Freesurfer

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Fwd:
by José Ángel Pineda 30 Oct '14

30 Oct '14

Notification of the “Isaac Peral” Program to contract one senior researcher associated with BBVA Foundation-UPM Industry-Academia chairs for scientific-technological research in Medical Imaging, within Marie Curie Action COFUND. This notice provides for a maximum of one position in the area of scientific-technological initiatives in Biotech indicated below, in accordance with the procedure established in the Regulatory Bases of 30 April 2009 for the ISAAC PERAL Program for Senior UPM Researchers (in the attached document). The candidate degree may be from any specialization in Engineering, Physics, Mathematics, Statistics, Biology, Biochemistry, etc. Location: The activities will be carried out in the Campus of International Excellence: Campus of Montegancedo at the CTB: Centre for Biomedical Technology (www.ctb.upm.es) in Madrid, Spain. Beneficiaries: 1. Have held a PhD for more than 10 years, effectively pursuing uninterrupted research activity during that time. 2. Have extensive research experience in the sphere of the profile of the contract announced, i.e. biomedical imaging. 3. Have pursued their research activity following the award of their PhD in relevant foreign Research Centers for at least six years or have studied the whole of the PhD and graduated in a foreign University or Research Centre and have pursued subsequent research activity in a relevant foreign research center for at least three years. 4. Have certified experience in the management of research groups in university institutions or relevant research centers. All the requirements demanded and the merits argued by candidates must have been fulfilled prior to the date of termination of the period for the submission of applications. Conditions of the position: 1. Gross remuneration shall not be less than 80000 € nor more than 90000 € per year. 2. Three year contracts for two young PhDs 3. Three positions for PhD studies (four years) 4. A 30000 € support for the Senior researcher during the first year of contract to facilitate the start of the research activities 5. A minimum of 100m2 space available in the Centre for Biomedical Technology N.B.: All the the details of the call can be consulted at the following link: *http://www.upm.es/sfs/Rectorado/Vicerrectorado%20de%20Investigacion/Servicio%20de%20Investigacion/Ayudas_y_Convocatorias/Convocatorias_Propias/Convocatoria-MedImaging-Eng.pdf <http://www.upm.es/sfs/Rectorado/Vicerrectorado%20de%20Investigacion/Servici…>* Interested candidates should send CV to the following email address francisco.delpozo(a)ctb.upm.es. [image: http://www.upm.es/sfs/Montegancedo/Noticias/imagenes/ctb.gif] Prof. Francisco del Pozo Director Center for Biomedical Technology (CTB) Universidad Politécnica de Madrid Parque Científico y Tecnológico de la UPM Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, ES Tfo: +34 913364632 (Tfo: +34 913364631) www.ctb.upm.es

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Error with asegstats2table function
by Claire Morley 30 Oct '14

30 Oct '14

Hello Freesurfer Experts, Thanks so much again for all of your help. I am trying to complete the Anatomical ROI Analysis Tutorial because I will need to use segmentation volumes for an experiment we`re running in the lab. In particular, I am trying to complete the group stats files part of the tutorial so that I know how to export this data in the future to excel for statistical analysis. However, I keep getting the following error: IOError: [Errno 13] Permission denied: 'aseg_stats.txt' I have tried to put in my password with sudo, make myself a superuser, and chmod, but nothing seems to work. When I do sudo it will tell me that my SUBJECTS_DIR isn`t defined although it is defined in the first two lines of every terminal window I open (because of my .profile). See here: IOError: [Errno 13] Permission denied: 'aseg_stats.txt' [dbm079-066:/Applications/freesurfer/subjects] claire% sudo asegstats2table --subjects 004 008 --meas volume --tablefile aseg_stats.txt Password: ERROR: SUBJECTS_DIR environment variable not defined! Additionally, sometimes I will also see the following error ERROR: output table name should be specified (use --tablefile FILE) after putting in the following: claire% asegstats2table --subjects 004 008 \ --segno 11 17 18 \ --tablefile aseg.vol.txt ERROR: output table name should be specified (use --tablefile FILE) Please help! I have tried everything I can think of. Thank you for everything, 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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Unknown problem with fsgd file
by Bronwyn Overs 30 Oct '14

