Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

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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Re: [Freesurfer] Choi's parcellation expansion inquiry
by Thomas Yeo 11 Feb '14

11 Feb '14

Hi Sooyun, It is possible that tri-linear might work better, but I have to caution that you will get non-integer values. Have you tried mri_label2vol? According to Doug in the last email, mri_label2vol might work better than mri_vol2vol. My suggestion is to first verify whether the transformation from Choi parcellation to the subject's native space is good enough. To do that, instead of transforming the Choi parcellation, try transforming the MNI152 template accompanying the Choi's parcellation (NOT the FSL MNI152 template). If the transformed MNI152 template does not match your subject's native anatomy to your liking, then you need to improve the transformations. Again, can you clarify where you are obtaining the transformation matrices? Recall that I previously told you that to convert the Choi's parcellation to the MNI152 template from FSL, you should just use mri_vol2vol, rather than FIRST. The command is as follows: "mri_vol2vol --mov original_choi_MNI152_parcellation.nii.gz --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader --o FSL_choi_MNI152_parcellation.nii.gz --no-save-reg --interp nearest". And the reason is that the Choi volume is in exactly the SAME space as the $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz, it's just that the header information is different. Therefore the "regheader" flag takes care of that. Cheers, Thomas On Tue, Feb 11, 2014 at 2:03 PM, 조수연 <syduam2452(a)kaist.ac.kr> wrote: > Hi, Thomas. > > > > > > I have circled the unmasked regions in the image with a red brush tool. > The yellow-red regions are the FreeSurfer space->MNI152 space->Subject > space transformed Choi's loose mask files, and the blue regions are the > subject's subcortical areas. My current ROI is the caudate and the putamen. > As you can see, there are multiple regions where the labels aren't big > enough to cover my subject data. I checked the original Choi's > parcellations in the original space and the MNI152 space but it's hard to > check whether the label in the specific location of my interest is missing > or not because the voxel numbers and dementions are different per space, > thus is hard to get the specific coordinates that lacks mask. > > I discussed with my lab members and concluded maybe the problem lies when > we are transferring the image from one space to another in that we used the > nearest neighbour when applying the transformation matrix. We are planning > to use tri-lear for interpolation instead so that the achieved image has a > looser intensity specificaton, so that it helps us to specify the lables of > the subject's regions which are not covered by Choi's masks. Hope this > helps. > > If you have any suggestions as of how to morph Choi's images best to our > subject's fit, please do inform me. Thanks! > > > > Best regards, Sooyun. > > > > > > -----------------------원본메일----------------------- > 보낸사람 : Thomas Yeo <ythomas(a)csail.mit.edu> > 받는사람: 조수연<syduam2452(a)kaist.ac.kr> > 참 조: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > 보낸날짜: 2014-02-11 00:11:48 GMT +0900 (ROK) > 제목: Re: [Freesurfer] Choi's parcellation expansion inquiry > > > Hi Sooyun, > > Which is the sky blue region you are referring to? Can you place your > fslview cursor in the location where you think is missing the label? > > Can you visually inspect the original Choi's parcellation to see if the > label is also missing at the corresponding MNI152 location? If the label is > not missing, then perhaps your transformation is not doing its job, which I > suspect might be the problem since the loose mask in Choi's parcellation is > already pretty loose. > > Regards, > Thomas > > > On Mon, Feb 10, 2014 at 12:20 PM, 조수연 <syduam2452(a)kaist.ac.kr> wrote: > >> Hi, all. >> >> I'm trying to apply Choi's parcellations onto my subjects' data. I used >> the 7-Network loose mask but it turns out that even the loose mask isn't >> capable of covering up the ROI. >> >> Is there a way I can further "expand" the loose mask and make it "looser"? >> >> The uncovered areas of my subject's image are colored skyblue. The rest >> are parcellated segments of Choi's image. >> >> FYI Choi's FreeSurfer grid images were linearly transformed by concat >> matrix which shifts FreeSurfer grid to Standard MNI152 grid to our >> subject's grid. >> >> >> >> Thanks. >> >> >> >> Best regards, Sooyun. >> >> _______________________________________________ >> 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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Freeview not working
by Saurabh Thakur 10 Feb '14

