Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

subfields segmentation FS v6.0
by Daniele Orlandi 03 Nov '15

03 Nov '15

Dear all I'm running the new pipleline for hippocampal subfields segmentation with FreeSurfer v6.0 on a T13D image. As results i can extract values for the Whole hippocampus and the following subfields: Hippocampal_tail, subiculum, CA1, hippocampal-fissure, presubiculum, parasubiculum, molecular_layer_HP, GC-ML-DG, CA3, CA4, fimbria, HATA but not for Alveus as reported in the paper of Iglesias, JE. et al. 2015. Was my computation wrong? Best, Daniele

2 1

recon-all crashing
by Biekman, Brian Darnell 02 Nov '15

02 Nov '15

To Whom It May Concern: I am conducting FreeSurfer analysis for a multi-site project and I'm unable to run recon-all on the T1 data for all but one of the sites. The problem I'm dealing with is identical for all of the subjects for which recon-all crashes. I do not want to speculate as to why recon-all works for one of the sites but it's worth mentioning that that site has a slightly different T1 protocol and that these images were uploaded via a physical backup disk while for the other sites, I downloaded the T1 data for the other sites from a database shared by all of the project investigators. I would like to upload the images for one the T1-weighted sequences that crashes recon-all. If somebody could let me know how to go about that, I would really appreciate it. Thank you. Here is the requested information for anyone reporting a bug: FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 15.0.0 x86_64 Subject Name: 14-140-0052 Command Line Executed: recon-all -all -i /users/brianbiekman/Desktop/Brain_Scope/14-140-0052/00001.dcm -s 14-140-0052 Error message generated: Screenshot of error message attached recon-all log: Attached

2 2

Mac Version and Output differs
by Kasper Jessen 02 Nov '15

02 Nov '15

Dear FreeSurfer group, I have tested the data output on the same subjects using the same FreeSurfer version but on different machines, a MacPro and a iMac. The output are different, which argues that it is important to run freesurfer on the same computer on all your subjects. Is it due to a randomisation in freesurfer (maybe because of seed points)? Is it possible to get the same results even though you run in on different computers? *MacPro:* build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin mac-pro-2014.regionh.top.local 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 *iMac: * build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin Nikolajs-iMac.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 Best regards, Kasper Jessen

2 1

Tracula ends with errors
by denizzgursel 02 Nov '15

02 Nov '15

Dear all, I am very new to using TRACULA and Freesurfer. I am trying to apply tracula on the provided tutorial data. When I ran the command trac-all -prep -c dmrirc.tutorial, after eddy current correction, I get this error: mv -f /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs.norot xfmrot /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.ecclog /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs.norot /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. n -sf /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/data.nii.gz mri_convert --frame 0 /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999278, -0.0375823, -0.00564044) j_ras = (-0.0367492, 0.917788, 0.395367) k_ras = (0.00968205, -0.395289, 0.918506) keeping frame 0 writing to /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz... mri_concat --i /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz --mean --o /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb.nii.gz bet /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain_mask.nii.gz /data_augus t/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff #------------------------------------- #@# Inter-subject registration Mon Nov 2 15:39:02 CET 2015 flirt -in /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain.nii.gz -ref /data_RAID/Kathrin/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain_mni.nii.gz -omat /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2mni.mat -cost corratio convert_xfm -omat /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/mni2diff.mat -inverse /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Mon Nov 2 15:39:20 CET 2015 flirt -in /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/lowb_brain_mask.nii.gz -ref /data_RAID/Kathrin/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/lowb_brain_mask.nii.gz -ref /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/brain_anat_orig.nii.gz -out /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Mon Nov 2 15:39:23 CET 2015 dtifit -k /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz -m /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs -b /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvals -o /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dtifit 0 128 0 128 0 64 terminate called after throwing an instance of 'NEWMAT::IndexException' Abort Linux slow.mri.tu-muenchen.de 3.7.10-1.40-desktop #1 SMP PREEMPT Thu Jul 10 11:22:12 UTC 2014 (9b06319) x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Nov 2 15:39:23 CET 2015 My config file is as simple as possible. I only defined the data path, output path, subject list and dcmlist. The problem seems to be related to bvecs file, I looked at it, and it seems to have 0.0000 in the beginning. Could this create a problem? Thank you. Best, -- D.

1 0

(no subject)
by denizzgursel 02 Nov '15

02 Nov '15

1 0

Hippocampal Subfields 6.0 with 5.3 recons
by O'Shea,Andrew 02 Nov '15

02 Nov '15

Hello all, I was wondering if anyone with knowledge of the new hippocampal subfield segmentation that is going to be released with version 6.0 could answer a quick question. We have previously processed subjects in v5.3 and would like to use the new hippocampal seg algorithm. How "standalone" is the new process? Does the new process use any inputs from the recon-all stream which have changed in the upcoming version? Thanks! -Andrew

1 0

wrong segmentation
by Thục Trinh 02 Nov '15

02 Nov '15

Hi Freesurfer experts, I ran recon-all for our subjects and there is a problem with the wrong segmentation between the white/gray matter. this error appears in couples continued slices. Picture are attached. Do you have any suggestion to fix this error. Thank you, Trinh

2 2

Timepoints and Analysis
by Kasper Jessen 02 Nov '15

02 Nov '15

Dear FreeSurfer group, I have a question regarding timepoints and analysis. For example, lets say we have a data-set of 80 subjects with the following timepoints: baseline, 6 weeks, 6 months, 1 year and 2 years follow-up. Two different studies on the same data needs to be performed. a) Study_1 with two timepoints (baseline and 6 weeks) b) Study_2 with all time timepoints (baseline, 6 weeks, 6 months, 1 year and 2 years follow-up). As i understand, the more time points the better the [BASE] you will get. The BASE is going to be edited Therefore, even though Study_1 only is going to be using two timepoints, do you still recommend to include all the 5 time points in creating the [BASE] even though only 2 time points will be used? Best regards, Kasper Jessen

2 1

center of gravity
by Shani Ben Amitay 01 Nov '15

01 Nov '15

Dear freesurfer, Is it possible to get center of gravity for each label/parcel in annotation file? Thanks, Shani

1 0

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Freesurfer November 2015