Freesurfer

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30132 discussions

tkregister question
by Shay Ohayon 01 Jun '12

01 Jun '12

Hi, Here's a question to Doug / anyone else who mastered the intricate way of volume transformations: I'm a bit puzzled. According to Free surfer's documentation (fscoordinates.pdf), the way two volumes are registered to each other using tkregister is always using the fixed transformation (tkvox2ras) (see page 6). However, when I do the following little experiment (using matlab's freesurfer API) A = '001.nii'; B = '002.nii'; X=MRIread(A); X.vox2ras0(1,4) = 40; MRIwrite(X,B); tkregister2 --targ 001.nii --mov 002.nii --regheader -reg R.reg The two volumes are not in alignment when they are loaded into tkregister. Now, what am I missing here? If both were loaded using the fixed transform, they should still be in alignment (i.e., vox2ras should be ignored for registration purposes). Thanks in advance, -- Shay Tsao lab Caltech

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qdec: selecting multiple continuous variables
by Laura M. Tully 01 Jun '12

01 Jun '12

Hi, I am using freesurfer 5.1.0 and qdec 1.4. I'm interested in looking at between group differences in thickness in relation to two other continuous measures whilst controlling for ICV. However, qdec doesn't seem to let me select more that one continuous variable even though I only have group selected (discrete) and ICV (nuisance) as additional variables (i.e. a total of three selected) - it's my understanding that qdec allows up to 4 variables, is there a method to selecting multiple continuous variables that I am missing (e.g. hold down shift and select)? Thanks! Laura. -- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully(a)fas.harvard.edu -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura

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recon all error MRISread: could not open file
by Diana Omigie 01 Jun '12

01 Jun '12

I am getting an error during the recon all step that I cannot figure out. It seems to occur in the stage where labels are being written as two label files are missing in the labels directory ( lh.entorhinal_exvivo.label and lh.entorhinal_exvivo.label ) and an error log message emerges in the labels directory which says: MRISread(/neurospin/meg/meg_ rep/anat/freesurfer_segmentation/lh.EC_average/surf/lh.sphere.reg): could not open file In the main directory,an rh.EC_average and lh.EC_average file appears with broken links... Does anyone know what the problem might be be. Sorry for my ignorance. Many thanks, Diana Omigie

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mri_surf2surf error
by mdkruepke＠uwalumni.com 01 Jun '12

01 Jun '12

To anyone who can help - I am trying to tun a GLM on a set of data and am currently receiving an error during the mri_surf2surf portion. When running this portion i receive an error ( could not scan # of lines from (path to rh.cortex.label)). This does not happen when running this portion for the lh, only the right. I am unable to find any information on this error on the mailing list so im hoping someone can help! Best- Michael Kruepke -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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transfer annot files from template to each subject
by Leon 01 Jun '12

01 Jun '12

Hi, FreeSurfer expert I am having difficulty finding the functions that transfer an annotation file I generated on a template to each subject. This template has been registered with several subjects using a surface-based registration method. Now what I want is to (1) transfer this annotation file from the template to each subject, through surface-based registration. and then (2) transfer the annotation file in each subject's surface to their T1 volume space. Could someone show me which functions I need to use? Do I have to convert the annotation files first to label files to do that? Many thanks in advance Leon

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[Fwd: mri_glmfit error]
by YUMI MAEDA 01 Jun '12

01 Jun '12

HI, I figured out, one of the cope file had problem... YUMI 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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open Post-doc position
by Esther Walton 01 Jun '12

