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30088 discussions

Conversion fMRI volumes to surface
by Marina Fernández 17 Dec '19

17 Dec '19

External Email - Use Caution Dear experts, I’ve done the fMRI preprocessing and now I would like to convert each file (that contains 250 volumes) to surface. Is it correct to use the function mri_vol2surf? Should I use any specific flag because they are 4D files? What is the best way to transform the volumes to surface? Thank you in advance. Best regards, Marina.

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Doctoral student positions in fMRI of visual illusions
by Zaretskaya, Natalia (natalia.zaretskaya＠uni-graz.at) 17 Dec '19

17 Dec '19

External Email - Use Caution Dear all, We are looking for three doctoral students to join our Experimental Psychology and Cognitive Neuroscience group in Graz to work on fMRI of visual illusions. You will find the official job ad below (Please note that doctoral students in Austria are employed under a work contract with health and pension benefits. There are no tuition fees associated with getting a PhD degree.) The Institute of Psychology of the University of Graz is looking for three Doctoral Candidates within the framework of the BioTechMed Young Researcher Group "Neural basis of subjective visual experience" (Project-Assistant; 30 hours a week; fixed-term employment for the period of 4 years; position to be filled as of now) Your profile * Master's degree or diploma in psychology, biology, neuroscience, medicine computer sicence or similar fields * Excellent English skills * Interest in the topic of the project and in neuroscience research in general * Scientific curiosity, ability and readiness to learn new things * Excellent organization, communication and social skills * Independence and reliability * Preferably sound knowledge in conducting/analyzing fMRI experiments and programming skills (MATLAB, Python, etc.) Your duties * Writing a dissertation and publishing activities in the research area of the Young Researcher Group * Participation in planning, preparing and conducting fMRI experiments, fMRI data analysis * Preparing scientific manuscripts and publications * Participation in scientific conferences and workshops * Contribution to supervising scientific thesis Our offer The project provides an opportunity to learn advanced (f)MRI techniques (including quantitative morphometry, surface-based analysis, pRF mapping, MVPA, high-resolution structural and functional MRI), while addressing exciting scientific questions. More information about the project can be found at https://psychologie.uni-graz.at/en/cognitive/researching/projects/neural-ba… Classification Salary scheme of the Universitäten-KV (University Collective Agreement): B1 Minimum salary The minimum salary as stated in the collective agreement and according to the classification scheme is EUR 2148.40 gross/month. This minimum salary may be higher due to previous employment periods eligible for inclusion and other earnings and remunerations. We offer you a job with a lot of responsibility and variety. You can expect an enjoyable work climate, flexible work hours and numerous possibilities for further education and personal development. Take advantage of the chance to enter into a challenging work environment full of team spirit and enthusiasm for your job. Application Deadline: January 1st 2020 Reference Number: MB/24/99 ex 2019/20 The University of Graz strives to increase the proportion of women in particular in management and faculty positions and therefore encourages qualified women to apply. Especially with regard to academic staff, we welcome applications from persons with disabilities who meet the requirements of the advertised position. If you are interested, please submit your application documents before the stated deadline. Make sure to indicate the reference number on your application (Motivation letter, CV, degree certificates, names of two scientists who can provide a reference letter upon request) to: bewerbung(a)uni-graz.at<mailto:bewerbung@uni-graz.at?subject=Bewerbung,%20Kennzahl:%20MB/24/99%20ex%202019/20> For further Information please contact Mrs Dr. Natalia Zaretskaya (http://bit.ly/2youGD6) -- Dr. Natalia Zaretskaya Institute of Psychology, University of Graz BioTechMed-Graz Universitaetsplatz 2 8010 Graz Austria +43 316 380 - 5117 natalia.zaretskaya(a)uni-graz.at<mailto:natalia.zaretskaya@uni-graz.at> http://bit.ly/2youGD6

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Problem with the segmentation of subregions
by Marina Fernández 17 Dec '19

17 Dec '19

External Email - Use Caution Hi experts, We are doing the segmentation of the subfields of the hippocampal and amygdala subfields, brainstem subestructures and thalamic nuclei. When we used segmentHA_T1.sh and segmentThalamicNuclei.sh, 'Command not found' appears. On the other hand, we used segmentBS.sh and we got the following message: 'Software requires 4 arguments: segmentSFnewT1.sh matlabRuntimeDirectory FShomeDirectory subjectName subjectDir'. But, when we typed 'segmentSFnewT1.sh' we got 'Command not found' again. Note: We have FS v6.0 and the runtime Matlab 2014b. Best wishes, Marina

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Topological Defect
by Kong Chuizheng 16 Dec '19

16 Dec '19

External Email - Use Caution Hello Freesurfer Developers, We are trying to construct a 3D cortex model of a tumour subject. The recon-all.log showed that the program froze at Correction of the Topology with "XL defect detected." I followed the procedure of the online tutorial page ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_free…) and found that there's lots of "holes" and sharp abnormal shapes in the lh/rh.smoothwm.nofix file. It will be very hard to fix this by hand, and we wonder if you can give us some advice. Sincerely, Chuizheng Kong Chuizheng Kong

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PETsurfer RBV-PVC strange values for some ROIs
by Jonathan DuBois 16 Dec '19

