Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

7T reconstruction
by B V 29 Oct '14

29 Oct '14

Hello, I am interested in using functional data collected from 7t using freesurfer and fsfast. We would like to use EPI field maps to warp this data to 3T anatomical space. Can anyone guide me as to how to do this. Best, B

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Local gyrification index
by Sterling, Nicholas 29 Oct '14

29 Oct '14

Hello, I am trying to obtain estimates for the local gyrification index (LGI) using Freesurfer. I have tried to compute LGI via two different commands... "mris_compute_lgi --i lh.pial" and " recon-all -lgi -s subjectName." Both of these return the same error after running for a while... .......... Saving label file /......../FS/subjects/test/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.029901.label Connecting and filling vertices in path at fillseed 69178 Finding path..................................................................................................................................................................................................................................................................................................................................................................................... done Filling 69178 nlabel 9709 Saving label file /......../FS/subjects/test/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.030001.label Connecting and filling vertices in path at fillseed 68070 Finding path.............................................................................................Killed ERROR: mri_path2label --confillxfn lh.pial /......../FS/subjects/test/surf/tmp-mris_compute_lgi-lh.pial/mri_path2label.input failed! I've tried a couple of subjects and I get the error above. Would anyone please be able to offer suggestions regarding how to resolve this issue? Many thanks for taking the time to read my inquiry. Nick

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Re: [Freesurfer] LGI fails for fsaverage
by Pierre Mégevand 29 Oct '14

