Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

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

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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

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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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How to combine attached commands into one run
by Erik Lindberg 10 Feb '14

10 Feb '14

Dear Freesufers, I want to use the following commands in my recon-all to try to improve my output some difficult images: -gentle to mri_normalize and -min_border_white 85 -min_gray_at_white_border 80 So far I only managed to do this by making one step at a time. I was wondering if there is a way to combine these commands so I do not have to run it step by step.

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scuba running problem.
by Saurabh Thakur 10 Feb '14

10 Feb '14

Hello Friends, I m facing problem in freeview and scuba. can anyone help me in this matter. //==========================================================// saurabh@saurabh-Precision-WorkStation-T3500:/$ cd $FREESURFER_HOME saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ scuba -v $SUBJECTS_DIR/bert/mri/T1 Error starting scuba: File: tkUtils.tcl scuba could not be loaded because a support file was missing. Please check your installation. Make sure that the FREESURFER_HOME environment variable is set. //==========================================================// Thanks in advance. cheers Saurabh Thakur,

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Freesurfer February 2014