Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

problem in building cortex mask
by lorenzo pasquini 30 Mar '12

30 Mar '12

Dear freesurfers, I have a problem in creating masks of the left and right cerebral cortexes. The message "found 0 values in range" is displayed and an empty mask is created. This is surprising as I am able to build masks of the right and left hippocampi and entorhinal cortexes using the same command without any problems. Further the satistic file aseg.stats indicates me a huge amount of voxels in the cerebral cortexes. I am using the segmentation ID 3 for the left cerebral corex and 42 or 53 for the right cerebral cortex. I am surprised as well to find two different IDs for the same region, 42 comes from the aseg.stats file, 53 comes from the FreesurferColorLUT table. Wich ID is the right one to use?Why can I build masks of hippocampal regions but not of the cerebral cortexes? Thank you very much and kind regards, Lorenzo Pasquini

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Now Hiring: Postdoc
by Juranek, Jenifer 30 Mar '12

30 Mar '12

We have a current opening for a post-doctoral associate in the areas of *image analysis* (structural and functional) and *developmental neuroscience*. Available resources include a research-dedicated 3.0T MRI scanner and analysis platforms based in MATLAB/UNIX. The successful candidate will be expected to work independently (with some supervision) to analyze multimodal neuroimaging data (volumetrics, cortical thickness, DTI, resting state connectivity with fMRI and MEG/EEG, lesion identification and analysis) obtained from typically-developing and atypically developing pediatric study participants. The successful candidate should have a strong publication record and a continued interest preparing manuscripts for publication in the field of pediatric neuroimaging using multimodal imaging data. The successful candidate should have a doctoral degree in a field related to developmental cognitive neuroscience (e.g., cognitive neuroscience, neuroscience, developmental psychology, medicine or psychology). Individuals with a background in electrical engineering, biomedical engineering or computer science will also be considered, as appropriate. The successful applicant must possess excellent English verbal and written communication skills. Applicants are expected to have a very strong research background in the design and statistical analysis of multimodal neuroimaging data. Experience with Freesurfer, FSL UNIX/LINUX/ and/or programming skills (MATLAB; Perl; bash) are highly desirable. For consideration please send a statement of interest, a CV and a list of three potential referees via email to Dr. Juranek at Jenifer.Juranek(a)uth.tmc.edu<mailto:Jenifer.Juranek@uth.tmc.edu>. This position is currently available; the search for a successful applicant will continue until the position is filled. ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Jenifer Juranek, PhD Assistant Professor UT Houston Developmental Pediatrics Children's Learning Institute Voice: 713.500.3813 Fax: 713.500.3878

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base.mgh file
by Tina Jeon 30 Mar '12

30 Mar '12

Freesurfer universe, I noticed that the newer version of freesurfer does not output a ?h.base.mgh file, which contains vertices, but no triangular meshes and corresponding gyral labels from the color look up table. Question: 1). Why does my cortical labels created using tksurfer correspond to the vertices in the base.mgh file and not the pial surface that I drew the surface on? 2). Is there a file in place of the ?h.base.mgh file in the newer version of freesurfer? My goal is to figure out which surface aligns with my manually created cortical labels for visualization. I am running version FSv5.0.0 on Centos4_x86_64 bit. Many thanks, Tina Jeon Biomedical Engineering Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center P: (214) 645-2892 F: (214) 645-2885 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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ICV estimation
by HOSSU Gabriela 30 Mar '12

30 Mar '12

Dear all, I am working with FreeSurfer version 5.10 from 2 months. I am interested in hippocampus volume measurements and I want to normalize them with the intracranial volume. We have scanned about 4 times the same 2 healthy subjects (3T GE HDxt, 8 channel coil). 3D acquisitions were made with the BRAVO GE sequence in coronal and sagittal planes (roughly with the same parameters) . On the hippocampus we obtained about 5% intra subject variation but for the ICV intra subject variation is around 15%. With the supra tentorial volume estimations, the variation is around 2%. Any idea to explain this so important difference for the ICV estimation? Can we use the supra tentorial volume in order to normalize our hippocampus estimations? Thanks, Gabriela HOSSU, Ph.D. Chef de projet CIC-IT Nancy (Inserm CIT801) CHU de Nancy Brabois 4ème étage Tour Drouet Rue du Morvan 54511 VANDOEUVRE-LES-NANCY FRANCE

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selxavg3-sess error
by Oya, Hiroyuki (UI Health Care) 30 Mar '12

30 Mar '12

Hi I got an error while running selxavg3-sess, "cannot find AFNI command 3dvolreg".(In ubuntu v11.). Any help would be appreciated. Hiroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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Re: [Freesurfer] [FREESURFER] atlas applicability. (fwd)
by Lilla Zollei 29 Mar '12

29 Mar '12

Hi Cheol, > I am using freesurfer for patients with various neural disease. I wonder the > the > freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB), > epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies > already > used freesurfer for some of the diseases in the list,) I believe epilepsy > patients with lobectomy cannot be applicable. If the malformation or the difference between normal control acquisitions and your scans is significant the FS pipeline, using the FS atlas is not going to be successful. Withuot seeing your data I cannot tell which population from the above is going to be affected, but if in doubt just try processing one or two representative samples from the different populations and assess how successful the processing is. > Also is there age limit for the freesurfer atlas? How young can the atlas > work > for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper > bound? 80 year-old? The lower bound, in our experience, is about 4-5 yrs. Of course, it depends on your data quality but we had success all the way down to that age. I am not aware of any upper limits. Again, if you are processing these kind of "extreme" populations, make sure that you inspect the outcome of the FS recon pipeline carefully before proceeding with any type of analysis. Lilla

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About the sample data
by bowang21＠mail.ustc.edu.cn 29 Mar '12

29 Mar '12

Dear All, I can't uncompress the data long-tutorial.tar.gz with command tar xzvf /mnt/workplace/long-tutorial.tar.gz /mnt/workplace. How can I uncompress the data?

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method for detecting neighboring labels?
by David Grayson 29 Mar '12

29 Mar '12

Is there a way to output a list of all the labels within a given annotation file which share a border with another specified label? Thank you very much, David

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sulci problem
by LAOUCHEDI MAKHLOUF 29 Mar '12

29 Mar '12

hi all i use mri_anot2label to extract sulci, is there a tool allowing to keep just the deepest line of the sulcus and if possible get the list of talairach coordinates of that line's points. thanks a lot for your help

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TRACULA and CVS space
by Antonella Kis 29 Mar '12

29 Mar '12

Hi, I would like to know if for a probabilistic tractrography using TRACULA I can use the CVS space as a common template to register the diffusion data instead of MNI template. How I should change for the CVS space the following: set doregmni = 1 which is the default for the MNI space. If I want to use both MNI template and CVS template for comparison purposeshow this can be done? THANKS. Antonella

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Freesurfer March 2012