Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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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Erasing, adding voxels in Freeview
by Denker, Alexander (NIH/NIMH) [F] 10 Feb '14

10 Feb '14

Hi all, This is probably a very elementary error in my use of Freeview, but I have been having trouble adding voxels to scans. I set the eraser value to "0", but when I draw, the voxel still shows up as a black box instead of grey. Am I not setting the right values or am I just in the wrong viewing mode? Thanks! Alexander

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Re: [Freesurfer] PET Partial volume correction
by Jonathan DuBois 10 Feb '14

10 Feb '14

Hi Doug, Thanks for replying. We are currently working on this analysis, is there anyway you could provide a beta version of the PVC code? Thanks, Jonathan

2 1

autorecon2-cp failure
by Maia Pujara 10 Feb '14

10 Feb '14

Hello, I came across two subjects who had incomplete surfaces because of an aggressive skull strip. After changing the watershed parameters to include the missing brain parts and running the subject through autorecon2 and autorecon3 again, the surfaces were included for one hemisphere but not the other. I've attached screenshots for these subjects. For one of the subjects, I tried including control points where necessary and running autorecon2-cp, and it still didn't fix the incomplete surfaces. Any ideas on what to do next? Thank you! Maia

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Fwd: OHBM Glass Brain Award: Call for Nominations
by Douglas N Greve 10 Feb '14

10 Feb '14

FYI -------- Original Message -------- Subject: OHBM Glass Brain Award: Call for Nominations Date: Mon, 10 Feb 2014 11:18:43 -0600 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu <mailto:info@humanbrainmapping.org> *ORGANIZATION FOR HUMAN BRAIN MAPPING GLASS BRAIN AWARD* /A lifetime achievement award in the field of human brain mapping/ Dear OHBM Member, The Organization for Human Brain Mapping Council is excited to announce that OHBM has established an award to recognize and reward a lifetime of achievement by gifted and talented researchers using neuroimaging to discover original and influential findings to the organization of the human brain. *Aw**a**r**d Criteria* 1. Nominee must be visibly engaged in OHBM activities 2. Nominee must have evidence of extraordinary lifetime accomplishments in the field of human brain mapping and hold the promise of future major contributions to the field 3. The nominee must be over the age of 40 4. The nominee must be present to accept the award given out at the Annual Meeting 5. No self-nominations are allowed *Nomination Process* Nominations for the Glass Brain Award should include a letter of nomination (no self-nominations are accepted) outlining the nominee’s lifetime accomplishments as well as a curriculum vita of the nominee. Additional letters of support are not required but will add to the strength of the nomination. Nominators are required to collate all nomination materials into one single Adobe Acrobat PDF document to be emailed to OHBM at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org>. Deadline for nominations is March 14, 2014. *Rev**i**e**w Process* The OHBM Council is charged with the selection of the Glass Brain Award recipient and will meet in mid-March to review the award criteria and discuss each nominee. The Council will then vote electronically on their top ranked candidates. If needed, the Council will meet again to discuss any split decisions and make a final selection. The award recipient will be notified electronically in April. *Aw**a**rd* The award recipient will be provided with an OHBM Glass Brain Award, gratis Annual Meeting registration, coach travel and two nights lodging at the host hotel. We look forward to your involvement in the nomination process. Please contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> with any questions. Sincerely, JoAnn Taie Executive Director Organization for Human Brain Mapping (OHBM) ------------------------------------------------------------------------ Organization for Human Brain Mapping (OHBM) 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> www.humanbrainmapping.org <http://www.humanbrainmapping.org> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org>.

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Color Bar options
by Jonathan Holt 10 Feb '14

10 Feb '14

Hi all, Would someone kindly point me toward color bar options, specifically for thickness maps. The color bar that appears by default includes negative values, and the bit with positive thickness values is very compressed. For reference I’m looking at surfaces in freeview brought up by freeview -f SUBJ_ID/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 jon

2 1

setting the useRealRAS bit
by Lilla Zollei 10 Feb '14

10 Feb '14

Hi, I have some FS-style surface files that were created using outside tools (from McGill). Due to some recent changes in FreeView they do not display properly though as the useRealRAS bit in the header is not set to 1. Do we have any C / Matlab code that I could use to change that? Thanks, Lilla

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QDEC Error
by pfotiad＠nmr.mgh.harvard.edu 10 Feb '14

10 Feb '14

Hi FS community, After I open QDEC, when I try to load my qdec data table, QDEC crashes for some reason. The error message that comes out at the terminal is: Returned Error on line 1: missing close-brace Stack trace: missing close-brace while executing ".vtkKWLoadSaveDialog5.vtkKWFileBrowserWidget0.vtkKWSplitFrame0.vtkKWFrame2.vtkKWSplitFrame0.vtkKWFrame0.vtkKWDirectoryExplorer0.vtkKWTreeWithScrollbar..." X Error of failed request: BadAlloc (insufficient resources for operation) Major opcode of failed request: 53 (X_CreatePixmap) Serial number of failed request: 611512 Current serial number in output stream: 611810 Exit 1 I was wondering whether you know why is this happening. I am using FS v5.3 and my OS is Linux Centos 6.5. Thanks in advance, Panos

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Choi's parcellation expansion inquiry
by 조수연 10 Feb '14

10 Feb '14

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.

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Freesurfer