01 Jun '12

Post-doc position within the Collaborative Research Centre 940 "Volition and Cognitive Control: Mechanisms, Modulators, and Dysfunctions" at the Department of Child and Adolescent Psychiatry, University Hospital C. G. Carus, Dresden University of Technology, Germany PLEASE REPOST FOR INTERESTED PARTIES Job Description: The Department of Child and Adolescent Psychiatry, Dresden University of Technology, Germany invites applications for a postdoctoral research position in neuroimaging of eating disorders. The new project is part of the aforementioned Collaborative Research Centre (CRC, Steering Committee: Profs. T. Goschke, C. Kirschbaum, M. Smolka, A. Strobel, H.-U. Wittchen and will focus on cognitive control, reward system and the processing of emotions in patients with anorexia nervosa. This is a full time position within the Translational Developmental Neuroscience Group. Responsibilities will include the coordination of our ongoing clinical research study and the acquisition and analysis of a range of behavioral and magnetic resonance imaging (MRI) data. Together with a doctoral student new functional MRI paradigms need to be implemented. Imaging sessions will take place on the Neuroimaging Center's 3T Siemens TIM-Trio scanner and data collected includes high-quality structural, diffusion, and functional MRI data. A variety of additional information will also be collected, including neuropsychological and psychiatric scales, physiological and endocrinological markers. Summarizing results and writing research articles will be another central aspect of the work. The successful applicant will work in a team of young investigators and also be responsible to supervise doctoral students, interns and medical students working in the project. Thanks to the CRC the applicant will have ample opportunity to work with peers and senior scientists in similar project in the Medical School and the Psychology Department. Applicants for the position must hold (a) a PhD, MD or comparable degree in a relevant field (Psychology, Neurosciences or Medicine; if you have additional qualifications a degree in Biology, Biomedicine, Biophysics, Computer Science or Electrical Engineering may also be sufficient), (b) have had some exposure to cognitive and emotional neurosciences, (c) participated in research activities within the past years (d) published in peer-reviewed journals, e) possess strong organizational skills and (f) be able to communicate in German with non-scientific staff members. Some experience in computer programming (Linux/Unix shell scripting, Python and/or MATLAB), neuroimaging analysis methods (FSL, SPM, FreeSurfer or others), advanced statistical analyses and scientific publishing is necessary. The successful applicant will join a multidisciplinary team of researchers and clinicians, will receive further training and train doctoral students (informally). The position is available for a start date as soon as July 1st 2012 (to be confirmed). Review of applications will begin immediately and will continue until the position is filled. The position is guaranteed for one year with the possibility of renewal after positive evaluation. The CRC funding has been granted for 4 years. Salary will be consistent with levels in accordance with the German Research Foundation (100% TV-L: E 13). Compensation includes health insurance, and vacation time. To apply you can use our online portal (https://www.uniklinikum-dresden.de/Bewerbung/?id=81ed34303f2d9930fe6a6cb5d3… application should include a cover letter detailing professional objectives and interests, CV (with grades and language skills), and the names and email addresses of two references. The application can be written in German or English. Applications from many disciplines may be considered. The position is open to qualified international applicants but the knowledge of some German is necessary since the position includes the coordination of an ongoing clinical study. Applicants with a disability will be given preference in the selection process. Prof. Dr. med. Stefan Ehrlich Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Universitätsklinikum Carl Gustav Carus Dresden an der TU Dresden E-Mail: KJPChefsekretariat(a)uniklinikum-dresden.de Please refer to our homepage: http://www.kjp-dresden.de/en/Eating-disorders, http://www.kjp-dresden.de/en/Schizophrenia and http://kjp-dresden.de/de/Publikationsliste-Prof-Dr-S-Ehrlich for more detailed information.

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open Research position (PhD)
by Esther Walton 01 Jun '12

01 Jun '12

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Re: [Freesurfer] long_qdec_table and LongQdecTable.py errors
by Martin Reuter 31 May '12

31 May '12

Great. Thanks for letting me know. I post this to the list, so that other know. Best Martin On May 31, 2012, at 21:11, Jiyagn <jiyang.jiang.email.lists(a)gmail.com> wrote: > Thanks for your reply Martin! > > I think I just found out where the problem was - a blank line at the end of the longitudinal table. The program works fine after deleting it. Probably the error is due to the different line break formats in Windows and Linux. > > Cheers, > Jiyang > > On 05/31/2012 10:39 PM, Martin Reuter wrote: >> Hi Jiyang, >> >> Must have missed Derin's mail. >> >> Can you send the table And command? >> I can then try to see if this bug is still in our dev version or if it got fixed in the meantime. >> >> Best Martin >> >> On May 30, 2012, at 22:06, Jiyang Jiang<jiyang.jiang.email.lists(a)gmail.com> wrote: >> >>> 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 >>> _______________________________________________ >>> 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. >> > >

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pial mesh decimation...
by Gonzalo Rojas Costa 31 May '12

31 May '12

Hi: How can I do a decimation to 10000 polygons aprox to the pial surface ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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