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using own average subject
by Schuster, Christina /DZNE 31 May '12

31 May '12

Dear FreeSurfer experts, I am trying to create an average subject based on a matched subsample (2 different scanners, patients and healthy controls). I successfully ran make_average_subject receiving a "newtemplate". Now I am unsure how to proceed: As far as I understand it, according to the SurfaceRegAndTemplates page (http://surfer.nmr.mgh.harvard.edu//fswiki/SurfaceRegAndTemplates) I should use mris_register for each subject from my subsample receiving ?h.sphere.reg.newtemple files with which I should make again an average subject, let's call it "newnewtemplate". Is that correct? Now, if I want to assemble the data into common space using mris_preproc: what do I need to specify? Would --target be the newtemplate or newnewtemplate? Do I need to specifiy the --surf-reg as well? On the other hand, I read in one of your tutorials that I only need to run make_average_subject receiving a "newtemplate" which I then specify using mris_preproc as --target and that --surf-reg is not needed. So what would be the correct way to use my own template for the group analysis? Many thanks for you help! Best wishes Christina *********************** Christina Schuster, M.Sc. Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Standort Rostock/ Greifswald Sitz am Zentrum für Nervenheilkunde (über Station N4) Gehlsheimer Straße 20 D- 18147 Rostock Tel: +49-381-494-9618 Fax: +49-381-494-9472 E-mail: christina.schuster(a)dzne.de Web: http://www.dzne.de *********************** Vorstand: Prof. Pierluigi Nicotera, MD PhD (Vorstandsvorsitzender und wissenschaftliches Vorstandsmitglied) und Ursula Weyrich (administratives Vorstandsmitglied) eingetragen in das Vereinsregister des Amtsgerichts Bonn (Az. VR 9021) ***********************

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Job advertisement
by Direktion, Institut f. Schlaganfall- und Demenzforschung 31 May '12

31 May '12

The Institute for Stroke and Dementia Research (ISD) is looking for a Post-doctoral Research Fellow: Imaging in Neurodegenerative Diseases RESPONSIBILITIES: The research fellow will acquire and analyze multimodal neuroimaging data on Alzheimer's disease, including structural and functional MRI, amyloid PET, and FDG-PET. The research project focuses on tracking structural and functional brain changes in preclinical Alzheimer's disease. The fellow will also have the opportunity to work on data from pre-existing data sets such as the Alzheimer's Disease Neuroimaging Initiative (ADNI) that will provide the basis for immediate data analysis and publications. REQUIREMENTS: The candidate should hold a PhD, MD or equivalent degree in relevant disciplines (informatics, engineering, mathematics, neuroscience). Skills in image registration and segmentation are desirable. Solid knowledge of programming and statistics is a plus. Familiarity with biological or clinical aspects of Alzheimer's disease is not a prerequisite. An enthusiastic, reliable and independent work style will provide a good fit for our team. OFFER: Our institute offers an excellent multidisciplinary environment (medical scientists, neuropsychologists, biologists, bioinformaticians, epidemiologists) with a powerful IT infrastructure and state-of-the-art scanners (3 & 7T MRI, molecular PET). The research fellow will have clearly defined task definitions, access to all data sets of the research project, and advanced technical support to facilitate efficient work conditions. The fellow will work in a friendly, dynamic, and highly productive team, headed by Prof. Michael Ewers, PhD. The University of Munich, Germany, and its clinics figure among Germany's premier and internationally competitive biomedical research sites funded by the government's German Universities Excellence Initiative. The Institute for Stroke and Dementia Research (ISD) is a thriving new research-dedicated institution (http://www.isd-muc.de) The ISD will be housed soon in a top-notch research facility that is currently being build and will eventually attract around 100 staff members, graduate students, scholars and foreign scholars. Salary is according to TV-L. The position is limited for two years, extension is desired. Disabled persons will be preferentially considered in case of equal qualification. Presentation costs can unfortunately not be refunded. For more information, please contact Mr. Frühauf, Tel.: +49 (0)89 7095 7800. HOW TO APPLY: Your application - preferably in electronic form - with the usual documents indicating the earliest possible starting date should be directed to: Klinikum der Universität München, Institute for Stroke and Dementia Research Markus A. Frühauf, Managing Director ISD Heiglhofstr. 55 81377 Munich | Germany E-Mail: isd(a)med.uni-muenchen.de