16 Dec '19

External Email - Use Caution Hi Doug, I have been running mri_gtmpvc RBV-PVC and have noticed that in a few regions the RBV corrected values are negative. This occurs when using –no-rescale so I don’t think it is a reference region issue. I also tried using the –wm-annot option in mri_gtmseg and this resulted in slightly more regions with a negative value following RBV PVC. This suggested to me that the matrix may be ill-conditioned, but I was wondering what you think and if you have seen this before? I included a screen shot showing a couple regions with negative values. The raw counts are slightly lower in these regions but not significantly below the average. The data is from an HR+ scan (~6mm FWHM) from AD subject so the cortex is pretty thin and regions that this is occurring in are fairly small (e.g. left caudal anterior cingulate, right vessel, right accumbens, right transverse temporal). If you think it is the case that the matrix is ill-conditioned is there a way to reduce the number of regions by combining them automatically? I can generate a new parcellation and feed it into mri_gtmseg, but I wasn’t sure if you had something set up already. Best, Jon

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(no subject)
by Marina Fernández 16 Dec '19

16 Dec '19

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Create translucent brain volume and save as matlab figure file
by Sparsh Jain 15 Dec '19

15 Dec '19

External Email - Use Caution Hi! Can I create a brain volume with about 40% opacity and save it as a matlab figure? The volume may not be very accurate. Why I need this: I want to 3D plot the RAS coordinates of electrodes inside this brain volume in Matlab and assign different colors corresponding to power values. I have attached a sample brain volume that might work for me. Please ignore the electrode color (it was obtained using a different pipeline). Thanks! Sparsh

2 2

ROI analysis with manually created labels
by 尹圆圆 14 Dec '19

14 Dec '19

External Email - Use Caution Dear FreeSurfer developers, I used Freesurfer QDEC for group comparisons and identified clusters with significance cortical thickness between the Patient group and the Control group. Then I created several ROIs manually, saved them as labels, and mapped them onto each subject.  I have learned how to get the cortical thickness of certain label (e.g., lh.precentral.label) from one subject (e.g. N001) using this command "mris_anatomical_stats -l lh.precentral.label -t lh.thickness -b -f N001/stats/lh.precentral.stats N001 lh".  But using this command for each label and each subject (one by one) to extract cortical thickness is rather time-consuming, I am wondering if there this a batch processing command for this (for all subjects, do the aforementioned command automatically, so that I can extract the cortical thickness values of the lh.precentral.label of all subjects)? I've searched the freesurfer wiki and the question list but found no help. Excuse me for this basic question. Thanks in advance. Best regards, Yuanyuan Yin

2 1

Thickness problem
by Gwang-Won Kim 13 Dec '19

13 Dec '19

2 1

Study specific template
by Joshi, Nandita 13 Dec '19

13 Dec '19

External Email - Use Caution Hello, I am trying to make a study specific template based on the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates However, on running the first step: make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ... I get an error while running the recon-all is trying to run the aparc to aseg step: #@# AParc-to-ASeg aparc Thu Dec 5 11:29:33 EST 2019 /Users/nandita/FreeSurfer_recon/newtemplate \n mri_aparc2aseg --s newtemplate --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt \n relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /Users/nandita/FreeSurfer_recon subject newtemplate outvol /Users/nandita/FreeSurfer_recon/newtemplate/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /Users/nandita/FreeSurfer_recon/newtemplate/surf/lh.white Reading lh pial surface /Users/nandita/FreeSurfer_recon/newtemplate/surf/lh.pial Loading lh annotations from /Users/nandita/FreeSurfer_recon/newtemplate/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /Users/nandita/FreeSurfer_recon/newtemplate/label/tmpdir.annot2std.41916/seg.1.100110189.ctab) Reading rh white surface /Users/nandita/reeSurfer_recon/newtemplate/surf/rh.white Reading rh pial surface /Users/nandita/FreeSurfer_recon/newtemplate/surf/rh.pial Loading rh annotations from /Users/nandita/ADRC/FreeSurfer_recon/newtemplate/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /Users/nandita/FreeSurfer_recon/newtemplate/label/tmpdir.annot2std.47059/seg.1.100110189.ctab) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /Users/nandita/FreeSurfer_recon/newtemplate/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /Users/nandita/FreeSurfer_recon/newtemplate/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter Segmentation fault Darwin Nanditas-MacBook-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Sun Jun 2 20:31:42 PDT 2019; root:xnu-4570.71.46~1/RELEASE_X86_64 x86_64 recon-all -s newtemplate exited with ERRORS at Thu Dec 5 11:29:52 EST 2019 On inspecting the mri folder, it seems the norm.mgz file has not been created at all. Looking at the flowchart of steps for the recon-all command, norm.mgz is supposed to be created in the CA Normalize step, which requires the talairach.lta in the newtemplate/mri/transforms folder, which seems to be missing as well. The only transform created in the transform folder is talairach.xfm. The talairach.lta is created in the EM GCA registration step. Do I re-run the EM GCA registration, CA normalize, and then contonue from aparc to aseg? I am not sure if since I am creating my own template, the EM GCA step requires any modifications? Any help will be appreciated. Thanks, Nandita

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