10 Feb '14

Hi all, My freeview is not working. //=============================================================// saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ freeview freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ /=============================================================// please suggest wht is going wrong. Thanks in advance, cheers Saurabh Thakur,

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Re: [Freesurfer] Fwd: trac-all -path error
by Anastasia Yendiki 10 Feb '14

10 Feb '14

We've generally seen better results with BBR, which is why it became the default setting. On Thu, 6 Feb 2014, Jon Wieser wrote: > HI Anastasia, > > I ran it again with the flirt registration and it finished ok. > We did not have a specific reason for running it both ways. we are using the default setting for the dmrirc file. > do you recommend one method over the other? > > thanks again > Jon > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Thursday, February 6, 2014 3:07:12 PM > Subject: Re: [Freesurfer] Fwd: trac-all -path error > > > That's entirely up to you, and whether you had a specific reason for > running it both ways. > > If you want to fix the bbr registration manually, check the trac-all.log > file for a command at the end of bbregister, where it says "To check > results, run". > > On Thu, 6 Feb 2014, Jon Wieser wrote: > >> Hi Anastasia, >> We used both flirt and bbr registration in the dmrirc file, the Aparc+seg I just showedd you was from the BBR resitration. I looked at the flirt registration. it looks OK. >> should I rerun tracula using only the flirt registration? >> Jon >> >> ----- Original Message ----- >> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >> Sent: Thursday, February 6, 2014 11:00:25 AM >> Subject: Re: [Freesurfer] Fwd: trac-all -path error >> >> >> So there's your culprit. You need to fix the intra-subject >> (diffusion-to-T1) registration. Did you use flirt or bbregister for that? >> >> On Thu, 6 Feb 2014, Jon Wieser wrote: >> >>> Hi Anastasia, >>> I looked at the dlabel/diff/Aparc+aseg overlayed on the dmri/dtifit_FA.nii.gz >>> the alignemenst is way off (in freeview, in the coronal view, the aparc+seg is rotated 45 degrees anti-clockwise), and parts of the FA map in the L ILF area are missing. the original DTI is not missing data in these areas. I have attached screenshots >>> Jon >>> >>> >>> >>> ----- Original Message ----- >>> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Sent: Wednesday, February 5, 2014 6:35:12 PM >>> Subject: Re: [Freesurfer] Fwd: trac-all -path error >>> >>> >>> Hi Jon - You need to look at the aparc+aseg after it has been mapped to >>> diffusion space. It's possible that it looks fine in its original space >>> but then maybe something goes wrong with the registration. So you should >>> look at the aparc+aseg and aparc+aseg_mask files from the tracula >>> dlabel/diff directory. These are in diffusion space and you can overlay >>> them on the FA map to see if there's anything strange in the ILF area. >>> >>> Hope this helps, >>> a.y >>> >>> On Tue, 14 Jan 2014, Jon Wieser wrote: >>> >>>> Hi anastasia >>>> I looked at the brainmask and the aparc+aseg. I did see anything missing in the area of the left ILF. >>>> I have attached the files. can you take a look at them? >>>> Thanks >>>> JOn >>>> >>>> ----- Original Message ----- >>>> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>>> Sent: Friday, January 10, 2014 6:15:23 PM >>>> Subject: Re: [Freesurfer] Fwd: trac-all -path error >>>> >>>> >>>> Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? >>>> Anything missing there that might affect the left ILF? >>>> >>>> a.y >>>> >>>> On Wed, 8 Jan 2014, Jon Wieser wrote: >>>> >>>>> >>>>> Dear freesurfer experts >>>>> I'm getting the following error when runing trac-all -c dmrirc_single_subject -path >>>>> >>>>> >>>>> Loading initial proposal SD's from /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt >>>>> Processing pathway 3 of 18... >>>>> Initializing MCMC >>>>> Segmentation fault >>>>> Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 >>>>> >>>>> >>>>> I have attached the trac-all.log and trac-all.error files >>>>> >>>>> I am running tracula 5.3 >>>>> >>>> >>>> >>>> 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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Freesurfer February 2014