourself, I went ahead and uploaded the subject's processed data to your FTP server (110107_L206.tgz) thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

3 5

mri_segstats output
by Marco Loggia 01 Mar '12

01 Mar '12

Dear all, Given a series of fsaverage-registered rCBF maps, I am trying to extract the average rCBF value from one specific region. This region, which was a significant cluster from a volumetric (fsl) analysis, was binarized and then converted to surface. When I run mri_segstats with the --avgwf I obtain two columns. Can you please remind me which one is the average extracted from that ROI, and what is the other column? Thanks! Marco mri_vol2surf --mov DMN_s1_RS1_correlates_with_ASL1_rating.gfeat/cope1.feat/cluster_mask_zstat1.nii.gz --mni152reg --hemi rh --o /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF/rh.RS1_correlates_ASL1.mgz cd /autofs/cluster/randy/6/users/marco/lbp/lbp_freesurfer_ASL/ASL_connectivity_SURF for f in `ls *.mgz` ; do mri_segstats --seg $f --in /homes/14/marco/cluster_6/lbp/lbp_freesurfer_ASL/patients+controls/analyses/rh.lbp+ctrl.session1.asl2-asl1_projfrac-max_nopaired-diff_sm7_03mm_OCT18.mgh --avgwf "$f"_RH_nopaired_diff.txt done nedit rh.RS1_correlates_ASL1.mgz_RH_nopaired_diff.txt & 38.2811 47.6476 40.3997 36.0856 42.6304 46.2465 44.4789 36.7066 69.2376 51.4098 66.0043 47.2098 34.5957 40.3854 36.8976 42.2028 38.2475 35.875 39.9503 37.0186 35.1582 36.6949 35.1924 38.874 43.4415 36.2505 43.3516 34.5041 58.3073 50.3295 61.8703 60.8415 61.1754 51.3476 47.9508 51.594 51.5809 48.2985 49.6545 50.974 62.9431 72.1211 54.0272 55.7234 35.0701 34.5995 37.9241 35.3844 37.2277 42.3105 38.2136 46.7896 45.0951 51.9831 45.4391 51.6242 46.2971 47.5424 44.3713 41.1725 37.4132 36.1166 36.7285 39.2947 44.0285 46.501 45.4698 50.5906 51.0392 48.2324 55.0885 50.9392 66.7224 67.7807 64.8932 68.5847 45.5101 45.6065 46.7002 45.232 40.6324 48.9768 44.3654 45.9017 39.4908 32.8936 39.5983 36.4909 55.9295 59.1527 55.6738 55.7016 44.7433 50.9412 42.6953 50.0857 42.4522 48.7366 43.5595 42.3424 43.9283 36.5026 41.9838 36.8662 39.9873 44.505 43.442 49.2243 57.6304 55.5628 53.3496 49.4215 43.2505 42.5797 43.5452 42.0694 50.4555 47.993 49.8977 49.6568 41.5077 42.8473 40.2357 42.3246 40.3846 39.1473 38.7073 41.502 ______________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School Psychiatric Neuroimaging Research Program CNY Building 120, suite 100 Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

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Re: [Freesurfer] hippocampus volume normalization question
by Douglas N Greve 01 Mar '12