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long_qdec_table and LongQdecTable.py errors
by Jiyang Jiang 31 May '12

31 May '12

Hi Martin, I came across a problem when shrinking longitudinal qdec tables with 345 subject in two time points, into cross sectional form. The error states as follows: ------------------------------------------ [jiyang@abc qdec]$ long_qdec_table --qdec ./long.qdec.table.dat --cross --out ./cross.qdec.table.test.dat Parsing the qdec table: ./long.qdec.table.dat Traceback (most recent call last): File "/usr/local/software/freesurfer/freesurfer-5.1.0/bin/long_qdec_table", line 142, in <module> longqdec = LongQdecTable(options.qdec) File "/usr/local/software/freesurfer/freesurfer-5.1.0/bin/LongQdecTable.py", line 30, in __init__ self.parse(stpmap) File "/usr/local/software/freesurfer/freesurfer-5.1.0/bin/LongQdecTable.py", line 58, in parse if strlst[0].upper() == 'SUBJECTS_DIR': IndexError: list index out of range ---------------------------------------------- I found Derin posted the same question on 20 Apr 2012, but it seems no following answers after. This error disappeared after deconstructing longitudinal qdec table. Any suggestion or clue will be appreciated. Thanks! Jiyang

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Converting labels into .annot
by Sam Carpenter 30 May '12

30 May '12

Hi all, We have a series of labels (over 100) that encompass the majority of the cortex, but some minute vertices remained unlabeled. We've tried several attempts to make this .annot file and as well as attempts to label the unlabeled vertices (from a previous post 'labeling unlabeled vertices..'). But still to no avail. Question: how to convert .label files to .annot file, when some vertices are still unassigned. Thanks!!!

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Re: [Freesurfer] [martinos-tech] checking talairach registration
by Douglas N Greve 30 May '12

30 May '12

Hi Suzanne, it does not mean that there is anything wrong with your data. I've seen this before on some data sets. I have a work-around that might work. How many data sets do you have to run? doug On 05/29/2012 02:35 PM, suzanne oosterwijk wrote: > > Hi, > > Recently I ran recon1 for several participants. After recon1 I checked > the talairach transform with tkregister2. I noticed that for about 5 > out of 7 participants the original surface did not line up with the > fuzzy moveable volume. Specifically, the fuzzy volume was too small > for the green surface, in such a way that the green lines would > overlap with the skull, the dura or the eyes. I adjusted the > registration, mostly by scaling the brain. I think I was able to > realign everything correctly, but after checking with some colleagues > I heard that they never had this kind of trouble with the > registration. Is this normal? Or is this a sign that somewhere in the > pipeline (or during scanning) something went wrong? > > My data can be found at: > > /autofs/space/boggart_001/users/oosterwi/oosterwi_feedback/feedback_structural > > Thanks in advance for any comments/advice on this! > > Suzanne > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Interdisciplinary Affective Science Lab > > Department of Psychology > > Northeastern University > > 114 Lake Hall > > Boston, United States > > s.oosterwijk(a)neu.edu <mailto:s.oosterwijk@neu.edu> > > https://sites.google.com/site/suzanneoosterwijk/ > > > __._,_.___ > Reply to sender > <mailto:suzanne.oosterwijk@gmail.com?subject=Re%3A%20checking%20talairach%20registration> > | Reply to group > <mailto:martinos-tech@yahoogroups.com?subject=Re%3A%20checking%20talairach%20registration> > | Reply via web post > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwNThjMnR2BF9TA…> > | Start a New Topic > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJlNjZpM2V0BF9TA…> > > Messages in this topic > <http://groups.yahoo.com/group/martinos-tech/message/5666;_ylc=X3oDMTM0cGxvZ…> > (1) > Recent Activity: > > Visit Your Group > <http://groups.yahoo.com/group/martinos-tech;_ylc=X3oDMTJlZmFzYnBmBF9TAzk3Mz…> > > Yahoo! Groups > <http://groups.yahoo.com/;_ylc=X3oDMTJkanUycTR0BF9TAzk3NDc2NTkwBGdycElkAzQ5O…> > > Switch to: Text-Only > <mailto:martinos-tech-traditional@yahoogroups.com?subject=Change%20Delivery%20Format:%20Traditional>, > Daily Digest > <mailto:martinos-tech-digest@yahoogroups.com?subject=Email%20Delivery:%20Digest> > • Unsubscribe > <mailto:martinos-tech-unsubscribe@yahoogroups.com?subject=Unsubscribe> > • Terms of Use <http://docs.yahoo.com/info/terms/> > . > > __,_._,___ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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mri_glmfit error
by YUMI MAEDA 30 May '12

