Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

file error
by LIEWALD David 09 Dec '15

09 Dec '15

OS Opensuse 13.2 Freesurfer 6 Dev Logfile Attached I have had no luck trying to get freesurfer to run. It is failing at the same point each time ( Please see log). I have tried with multiple datasets in multiple locations both on the local machine and across the network. I have also verified that the permissions of the dir are correct and I can manually read and write to the. I'm at a loss? Dave Liewald The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

1 0

ASCII Error
by Marc Callison 08 Dec '15

08 Dec '15

Good day, I'm getting the following error when I try to convert my DICOM files. Some of the files do not have the issue, but others do. The error is below. WARNING: file /Users/marc/Desktop/brainscan/DICOM/PA000000/ST000000/SE000001/IM000000 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header Darwin Marcs-MacBook-Air.local 15.0.0 Darwin Kernel Version 15.0.0: Sat Sep 19 15:53:46 PDT 2015; root:xnu-3247.10.11~1/RELEASE_X86_64 x86_64 recon-all -s my_brain exited with ERRORS at Fri Dec 4 20:02:27 CST 2015 For more details, see the log file /Applications/freesurfer/subjects/my_brain/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I need help figuring out how to solve this if anyone can. I'd really appreciate it. Thanks, Marc

3 5

3dClustSim and Gaussian filter width
by Emma Thompson 08 Dec '15

08 Dec '15

Dear Freesurfers, I am trying to use 3dclustsim in AFNI to determine the minimum number of voxel in a cluster to reach significance, my understanding is that in the command line the -fwhm s flag refers to the gaussian filter width and NOT the Gaussian Kernel, can anyone point me to how I might be able to obtain this for each hemisphere in freesurfer? I am using my own average brain that I created, but it would help to know how to do this for the fsaverage as well. Many thanks for your help! http://afni.nimh.nih.gov/pub../pub/dist/doc/program_help/3dClustSim.html

3 6

edits in a subjects
by angela.favaro＠unipd.it 08 Dec '15

08 Dec '15

Hi Freesurfer experts, I am checking quality of recon of some new scan and I need some advice about the needed edits. I attached two snapshots showing the problems: 1. a problem with white matter recon (surface seems good, but volume not) 2. a problem in the right medial subcortical wall (a lot of confusion in sufaces). My questions are whether I have to discard this subjects or try to edit and which type of edits do you suggest Thank you! Angela

2 3

recon-all reconstruction problems
by salvatoreandrea.92＠libero.it 08 Dec '15

08 Dec '15

Hi Freesurfer experts! I had run recon-all over 5 T1s acquired in different time-points in a patient affected by Multiple Sclerosis. Looking at the surfaces created by recon-all it appears that almost all the frontal lobe is missing, probably due to the big demyelinating lesion that she has. However this lesion does not affect the gray matter, which is still there, as I could see by the T1 images. Can I do something to correct for this error? Also because these distortions may have contaminated the stats files that, if I am not wrong, contain the volumes of several areas in the brain. Attached you can find a snapshot of the left hemisphere of the patient. Thank you all, Salvatore

1 0

Recon-all -bigventricles option : general use or not in Alzheimer cases ?
by Matthieu Vanhoutte 08 Dec '15

08 Dec '15

Dear FreeSurfer experts, My question is in the title. I'm working on Alzheimer case where most of the cases have large ventricles. Is it better in general use to apply -bigventricles option on all subjects (for homogeneous calculus or something like that...) or to distinct subtle cases of patients with not so big ventricles ? Thanks in advance for helping ! Best regards, Matthie

