Freesurfer

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30099 discussions

Hemispherectomy Surgery
by Kristian Eschenburg 11 Feb '14

11 Feb '14

Hi I have a dataset of children who have had hemispherectomy surgery to treat epilepsy. I want to be able to run recon-all on these children. I have masked out the remaining tissue from the excised side so that only tissue from the healthy hemisphere remains, and aligned this single hemisphere to a template. To mimic a whole brain, I have flipped the single hemisphere over the X-axis and added it to the other half. Thus, I have the original hemisphere, and the "mirrored" hemisphere in one scan. This is my input to recon-all. However, as the scans were acquired some time after surgery, the remaining hemisphere was not perfectly aligned at the midline and expanded / grew into to the empty cranial space, and there are gaps and overlap between the mirrored side and the original side. Is there a way to run recon-all on the single hemisphere alone, so that I do not have to mirror the brain? Perhaps by supplying a mask, to apply to the FreeSurfer atlases? Thanks Kristian

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Cortical Thickness values
by Natasha Haris 11 Feb '14

11 Feb '14

Dear Freesurfers, Is there anyway to get a compiled list of all the significant clusters with information about their maximum thickness value, x/y/z vertices, t statistic etc on QDEC? Does this have anything to do with a SaveClusterFile command? All of this information must be stored somewhere for the significant clusters to appear - wondering what's the easiest way to extract this info. Thanks, Natasha

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FreeSurferWiki RecentChanges
by Kaiming Yin 11 Feb '14

11 Feb '14

Dear guys, Is there some way to have a more detailed look of the recent changes on the FreeSurfer Wiki page? I click on the recent changes option but can only see the latest 13 updates within around 10 days. Could I have a check of that from further past days? Thanks a lot, Kaiming

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Program Director job opening at the NINDS (fwd)
by Bruce Fischl 11 Feb '14

11 Feb '14

FYI ---------- Forwarded message ---------- Date: Tue, 11 Feb 2014 16:50:15 +0000 From: "Babcock, Debra (NIH/NINDS) [E]" <dbabcock(a)ninds.nih.gov> To: "Babcock, Debra (NIH/NINDS) [E]" <dbabcock(a)ninds.nih.gov> Subject: Program Director job opening at the NINDS Dear Colleagues, The NINDS is currently seeking to hire several program directors. In particular, we are searching for a motivated and energetic PhD or MD with a background in cognitive neuroscience or a related field to administer our Behavioral and Cognitive Neuroscience program. Familiarity with neuroimaging science is a plus, but not required. Applications will be accepted through USAJOBS starting on February 14, 2014 and closing on February 23, 2014. There will be a separate job ad specifically for a similar Medical Officer (MD) position to follow this one; however, both MDs and PhDs may apply to the ad opening on Feb. 14. For more details, please see: http://jobs.sciencecareers.org/job/324934/health-scientist-administrator/ If you know of anyone who might be interested in this position, please forward this information to them. I’m happy to answer questions about the position or the application process. Thanks for your assistance, Deb Babcock Debra J. Babcock, Ph.D., M.D. Program Director, Behavioral & Cognitive Neuroscience NINDS/NIH 6001 Executive Blvd., Room 2108, MSC 9521 Bethesda, MD 20892-9521 Rockville, MD 20852 (for UPS, FedEx, etc.) Phone: 301-496-9964 Fax: 301-402-2060 Email: dbabcock(a)ninds.nih.gov

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Re: [Freesurfer] creating specific files
by Borzello, Mia 11 Feb '14