29 Oct '14

Unfortunately, our pre-implant MR was acquired with double-dose gadolinium and we can't seem to extract the pial surface from it. have you tried using bbregister to register post-op MRI with the pre-op surfaces? On Wed, 29 Oct 2014, Pierre M?gevand wrote: > Our usual method for electrode localization remains in the patient's space: > co-register post-op MR and CT with pre-op MR brainmask (our reference space) > and snap electrodes to patient's outer pial surface. > > My idea was: register the patient's (crappy) brainmask volume to the > "Talairach" fsaverage volume (not surface), which I can correct manually; > use the Talairach.xfm transform to bring the electrodes into that same > fsaverage volume, and then snap the electrodes to fsaverage's outer pial > surface. But that last step I can't perform. I'm aware that the localization > would be pretty inaccurate. > I'll look into what you suggest Marie. In case all else fails, the last > resort is to show the actual post-op MR and CT slices for electrodes of > interest, but that just does not look as appealing as pial surfaces! > > -- > Pierre M?gevand, MD, PhD > PLOS Neuro Community editor - Follow us on Twitter > Postdoc @?Feinstein Institute for Medical Research (NY, USA) > Follow me on Twitter - Read my blog here > > On Wed, Oct 29, 2014 at 12:29 AM, Marie Schaer <Marie.Schaer(a)unige.ch> > wrote: > > So what I don't get in your pipeline is how you'll register the > post-op brain to fsaverage if you don't have any cortical surface in > the post-op?? > > If I were you, if you want precise registration that includes the > sulci, I'd go with the white surface from the pre-op gadolinium scan. > And if you just want a rough registration of the skull shape, then you > can probably find a way to create the outer surface directly on the > gadolinium scan: if your brain mask is good, then mris_fill should > work (maybe you need to binarize the data first (in any case a few > lines of code in matlab should do the trick). If the brain mask is not > good due to gadolinium, then either playing with mri_watershed (and > maybe try mri_fill to separate the hemispheres / pons and cerebellum) > and then mris_fill for the tessellation. Or if it doesn't work with > mri_watershed,?playing a bit with threshold with another > skull-stripping program (e.g. MRIcro), then importing the volume back > in FreeSurfer and use mris_fill to get a good tessellation. Both > solutions will need you to play a bit, but I guess you cannot really > afford to simply throw these data and take another subject!? > > Good luck, > > Marie > > > > On Oct 28, 2014, at 2:57 PM, Pierre M?gevand > <pierre.megevand(a)gmail.com> wrote: > > You're right, we can't use the post-op surface because of > the deformation caused by surgery and the electrode > artifacts. > Getting a surface right from the brainmask would be OK, if we > can't get anything better, but the nice thing about using the > fsaverage surface is that you can plot and compare electrode > locations from multiple patients. Just in case we have nothing > better, though, how would you do it? > > Thanks again! > > -- > Pierre M?gevand, MD, PhD > PLOS Neuro Community editor - Follow us on Twitter > Postdoc @?Feinstein Institute for Medical Research (NY, USA) > Follow me on Twitter - Read my blog here > > On Tue, Oct 28, 2014 at 5:23 PM, Marie Schaer > <Marie.Schaer(a)unige.ch> wrote: > > Hi Pierre, > > Tricky question. So you can't really use the?post-op > cortical surface for this participant, right? Otherwise I > would simply use the outer smoothed pial for this subject > directly, which would be much more similar to the pre-op > than the outer surface from the fsaverage (?).?Otherwise, > with the gadolinium MRI, maybe you can still get an > adequate white surface, but I'm not sure that it would > help you. The other option is to use the brain mask volume > (which may work even with gadolinium if you are lucky, > otherwise you can play with the watershed parameters), and > tesselate a surface directly on this volume. But you'll > get the two hemispheres at once (and probably the > cerebellum as well), which may not be what you want? > > Best, > > Marie > > > On Oct 28, 2014, at 2:10 PM, Pierre M?gevand > <pierre.megevand(a)gmail.com> > ?wrote: > > Thanks Marie. Here is what I'm trying to do. > In fact, all I need from LGI are the first few > steps, until ?h.pial-outer-smoothed has been > generated. I'm not actually interested in the > local GI for fsaverage. > > Our intra-cranial electrode localization > method relies on post-implant CT and MRI scans > to localize the electrodes, and a pre-implant > MR scan to which we co-register the post-op > exams and to whose smoothed outer pial surface > we then "snap" the electrodes to, in order to > account for the brain shift caused by the > implantation procedure (Dykstra et al., 2012). > > Now, for one of our patients, the pre-op MRI > was acquired with a lot of gadolinium, and we > can't get Freesurfer to compute the pial > surface. So I thought I would co-register the > post-op exams to the fsaverage brain, and then > snap the electrodes to fsaverage's outer > smoothed pial surface as an approximation. Any > idea how else I could do this? > > Thanks, > > Pierre > > On Oct 28, 2014 3:06 PM, "Marie Schaer" > <Marie.Schaer(a)unige.ch> wrote: > > Hi Pierre, > > I'm not sure exactly what you are trying to > do, but it's true that LGI fails for fsaverage > at the mris_fills step, where the volume looks > "cut". It seems to be something in the > properties of the fsaverage surfaces. Maybe > Doug or Bruce have an idea where it comes > from. > > But in any case, I wouldn't advice to run the > LGI on the fsaverage, as the pattern of > cortical folding is lost from the averaging of > the subjects. So I'm not even sure that the > algorithm will work even if you get mris_fill > to work.? > > Can you tell us more precisely what you are > trying to do? And why on the fsaverage rather > than on your individual subject? > > Best, > > Marie > > On Oct 28, 2014, at 5:31 AM, Pierre M?gevand > <pierre.megevand(a)gmail.com> wrote: > > Dear all, > I've looked a little bit further into > why LGI fails for fsaverage. I > previously tried simply running > recon-all -s fsaverage-localGI but the > script exited with errors after a good > while. More importantly for me, the > lh.pial-outer-smoothed surface, which I > am after, did not look right. > > It seems that the first step, mris_fill, > produces a volume that does not look > very much like a brain anymore (cf. > attached screenshot). Any idea why that > would happen? > > Thanks, > > Pierre > -- > Pierre M?gevand, MD, PhD > PLOS Neuro Community editor - Follow us > on Twitter > Postdoc @?Feinstein Institute for > Medical Research (NY, USA) > Follow me on Twitter - Read my blog here > <screenshot3.png>_______________________________________________ > 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. > -- Pierre Mégevand, MD, PhD PLOS Neuro Community <http://neuro.plos.org> editor - Follow us on Twitter <http://twitter.com/PLOSNeuro> Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter <http://twitter.com/pierre_vanmedge> - Read my blog here <http://neuroscimed.wordpress.com>

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FLASH protocol
by Le Wang 29 Oct '14

29 Oct '14

Hi, I want to do source localization on 128-channel EEG. For that, I need to create 3-layer head models for our subjects. However, our current MRI protocol only includes MPRAGE. I've talked with the (f)MRI team on our project about adding a single FLASH scan in their protocol. They are mainly concerned about the time requirement. So my questions are: 1) Is it possible to get a decent 3-layer head model just from MPRAGE using FreeSurfer or other tools like SPM? 2) If we have to use FLASH, which protocol we should use? I found one at https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&… I don't know if this is the most recent one -- is there a newer FLASH protocol that can produce decent skull boundaries and takes less time to run. 3) Is there a FLASH protocol already imported on Bay 1 (Skyra scanner) at Martinos (where the MPRAGE was run)? If not, is it ok to run FLASH and MPRAGE on different scanners for the same subject? I know this is a lot of questions. I really appreciate any responses. Thanks! Le