30 Oct '14

Dear Freesurfer Mailing list, I have been attempting to run mri_glmfit using a complicated fsgd file (1 categorical varible with 5 levels, 3 categorical variables with 2 levels, age as covariate). When I run the command, I receive the following error: gdfReadHeader: reading site-gender-group-riskhaplotype.fsgd Input line 5, subjid = 100121, class siteMelbourne-anyRiskAnyRisk-genderFemale-groupControl not defined FSGDF Format Error: file = site-gender-group-riskhaplotype.fsgd, tag=Input I have double checked the fsgd file and confirmed that the class for participant 100121 was specific correctly at the beginning of the file (correct spelling and case was used). So I cannot identify the source of the error. Can you advise me as to what may be going wrong? My full fsgd file begins like this (I have 389 subjects but have provided only the first 20 for brevity): GroupDescriptorFile 1 Title GLM_SiteGender Class siteBrisbane-anyProtNoProt-genderMale-groupCase Class siteBrisbane-anyProtNoProt-genderFemale-groupCase Class siteBrisbane-anyProtNoProt-genderMale-groupControl Class siteBrisbane-anyProtNoProt-genderFemale-groupControl Class siteBrisbane-anyProtAnyProt-genderMale-groupCase Class siteBrisbane-anyProtAnyProt-genderFemale-groupCase Class siteBrisbane-anyProtAnyProt-genderMale-groupControl Class siteBrisbane-anyProtAnyProt-genderFemale-groupControl Class siteMelbourne-anyProtNoProt-genderMale-groupCase Class siteMelbourne-anyProtNoProt-genderFemale-groupCase Class siteMelbourne-anyProtNoProt-genderMale-groupControl Class siteMelbourne-anyProtNoProt-genderFemale-groupControl Class siteMelbourne-anyProtAnyProt-genderMale-groupCase Class siteMelbourne-anyProtAnyProt-genderFemale-groupCase Class siteMelbourne-anyProtAnyProt-genderMale-groupControl Class siteMelbourne-anyProtAnyProt-genderFemale-groupControl Class siteNewcastle-anyProtNoProt-genderMale-groupCase Class siteNewcastle-anyProtNoProt-genderFemale-groupCase Class siteNewcastle-anyProtNoProt-genderMale-groupControl Class siteNewcastle-anyProtNoProt-genderFemale-groupControl Class siteNewcastle-anyProtAnyProt-genderMale-groupCase Class siteNewcastle-anyProtAnyProt-genderFemale-groupCase Class siteNewcastle-anyProtAnyProt-genderMale-groupControl Class siteNewcastle-anyProtAnyProt-genderFemale-groupControl Class sitePerth-anyProtNoProt-genderMale-groupCase Class sitePerth-anyProtNoProt-genderFemale-groupCase Class sitePerth-anyProtNoProt-genderMale-groupControl Class sitePerth-anyProtNoProt-genderFemale-groupControl Class sitePerth-anyProtAnyProt-genderMale-groupCase Class sitePerth-anyProtAnyProt-genderFemale-groupCase Class sitePerth-anyProtAnyProt-genderMale-groupControl Class sitePerth-anyProtAnyProt-genderFemale-groupControl Class siteSydney-anyProtNoProt-genderMale-groupCase Class siteSydney-anyProtNoProt-genderFemale-groupCase Class siteSydney-anyProtNoProt-genderMale-groupControl Class siteSydney-anyProtNoProt-genderFemale-groupControl Class siteSydney-anyProtAnyProt-genderMale-groupCase Class siteSydney-anyProtAnyProt-genderFemale-groupCase Class siteSydney-anyProtAnyProt-genderMale-groupControl Class siteSydney-anyProtAnyProt-genderFemale-groupControl Variables age Input 100105SA sitePerth-anyProtNoProt-genderMale-groupCase 23 Input 100112SA siteBrisbane-anyProtAnyProt-genderMale-groupCase 22 Input 100117SA siteBrisbane-anyProtNoProt-genderMale-groupCase 39 Input 100118 siteBrisbane-anyProtNoProt-genderFemale-groupCase 30 Input 100121 siteMelbourne-anyProtAnyProt-genderFemale-groupControl 21 Input 100122 siteMelbourne-anyProtAnyProt-genderMale-groupControl 53 Input 100151 siteMelbourne-anyProtNoProt-genderFemale-groupControl 58 Input 100185SA siteBrisbane-anyProtNoProt-genderFemale-groupControl 24 Input 100187 siteBrisbane-anyProtNoProt-genderMale-groupCase 24 Input 100189 siteBrisbane-anyProtNoProt-genderFemale-groupCase 21 Input 100190 siteSydney-anyProtNoProt-genderMale-groupControl 41 Input 100191 siteMelbourne-anyProtAnyProt-genderFemale-groupControl 19 Input 100193SA siteSydney-anyProtNoProt-genderMale-groupControl 26 Input 100196 siteBrisbane-anyProtNoProt-genderMale-groupControl 55 Input 100197SA siteBrisbane-anyProtNoProt-genderFemale-groupCase 30 Input 100200SA siteBrisbane-anyProtNoProt-genderMale-groupControl 39 Input 100204 siteSydney-anyProtAnyProt-genderFemale-groupControl 50 Input 100208 siteBrisbane-anyProtNoProt-genderMale-groupControl 25 Input 100209SA siteBrisbane-anyProtAnyProt-genderMale-groupCase 35 Input 100214 siteSydney-anyProtAnyProt-genderMale-groupCase 44 The mri_glmfit command I am using is as follows: mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd site-gender-group-prothaplotype.fsgd dods --C gender.mtx --C group.mtx --C haplotype.mtx --C groupXgender.mtx --C haplotypeXgender.mtx --C groupXhaplotype.mtx --C genderXgroupXhaplotype.mtx --surf fsaverage lh --cortex --glmdir site-gender-group-prothaplotype.thick.lh.glmdir -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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Name external disk not recognized
by Righart, Ruthger 30 Oct '14