2 3

Re: [Freesurfer] Freesurfer 6 - exited with errors
by Scott Quadrelli 08 Dec '15

08 Dec '15

Thanks Doug and Bruce for your response. Here is the result of the command Doug requested: $ mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab C02DL_t1 rh white INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/mri/wm.mgz... reading input surface /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.white... Using TH3 vertex volume calc Total face volume 229272 Total vertex volume 224839 (mask=0) reading input pial surface /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.pial... reading input white surface /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.white... reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/6.0.beta/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1539395 mm^3 (det: 1.265500 ) lhCtxGM: 216981.653 216526.000 diff= 455.7 pctdiff= 0.210 rhCtxGM: 224488.981 223971.000 diff= 518.0 pctdiff= 0.231 lhCtxWM: 221893.625 222489.000 diff= -595.4 pctdiff=-0.268 rhCtxWM: 224605.205 224852.000 diff= -246.8 pctdiff=-0.110 SubCortGMVol 51078.000 SupraTentVol 967354.464 (965462.000) diff=1892.464 pctdiff=0.196 SupraTentVolNotVent 940904.464 (939012.000) diff=1892.464 pctdiff=0.201 BrainSegVol 1111453.000 (1108301.000) diff=3152.000 pctdiff=0.284 BrainSegVolNotVent 1080460.000 (1080411.464) diff=48.536 pctdiff=0.004 BrainSegVolNotVent 1080460.000 CerebellumVol 141268.000 VentChorVol 26450.000 3rd4th5thCSF 4543.000 CSFVol 1413.000, OptChiasmVol 158.000 MaskVol 1614399.000 663 321 1164 2.414 0.317 0.126 0.029 10 0.7 BA1_exvivo 1878 1200 2522 2.055 0.423 0.096 0.018 13 1.5 BA2_exvivo 846 653 728 1.608 0.324 0.159 0.035 9 1.3 BA3a_exvivo 1782 1155 1902 1.588 0.371 0.089 0.018 9 1.5 BA3b_exvivo 930 539 1396 2.423 0.439 0.108 0.030 8 1.4 BA4a_exvivo 1048 718 1669 2.480 0.403 0.093 0.021 4 1.0 BA4p_exvivo 6264 3392 9732 2.494 0.482 0.103 0.030 66 7.5 BA6_exvivo 951 631 1818 2.403 0.428 0.123 0.027 16 1.1 BA44_exvivo 915 650 1780 2.212 0.349 0.139 0.031 16 1.0 BA45_exvivo 3074 2189 3724 1.675 0.473 0.134 0.035 33 4.8 V1_exvivo 4690 2886 4907 1.698 0.528 0.151 0.041 79 8.3 V2_exvivo 324 198 535 2.216 0.477 0.135 0.036 5 0.5 MT_exvivo 285 170 847 3.400 0.783 0.132 0.036 4 0.4 perirhinal_exvivo 245 177 522 2.386 0.732 0.126 0.020 2 0.2 entorhinal_exvivo The annotation seems to be fine, I have attached a screenshot of the second command. The initial command I ran was: "recon-all -all -s bert -hippocampal-subfields-T1” However I noticed there was no [lr]h.hippoSfLabels-T1.v10.mgz output. When I tried to run the just the hippocampal segmentation I got an error that the matlab dependencies weren’t installed, so presumably that is why I received the original message ?! Cheers, Scott From: "quadrellis(a)me.com" <quadrellis(a)me.com> Date: Tuesday, 8 December 2015 8:57 am To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer 6 - exited with errors Hi All, I am trying to track down the source of an error on one of my first runs using freesurfer 6. I have attached the relevant logs. Any help would be much appreciated. Cheers, Scott

2 1

Freesurfer 6 - exited with errors
by Scott Quadrelli 07 Dec '15

07 Dec '15

Hi All, I am trying to track down the source of an error on one of my first runs using freesurfer 6. I have attached the relevant logs. Any help would be much appreciated. Cheers, Scott

3 2

Freesurfer V6 (beta) and MacOS 10.11 (El Capitan)
by Kevin Aquino 07 Dec '15

07 Dec '15

Dear all, I was wondering if many users have had freesurfer 6 (beta) working (well) with Mac OS 10.11? (or Freesurfer V5.3) Thanks! *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* Kevin.aquino(a)nottingham.ac.uk, aquino(a)physics.usyd.edu.au | *W* www.physics.usyd.edu.au/~aquino/ ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

2 1

Left and right white matter intensity ratio
by Sabrina Yu 07 Dec '15

07 Dec '15

Hi there, Would it be possible to use pctsurfcon to calculate the ratio of white matter signal intensity between left and right hemispheres? Thank you Sabrina

3 10

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer December 2015