11 Feb '14

woops- sorry meant to include everyone. The name of the file I use to plot is "lh.pial-outer-smoothed." So I either want to create this file or figure out another way to plot. Do i need lh.pial to make lh.pial-outer-smoothed? ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Tuesday, February 11, 2014 10:51 AM To: Borzello, Mia Subject: Re: [Freesurfer] creating specific files Hi Mia can you keep ccing the list? I don't know what the "outer smoothed pial surface" is. Is this something we create? I don't think so Bruce On Tue, 11 Feb 2014, Borzello, Mia wrote: > Plotting the electrodes on the surface using matlab. I usually use the outer smoothed pial surface- do I first need the normal pial surface to create this? > > > >> On Feb 11, 2014, at 10:42 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >> >> what kind of plotting do you mean? >>> On Tue, 11 Feb 2014, Borzello, Mia wrote: >>> >>> Okay and is there a way to check if the files I currently have are sufficient to plot with? >>> >>> Thanks, >>> m >>> >>> >>> >>>> On Feb 11, 2014, at 9:58 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >>>> >>>> if they are zero length there is nothing there now >>>>> On Tue, 11 Feb 2014, Borzello, Mia wrote: >>>>> >>>>> Is this okay to do even if I've done a coregistration, nothing will be deleted? Also, are the pial surfaces necessary for plotting? I'm wondering if I can just use the files that I have to create a plot without having to rerun anything. >>>>> >>>>> Thanks, >>>>> Mia >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> On Feb 10, 2014, at 4:31 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>> Hi Mia >>>>>> >>>>>> delete the 0 length files and run recon-all -make all -s <subject> >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>>> On Mon, 10 Feb 2014, Borzello, Mia wrote: >>>>>>> >>>>>>> Hi Freesurfers, >>>>>>> I was wondering if there was a way to kind of fill in the blanks for a >>>>>>> Surfer Output folder. I am working with an old data set, and it seem that >>>>>>> some of the files are empty (0 bytes), "rh.pial" for example. Is there a way >>>>>>> to pass the SurferOutput folder in and recreate what's missing? >>>>>>> Thanks, >>>>>>> Mia >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> > > >

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creating specific files
by Borzello, Mia 11 Feb '14

11 Feb '14

Hi Freesurfers, I was wondering if there was a way to kind of fill in the blanks for a Surfer Output folder. I am working with an old data set, and it seem that some of the files are empty (0 bytes), "rh.pial" for example. Is there a way to pass the SurferOutput folder in and recreate what's missing? Thanks, Mia

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How to caulculate the differences in subcortical volumes and display it?
by Wang, Guoying 11 Feb '14

11 Feb '14

Dear freesurfer experts, I am trying to compute the differences in subcortical volumes between two groups. I have read previous mail, https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17597.html , and in this mail, your answer was 'you can do a subcortical volume analysis by working with the aseg.stats file directly or compute with mri_glmfit'. So, I tried to use 'mri_glmfit' to calculate it . but without specifying the argument '-surf' (because it is mentioned in your webpage that 'if -surf is not specified, then mri_glmfit will assume that the data are volume-based and use the geometry as specified in the header to make spatial calculations'). However, when I ran the command, it gave me the error message which said :' you must use-surface subject hemi' with surface data'. Do I misunderstanding some point? On the other hand, if there is statistical differences in subcortical volumes. How to display them in freesurfer? Sorry, I am a beginner. I know someone asked this question before, but I am still not fully understand it . Thank you for your help and reply in advance ! Please find the command and error message attached --------------------------------------------------------------------- $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /gdata1/freesurfer_data/subjects/gy_stat/time1_average_cross/aseg_test cmdline mri_glmfit --y lh.volume.average.fwhm10.mgh --fsgd y_fsgd.txt doss --C lh-volume-age-gender-ICV-cor.mtx --glmdir lh.seg_volume_sexageicv.glmdir sysname Linux FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /gdata1/freesurfer_data/subjects/gy_stat/time1_average_cross/aseg_test/lh.volume.average.fwhm10.mgh logyflag 0 usedti 0 FSGD y_fsgd.txt glmdir lh.seg_volume_sexageicv.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from/........./ lh.volume.average.fwhm10.mgh ERROR: you must use '-surface subject hemi'with surface data ------------------------------------------------------------------------------------------------------ Guoying

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wmparc
by sujith vijayan 11 Feb '14

11 Feb '14

Hi All, I have a few questions about wmparc: What rule is used to determine what grey matter structure corresponds to a white matter point? What exactly has to be the case when UnsegmentedWhiteMatter is reported? Is there a reference you could point me to? Thanks, Sujith

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combining FS commands
by Erik Lindberg 11 Feb '14

11 Feb '14

Dear Freesurfers, I want to run: mri_normalize gentle, And mris_make_surfaces min_border_white 85 -min_gray_at_white_border 80 in MY recon-all script. I understand that I have to put the flag -expert to do this - but I seem to make errors in my command It would be greatly appreciated if you can tell me how the command should be written Thanks in advance! Erik

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Combining FS commands
by Erik Lindberg 11 Feb '14

11 Feb '14

Dear Freesufers, I want to run: mri_normalize gentle, And mris_make_surfaces min_border_white 85 -min_gray_at_white_border 80 In as few steps as possible as I will run around 800 images. So far I only managed to this by braking up the process several subparts (like doing autorecon1 before mri_normalize, and autorecon2 before mris_make_sufaces If this could be combined somehow it would of course be a lot easier than running step by step 800 times. Thanks in advance Erik

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