30 Oct '14

Dear Freesurfers, Not sure if my question is at the right place here but I'll give it a try. I have a memory disk with white spaces in the name: Seagate Expansion Drive. There is no simple way to rename the disk on my Linux machine. In Unix shell scripting problems with finding the directory can be prevented by putting the whole name in quotation marks, e.g., f1=”Seagate Expansion Drive” and then after that calling f1 with quotation marks (e.g., cp “$f1”/file.xxx /destination/ ). However, if I want to use bbregister then it does not recognize the quotation marks. For example, behind the flag --reg /”$f1”/fsreg.dat Freesurfer tells me that it does not recognize “Expansion” as a flag (probably because it still reads the white space in the name). I was wondering if there is any simple solution around or if the only option seems to try to rename the disk. Best, Ruthger

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Venous system on 3D models
by rwlodar2＠uic.edu 30 Oct '14

30 Oct '14

Hello my names Rich. I am working on a project that involves creating 3D models of patient brains and placing ECoG (Electrocorticography) leads on these models. I have intra-operative pictures of the leads placed on the subjects and I'm using these pictures to attempt to accurately place the leads. However, as you might guess, the 3D models are very different from looking at a live brain and the true sulcal and gyral pattern is difficult to determine from the pictures. I was wondering if it is possible to have freesurfer create or mark, in some way, the veins on the models so that I can use the venous system as points of reference when placing the leads. If not, is there a better way to do so that you can think of? I am relatively new to freesurfer so I don't fully understand its capability yet. Thanks!!

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Re: [Freesurfer] adding insula voxels
by Adam Mezher 30 Oct '14

30 Oct '14

Hi Bruce, Sorry for not clarifying. A number of subjects in our set have underestimated insula (usually anatomical right insula but sometimes both). I just uploaded an example to the ftp. I don’t think control points or wm edits can help with some of these so I wanted to see how we could go about editing them manually by adding the correct label to the empty voxels with the Edit Segmentation tool in tkmedit. Thank you, Adam

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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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