Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

Loading T1 maps onto inflated surfaces
by S Mian 08 Jul '13

08 Jul '13

Hi, I am new to FreeSurfer and I'm trying to figure out how to view T1 volumes on inflated surfaces in FreeSurfer. Any guidance would be appreciated! Thank you!

1 0

Xhemi results
by amirhossein manzouri 08 Jul '13

08 Jul '13

Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? 2) If yes, shouldn't I see the similar mapping by overlaying this to lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh) 3) How do you interpret the result after analyzing within one group? ( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh) 4) Is there any way to look at the results through the brain per slice and also the whole brain? -- Best regards, Amirhossein Manzouri

1 0

Tumor segmentation...
by Dov Sadan 08 Jul '13

08 Jul '13

Hi all, I Have MRI scans (T1/T2/Flair) with (manually) segmented tumors and I would like 2 use Freesurfer to estimate the brain locations of those Tumors. (I.e. What area of the brain "affected" by these tumors) .. Of course thisis not for clinical use, but "research" -- Is this task possible with Freesurfer ? If so, how this can be done ? Thanks, Dov [Please excuse me for my English...:]

2 1

recon-all
by 小麦 08 Jul '13

08 Jul '13

Hi expert, When I excuted the recon-all,I got the result that the final result is without error but the process is with error.The recon-all.log is attached.I want to get the cortical thickness,so I want to know that is the process's error affect my final result? Thanks in advance, Bella

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freesurfer skull strip removes brain except brainstem, and then has retesselation error
by Salil Soman 06 Jul '13

06 Jul '13

Hi, I have a study for which the original T1 looks good, was obtained identically to dozens of other studies that went through freesurfer without problem. For some reason this study keeps getting stripped down to a little more than its brainstem. Then the rest of the processing fails with an error of retesselation. Log files attached. Any suggestions on how I can properly process this data? Best wishes, Sal

2 1

T2pial refinement bbregister error
by Satrajit Ghosh 05 Jul '13

05 Jul '13

hi doug, bbregister was running into an error trying to do T2pial refinement sequence of commands and output here: https://gist.github.com/satra/5934639 and it looks like the absence of FSLDIR i didn't have FSL installed on this machine - i thought that freesurfer had it's own version of flirt. is FSL necessary? cheers, satra

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libboost_programs_options.so.5 problem solved, at least for me
by Hoptman, Matthew 05 Jul '13

05 Jul '13

Hi, I never got an answer to this problem, which affected numerous programs including mris_resample, but I solved it with help from my local sysadmin. I think the problem is that there is a versioning difference between Centos and other Linux "flavors" (I use Linux Mint 14). But anyway, I: 1) got the following RPM: boost-program-options-1.41.0-17.el6_4.x86_64.rpm 2) Extracted the relevant file: sudo rpm2cpio boost-program-options-1.41.0-17.el6_4.x86_64.rpm | cpio -ivd /usr/lib/libboost_program_options.so.5 3) Verified the file (libboost_program_options.so.5) was in /usr/lib And then I was good to go. Hope this helps others. --Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ________________________________ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

1 0

Parameterization Optseq
by Laura Dekkers 05 Jul '13

05 Jul '13

Dear Dr Greve, Together with Dr Hilde Huizenga I am implementing an fMRI study in which we would like to optimize the design by using Optseq2. We have a few questions. Could you please help us out? Our task consists of 3 runs of 72 trails each, in which participants are presented with a fixation cross that remains on the screen for a fixed duration of 1 sec, followed by one out of nine different stimuli that remains on the screen for a fixed duration of 4 sec. This gives a scan duration of 360 sec. We would then like to add 25% jitter, which results in a scan duration of 450 sec, and as TR = 2.0, this results in 225 time points. However, Optseq yields an error if ntp is set to 225, ev duration set to 4.0, psdwin dPSD to 1.0 , tnullmin to 1.0 and tnullmax to 6.0 ERROR: could not enforce tNullMax=6 (ntries=100000) You will need to reduce the number of time points or increase the number of presentations. However, reducing the number of time points makes Optseq to only insert null events of 1.0 or rarely 2.0 sec without much variation. Optimization with ntp set to 225, ev duration set to 5.0 (=fixed duration of fix + stimulus), psdwin dPSD to 1.0 , tnullmin to 0.0 (1.0 does not work) and tnullmax to 6.0 does work. However, this renders Optseq to insert null events of a fixed duration op 1.0 sec, which is not what we want. Could you please advise us in how to set these parameters? Thank you in advance. Best regards, Laura Dekkers -- Laura M.S. Dekkers, MSc Research assistant University of Amsterdam - Department of Developmental Psychology Weesperplein 4 1018 XA Amsterdam - The Netherlands E-mail: lmsdekkers(a)gmail.com

3 10

recon-all error
by LAOUCHEDI MAKHLOUF 05 Jul '13

05 Jul '13

Hi i run recon-all on 13 subjects (severe TBI) using the condor cluster environment, 10 of them were stopped with, mostly ending with this error (found in SUBJECTS_DIR/subj/scripts/recon-all.log) : ncvarput: ncid 4: Input/output error miicv_put: MINC package entry point nu_evaluate: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_evaluate (termination status=768) ERROR: nu_correct Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s gdd8 exited with ERRORS at Thu Jul 4 19:38:19 CEST 2013 thank you for help

3 2

zones of zero thickness
by Sebastian Urchs 05 Jul '13

05 Jul '13

Hi, I found that in some of my subjects there are - after manual correction - focal regions with zero cortical thickness. On closer inspection, I can see that the white matter and pial boundaries are touching in these regions - hence probably the zero thickness. My question is: should I manually force these boundaries to separate and if so, what would be the best way to do so and by what margin? I attached a link to a shared image explaining the problem. Thanks a lot, Sebastian 019402_thickness.png - https://docs.google.com/file/d/0B2xRN4FkuGF9S2dHVm1lYjB4OUE/edit?usp=sharing

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Freesurfer July 2013