01 Mar '12

It is whole-brain minus cerebellum and brain stem. But the current release has a bug and should not be trusted. See the email I sent out last week or look at the Release Notes page on our wiki for how to download a patch and regenerate the results. doug Rashmi Singh wrote: > Thanks so much Doug, > Just a last question. > Is supratentorial volume present in the aseg.stat file anyway related to > the whole brain volume? > Thanks, > Rashmi. > > > On 2/29/12 10:33 AM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > > >> You'll have to run it on each subject. Easy to do with a script. You can >> then cat the data into one fine (they are just text files). >> doug >> >> Rashmi Singh wrote: >> >>> Thanks Doug, >>> Do I need to run the following for each subject or can is there a way >>> to >>> run it with input for all my subjects in one go to get the brain volume >>> of >>> all my subject in one output file. >>> Thanks, >>> >>> >>> >>> On 2/29/12 10:15 AM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>> >>> >>>> oh, sorry, I do remember now that we took that out (I think we put it >>>> back in for the next release). The work-around is to run >>>> >>>> mri_binarize --i brain.mgz --min 0.00001 --count count.dat --o junk.mgh >>>> >>>> You can delete junk.mgh. The file count.dat will have info about the >>>> number of voxels in the brain. It will have 4 numbers: >>>> #voxels in brain, brain volume (mm3), total # voxels in volume, and >>>> brain volume as a percent of total volume in the 3d a field of view. >>>> >>>> doug >>>> >>>> >>>> Rashmi Singh wrote: >>>> >>>> >>>>> Hello doug, >>>>> In the asegstats. Txt ( that got as in the table format with >>>>> information >>>>> on all subjects grouped together in a single .Xls file) I found >>>>> information on Total Gray vol but I don't see whole Brain volume. >>>>> Can you please suggest me where to get the whole brain volume. >>>>> Thanks, >>>>> Rashmi. >>>>> >>>>> >>>>> On 2/28/12 3:22 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>> wrote: >>>>> >>>>> >>>>> >>>>> >>>>>> In the aseg.stats file there is a value for the whole brain volume. >>>>>> doug >>>>>> >>>>>> Rashmi Singh wrote: >>>>>> >>>>>> >>>>>> >>>>>>> I would like know how can I get the sub-cortical volumes normalized >>>>>>> it >>>>>>> to >>>>>>> the whole brain. >>>>>>> Thanks, >>>>>>> Rashmi. >>>>>>> >>>>>>> On 2/28/12 3:14 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> No, it does not. All volumes are volumes in native anatomical >>>>>>>> space. >>>>>>>> doug >>>>>>>> >>>>>>>> Rashmi Singh wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Hello. >>>>>>>>> I am using FreeSurfer to generate subcortical volumes and >>>>>>>>> cortical >>>>>>>>> thickness for my subjects. >>>>>>>>> Does FreeSurfer normalizes the subcortical volumes to the whole >>>>>>>>> brain >>>>>>>>> volume for each subjects. >>>>>>>>> Let me know. >>>>>>>>> For among subjects comparison I am assuming that the sub >>>>>>>>> cortical >>>>>>>>> volumes generated for each subject are normalized to its own whole >>>>>>>>> brain volume. >>>>>>>>> >>>>>>>>> Thank you, >>>>>>>>> Rashmi. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> ------------------------------------------------------------------- >>>>>>>>> -- >>>>>>>>> -- >>>>>>>>> - >>>>>>>>> >>>>>>>>> This document may contain information covered under the Privacy >>>>>>>>> Act, 5 >>>>>>>>> USC 552(a), and/or the Health Insurance Portability and >>>>>>>>> Accountability >>>>>>>>> Act (PL 104-191) and its various implementing regulations and must >>>>>>>>> be >>>>>>>>> protected in accordance with those provisions. Healthcare >>>>>>>>> information >>>>>>>>> is personal and sensitive and must be treated accordingly. If this >>>>>>>>> correspondence contains healthcare information it is being >>>>>>>>> provided >>>>>>>>> to >>>>>>>>> you after appropriate authorization from the patient or under >>>>>>>>> circumstances that don't require patient authorization. You, the >>>>>>>>> recipient, are obligated to maintain it in a safe, secure and >>>>>>>>> confidential manner. Redisclosure without additional patient >>>>>>>>> consent >>>>>>>>> or as permitted by law is prohibited. Unauthorized redisclosure or >>>>>>>>> failure to maintain confidentiality subjects you to application of >>>>>>>>> appropriate sanction. If you have received this correspondence in >>>>>>>>> error, please notify the sender at once and destroy any copies you >>>>>>>>> have made. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> ------------------------------------------------------------------- >>>>>>>>> -- >>>>>>>>> -- >>>>>>>>> - >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>> Phone Number: 617-724-2358 >>>>>>>> Fax: 617-726-7422 >>>>>>>> >>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 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. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> ________________________________ >>>>>>> >>>>>>> This document may contain information covered under the Privacy >>>>>>> Act, 5 >>>>>>> USC 552(a), and/or the Health Insurance Portability and >>>>>>> Accountability >>>>>>> Act (PL 104-191) and its various implementing regulations and must >>>>>>> be >>>>>>> protected in accordance with those provisions. Healthcare >>>>>>> information >>>>>>> is >>>>>>> personal and sensitive and must be treated accordingly. If this >>>>>>> correspondence contains healthcare information it is being provided >>>>>>> to >>>>>>> you after appropriate authorization from the patient or under >>>>>>> circumstances that don't require patient authorization. You, the >>>>>>> recipient, are obligated to maintain it in a safe, secure and >>>>>>> confidential manner. Redisclosure without additional patient consent >>>>>>> or >>>>>>> as permitted by law is prohibited. Unauthorized redisclosure or >>>>>>> failure >>>>>>> to maintain confidentiality subjects you to application of >>>>>>> appropriate >>>>>>> sanction. If you have received this correspondence in error, please >>>>>>> notify the sender at once and destroy any copies you have made. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve(a)nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> ________________________________ >>>>> >>>>> This document may contain information covered under the Privacy Act, 5 >>>>> USC 552(a), and/or the Health Insurance Portability and Accountability >>>>> Act (PL 104-191) and its various implementing regulations and must be >>>>> protected in accordance with those provisions. Healthcare information >>>>> is >>>>> personal and sensitive and must be treated accordingly. If this >>>>> correspondence contains healthcare information it is being provided to >>>>> you after appropriate authorization from the patient or under >>>>> circumstances that don't require patient authorization. You, the >>>>> recipient, are obligated to maintain it in a safe, secure and >>>>> confidential manner. Redisclosure without additional patient consent >>>>> or >>>>> as permitted by law is prohibited. Unauthorized redisclosure or >>>>> failure >>>>> to maintain confidentiality subjects you to application of appropriate >>>>> sanction. If you have received this correspondence in error, please >>>>> notify the sender at once and destroy any copies you have made. >>>>> >>>>> >>>>> >>>>> >>>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> >>>> >>>> >>> ________________________________ >>> >>> This document may contain information covered under the Privacy Act, 5 >>> USC 552(a), and/or the Health Insurance Portability and Accountability >>> Act (PL 104-191) and its various implementing regulations and must be >>> protected in accordance with those provisions. Healthcare information is >>> personal and sensitive and must be treated accordingly. If this >>> correspondence contains healthcare information it is being provided to >>> you after appropriate authorization from the patient or under >>> circumstances that don't require patient authorization. You, the >>> recipient, are obligated to maintain it in a safe, secure and >>> confidential manner. Redisclosure without additional patient consent or >>> as permitted by law is prohibited. Unauthorized redisclosure or failure >>> to maintain confidentiality subjects you to application of appropriate >>> sanction. If you have received this correspondence in error, please >>> notify the sender at once and destroy any copies you have made. >>> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> > > > ________________________________ > > This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

length of a label
by Ritobrato Datta 29 Feb '12

29 Feb '12

Hi All, Is there a way to calculate the length and width of a label ? Please let me know. Thanks a lot Ri

2 1

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Freesurfer March 2012