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NIH funded postdoctoral position at Harvard Medical School/Brigham and Women's Hospital
by Emily Goard Jacobs 29 Oct '14

29 Oct '14

Professor Jill Goldstein is recruiting a postdoctoral fellow with expertise in affective or cognitive neuroscience to join her lab, the CNL-SD ( http://cnl-sd.bwh.harvard.edu) *Job Description* This position requires the individual to have expertise in functional MRI. Experience with psychiatric disorders is preferable. Knowledge of paradigm development, data analytic software (e.g., SPM, FSL), and statistical underpinnings of fMRI are required. Responsibilities of this position include analyses of fMRI studies of the stress response, mood and anxiety, and hormonal responses; fetal programming of sex differences in mood and psychotic disorders; and implementation and analyses involved in a new neurostimulation study of mood and autonomic nervous system function. Thus, the position includes implementing methods for the analysis of fMRI data; developing project-specific methods when necessary (i.e., ROI analysis); utilization of advanced statistical methods to analyze fMRI, psychophysiological and serology data; preparation of manuscripts for publication; preparation of study findings and presentation at professional meetings; review and summarization of relevant literature for manuscript background and grant preparation; supervision of research assistant working on the study. There are many opportunities for education and growth in multiple domains in which we operate: neuroendocrinology, further neuroimaging training, neuroanatomy, neuro-immune interface. We collaborate with world-class scientists who are part of Brigham and Women’s Hospital, Massachusetts General Hospital, and others outside of the Harvard system. Applicant should have a PhD or ScD in clinical psychology, neuropsychology, and/or neuroscience or have an MD with fMRI expertise. We are committed to diversity, and qualified women and minorities are strongly encouraged to apply. Please email a CV, cover letter of interest, 2-3 written references, and a *brief *writing sample to Ms. Abby Brockman*, (abrockman(a)partners.org <abrockman(a)partners.org>), *Administrative Assistant to Jill Goldstein, PhD, Professor of Psychiatry and Medicine, Harvard Medical School, Director of Research, Connors Center for Women’s Health and Gender Biology, Brigham and Women’s Hospital, Boston, MA 02120.

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Re: [Freesurfer] LGI analysis of single subject
by Maria Holland 29 Oct '14

29 Oct '14

Hi Marie - Thanks for your response. After sending my email I found the hemisphere average values, but the values at each vertex and in each ROI will be very helpful! I tried the command you provided in tkmedit and it looks perfect - thanks! But when I try what I think is the corresponding command in freeview: freeview -v <SUBJ>/mri/brainmask.mgz <SUBJ>/mri/T1.mgz -f <SUBJ>/surf/lh.pial-outer-smoothed the images don't align (see attached). Am I doing something wrong? ~ Maria

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Pial surface with point-to-point correspondance between subjects
by Alexandre Routier 29 Oct '14

29 Oct '14

Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre

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LGI fails for fsaverage
by Pierre Mégevand 29 Oct '14

29 Oct '14

Dear all, I've looked a little bit further into why LGI fails for fsaverage. I previously tried simply running recon-all -s fsaverage-localGI but the script exited with errors after a good while. More importantly for me, the lh.pial-outer-smoothed surface, which I am after, did not look right. It seems that the first step, mris_fill, produces a volume that does not look very much like a brain anymore (cf. attached screenshot). Any idea why that would happen? Thanks, Pierre -- Pierre Mégevand, MD, PhD PLOS Neuro Community <http://neuro.plos.org> editor - Follow us on Twitter <http://twitter.com/PLOSNeuro> Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter <http://twitter.com/pierre_vanmedge> - Read my blog here <http://neuroscimed.wordpress.com>

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adding insula voxels
by Adam Mezher 29 Oct '14

29 Oct '14

Hi Bruce and FS group, Thanks again for the speedy replies and help with everything. Quick question about editing voxels (specifically those in the lh/rh insula). Should I simply add specific voxels to the aparc+aseg for this step? It was a little unclear on the wiki. Also, is there a specific command to re-run the stats/etc. after these edits are performed? Thanks a lot, Adam

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Error when completing cortical thickness analysis
by Claire Morley 29 Oct '14

29 Oct '14

I am conducting cortical thickness analyses between hundreds of individuals for a study we are conducting. I was getting this error Unrecognized sub-option flag 'annot_outline'. and so I tried to do the group analysis tutorial and input the command from the end of it (please see command below) but still got the same error. Freeview would open but it would not show any images. Could you help me to resolve this issue please? Also, what does it mean when it spits out invalid drawable? freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d Thank you so much for your help! Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot*

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Freesurfer