30 May '12

HI, I am trying to see difference in groupmap between 2 time-point within 1 group with glmfit. I followed the instruction"PairedAnalysis". mris_preproc .... --paired-diff mri_glmfit --surf fsaverage "$hemi" --y "$hemi"_cope1_"$grp".sm"$fwhmsrc".mgh --yffxvar "$hemi"_varcope1_"$grp".sm"$fwhmsrc".mgh --glmdir $fsdir/group_surf//"$hemi"_cope"$num"_"$grp".sm"$fwhmsrc"_ffx --ffxdof 1872 --osgm When I checked the output of the mri_glmfit, the mask file does not cover the entire brain as the cope/varcope does. it is much smaller and missing parietal brain. the log file says "Reshaping mriglm->mask..." Is this the issue? YUMI

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subcortical segmentation
by Richter, Julia 30 May '12

30 May '12

Dear FreeSurfer experts, I have a question regarding the subcortical segmentation. In the paper by Fischl et al (2002), I've read that the neuroanatomical labels are assigned to the voxels based on probabilistic information automatically estimated from a manually labeled training set. I don't understand which atlas is used though. Is it an atlas of the Center for Morphometric Analysis? How shall I cite it? Thank you very much for your help in advance, Julia

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read_surf - update
by Shay Ohayon 29 May '12

29 May '12

Hi again, OK. I managed to reverse engineer things back from mri_tessalate.c Here is the code snippet that should be added to read_surf to parse these new files: NEW_QUAD_FILE_MAGIC_NUMBER =16777213; elseif (magic == NEW_QUAD_FILE_MAGIC_NUMBER) vnum = fread3(fid); fnum = fread3(fid); vertex_coords = fread(fid, vnum*3, 'float32') ; tmp = fread(fid, fnum*3*3, 'uchar') ; tmp = reshape(tmp, 3, 3, fnum) ; faces = reshape(bitshift(tmp(1,:,:), 16) + bitshift(tmp(2,:,:),8) + tmp(3,:,:),3, fnum)'; end -- Shay

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read_surf and free surfer 5.0
by Shay Ohayon 29 May '12

29 May '12

Hi, I am trying to read a surface generated by mri_tessellate using matlab's API (read_surf.m) However, it seems like the function is not up-to-date, because the magic number in the surface file is 16777213, and the two magic-numbers recognized by read_surf are 16777214 and 16777215. Is there a newer version of read_surf.m out there? Thanks, -- Shay

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wmparc
by Christopher Bell 29 May '12

29 May '12

How much is the dilation (perpendicular to the cortical surface) for the creation of the white matter ROIs? Is there a citation for this? Chris Bell

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