Freesurfer October 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
170 discussions

qdec long parsing table to look in non-existant directory
by Katherine Damme 09 Oct '16

09 Oct '16

Hello everyone, I am running qdec for longitudinal data for the first time and although I have a file that matches the guide on the wiki, the script is looking in a non-exsistant file location (see below). While there is a 1001 file and a 1001_MR1, I am not sure where it is getting the 1001_MR1.long.1001 dir. Any ideas? "long_mris_slopes --qdec long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-stack --do-label --time years --qcache fsaverage --sd /home/adapt/Cortical_Thickness_Data Parsing the qdec table: long.qdec.table.dat Working in SUBJECTS_DIR: /home/adapt/Cortical_Thickness_Data Working on hemi: lh Subject-Template: 1001 INFO: 2 TPs in 1001 , mean age: 0.487704918 =============================================================================== SUBJECT 1001 Intersecting Within-Subject Cortex Label ERROR: /home/adapt/Cortical_Thickness_Data/1001_MR1.long.1001/label/lh.cortex.label does not exist!"

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QAtools - tkmedit and detailed snapshots all black
by Sneha Pandya 07 Oct '16

07 Oct '16

Dear experts, I am running QA tool on our current recon runs and am getting black image for all tkmedit and detailed snapshots. While running the tool, tkmedit window pops up and everything looks fine. Per instruction I am making sure that no other interactive window is open. Even otherwise when I take screen shot from within tkmedit window using screen shot button, it is still black. Please see QA tool summary . Can anyone advice what is wrong? [cid:bef1900c-65af-44e4-85fe-3a26322c7a23] Thanks, Sneha

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Extracting thickness values using labels
by Anders Hougaard 07 Oct '16

07 Oct '16

Dear Freesurfers, This is probably a very basic question, but I was unable to find an answer in the mailing list: I did a paired cortical thickness group analysis: mris_preproc --fsgd /home/paired.fsgd --target fsaverage --hemi lh --meas thickness --out lh.paired.00.mgh --paired-diff (smoothing) mri_glmfit --y lh.paired.05.mgh --fsgd diff.fsgd --osgm --surf fsaverage lh --cortex --glmdir lh.05_diff.glmdir I found an area of difference in cortical thickness and I would like to know the thickness values of this area for all of the input in paired.fsgd, not just the differences I get from the y.ocn.dat file. How do I extract thickness values from the lh.paired.00.mgh file using the label file of the significant cluster? All the best, Anders

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mris_make_face_parcellation
by Mamashli, Fahimeh 07 Oct '16

07 Oct '16

Dear Freesurfers, I have used mris_make_face_parcellation to divide the brain into smaller parcellations and then used mri_annotation2label to generate the labels. However, the problem is that the labels are ordered based on numbers and it is not clear which label belongs to which parcellation. For example, I would like to use lh.aparc.annot as parcellations. Can you please help me what should I do? Or is there anyway to figure out how to assign a parcellation (e.g. superior temporal) to the small labels generated based on mris_make_face_parcellation? Thank you very much, Fahimeh

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Research Position in Genetics and Neuroimaging
by Juan Domingo Gispert López 07 Oct '16

07 Oct '16

The Barcelonaβeta Brain Research Centre (BBRC), research institution of the Pasqual Maragall Foundation (PMF) and the Centre for Genomic Regulation (CRG) invites applications for a full-time research position to study the genetic modulation of cerebral phenotypes based on genome-wide associations with neuroimaging data, as part of its clinical research program. The primary responsibility of this position includes the analysis and interpretation of genome-wide association studies (GWAS) data in association with quantitative phenotypes extracted from neuroimaging modalities. The candidate will be working under the guidance of the Principal Investigators Roderic Guigó and Stephan Ossowski of the CRG and the Neuroimaging Group Principal Investigator of the BBRC, Juan-Domingo Gispert. The aim of this project is to improve our understanding of genetic modulation of cerebral phenotypes in healthy subjects and to identify spatially varying patterns of genetic control that may not be evident from summary variables. For additional details please visit: https://fpmaragall.org/wp-content/uploads/2014/07/ Postdoc_CRG_BBRC_Oct2016.pdf Deadline: Please submit your application by November 18th, 2016. -- *Juan D Gispert* Head Neuroimaging Research *Barcelona**β**eta **Brain Research Center - Fundació Pasqual Maragall* T. (+34) 93 326 31 90 C/ Wellington, 30 08005 Barcelona *www.fpmaragall.org <http://www.fpmaragall.org/>*

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Processing 7T data
by Damien MARIE 07 Oct '16

07 Oct '16

Dear experts, I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim is to look a R1 maps. I was wondering what was your opinion concerning the downsampling to 1 mm^3 (performed by the current FreeSurfer version if I am correct). What do you think would be the best: FreeSurfer 5.3 , FreeSurfer 5.3-HCP or FreeSurfer beta 6.0? Thank You and Best, Damien

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Question about Cortical Thickness
by Funk, Quentin 06 Oct '16

06 Oct '16

I have a few questions regarding the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness The instructions assume that there is an ROI in the same space as the T1.mgz map. Then they do the following: 1) Register the T1 to fsaverage 2) resample the ROI to the cortical surface of fsaverage 3) map the thickness data of the subject to fsaverage 4) measure the thickness data Why is the registering to fsaverage helpful? It seems as if this computation could be done in the native space. Why couldn't one make the following changes: 1) in mri_vol2surf, the reg option could be replaced with regheader MYSUB. 2) Then the surf2surf command becomes unnecessary. -- Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003 Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 1

mris_divide_parcellation
by Mamashli, Fahimeh 06 Oct '16

06 Oct '16

Dear Freesurfer group, I am going to divide a brain parcellation into divisions using mris_divide_parcellation. As far as I know from the help comment, this function "divides one or more parcellations into divisions perpendicular to the long axis of the label". Is there any other program that does not make the divisions perpendicular to the long axis? Thank you, Fahimeh

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[Dev Build] Processing very high resolution dataset
by Falk Lüsebrink 06 Oct '16

06 Oct '16

Dear all, I am currently trying to process a MPRAGE with an isotropic resolution of 250 µm acquired in vivo. Downsampling the data to .5 and 1 mm resulted in no errors and surfaces look good. However, while processing the data at native resolution I receive a segmentation fault during topology fixation. May this be related to the number of vertices / faces? Surfaces look okay and not totally corrupted. Memory and disk space are available plentiful. INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781 2016/06/13 21:20:50 fischl Exp $ before topology correction, eno=-2042 (nv=2743306, nf=5490696, ne=8236044, g=1022) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 1461809 ambiguous faces found in tessellation segmenting defects... Segmentation fault Uploading of the dataset is currently not possible. Best, Falk

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Job opening: AFNI group (NIMH, NIH, USA)
by P Taylor 06 Oct '16

06 Oct '16

There is a job opening in the AFNI group at NIHM, NIH, USA. Please see this link if you or someone you know is a scientific programmer: https://kelly.secure.force.com/CandidateExperience/CandExpJobDetails?id=a7V… Applications are made directly through the Kelly Services company (not through the AFNI group itself). If you have questions, please feel free to email: Robert W Cox, PhD Director, Scientific and Statistical Computing Core (AKA the AFNI group) NIMH & NIH email: robertcox(a)mail.nih.gov http://afni.nimh.nih.gov

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Freesurfer October 2016