Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

overlay cortical thickness estimates
by forsteca＠hu-berlin.de 19 Feb '19

19 Feb '19

External Email - Use Caution Hello Freesurfer Community, I want to view my cortical thickness estimates (I calculated standard deviations for different subjects) on a 3D file. I thought I could replace the lh.thickness part in the following code by my own estimations: freeview -f \ /Datasets/sSUBJ_DAY_01_01/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ /Datasets/sSUBJ_DAY_01_01/surf/lh.pial:annot=aparc.a2009s.annot:name=pial_aparc_des:visible=0 \ /Datasets/SUBJ_DAY_01_01/surf/lh.inflated:overlay=lh.thickness.asc:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ /Datasets/sSUBJ_DAY_01_01/surf/lh.inflated:visible=0 \ /Datasets/sSUBJ_DAY_01_01/surf/lh.white:visible=0 \ /Datasets/sSUBJ_DAY_01_01/surf/lh.pial \ --viewport 3d I tried loading a binary mat, as lh.thickness is a binary file as well. I got the following error: couldn't determine type of file Can you clarify what file structure the thickness overlay file should be, so that Freesurfer is able to read the thickness information ? Thank you so much. (addional info: mat file 163842x1 double)

2 1

hippocampal subfield segmentation input mask?
by Malone, Ian 19 Feb '19

19 Feb '19

External Email - Use Caution Dear FreeSurfer list, I'm wondering if there is any way to input different starting segmentations for the hippocampus into the hippocampal subfield segmentation? We've got a hippocampus specific segmentation algorithm which we'd like to try as input to see if it provides a better starting point than whole brain labels. Are there any other inputs we'd need? Best wishes, Ian Malone -- Research Associate Dementia Research Centre Queen Square Institute of Neurology UCL London WC1N 3BG

1 0

Qdec tutorial video
by Korom, Marta 19 Feb '19

19 Feb '19

External Email - Use Caution Hello Freesurfers, I was wondering if anyone has access to a Qdec tutorial, other than the one on the Freesurfer website. The one on the website only covers the basics and it does not have a video component. In case you have a better tutorial available or a video that goes into detail, please send it to me. Thank you, Marta -- *Marta Korom | *PhD Candidate University of Delaware, Clinical Science e-mail: mkorom(a)udel.edu phone: 646 861 8461 http://www.abcintervention.org/

1 0

mri_surf2surf QC
by Winkelbeiner, Stephanie A 19 Feb '19

19 Feb '19

External Email - Use Caution Hi Freesurfers, I ran mri_surf2surf and registered self-created parcels from fsaverage to all my subjects. What is the best way to do QC and check if everything went right? Thanks for your help! Stephanie The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

2 4

recon-all tries to call mri_relabel_hypointensities -all-info
by Drucker, Daniel 19 Feb '19

19 Feb '19

freesurfer-6.0.1/bin/recon-all line 630 calls: mri_relabel_hypointensities -all-info However, -all-info is not a valid option: $ mri_relabel_hypointensities usage: mri_relabel_hypointensities [options] <input aseg> <surface directory> <output aseg> This program measures a variety of anatomical properties valid options are: -l <label file> - limit calculations to specified label -a <annotation file> - compute properties for each label in the annotation file separately $ mri_relabel_hypointensities -all-info unknown option -all-info -- Daniel M. Drucker, Ph.D. Director of IT, McLean Imaging Center

2 1

Information about argument -erode in command mri_extract_label
by Viktor Domazetoski 19 Feb '19

19 Feb '19

External Email - Use Caution Dear FreeSurfer experts, I would like to enquire about the command mri_extract_label. More specifically I am looking for information about the -erode argument. Therefore I have a few questions: 1. Is a 3D erosion of the entire brain or a 2D slice by slice erosion used? 2. What structuring element (regarding the shape and size of the kernel) is used for the erosion for a given argument value (e.g. for the command mri_extract_label -erode 1)? Thank you in advance! Kind regards, Viktor

2 1

Average subject
by Laboratorio de Neurociencia Funcional 19 Feb '19

19 Feb '19

External Email - Use Caution Dear all, I am planning to run separate regression analysis with cortical thickness in two very different populations (young and elderly subjects). Depending on results, it may happen that I am interested in comparing regression slopes between the two groups. My question is: should I build one average subject for each within-group regression analysis (one for young and another for elderly), and another different average subject merging all subjects of the two samples to compare regression slopes? Or I should preferably use only one average subjects with all subjects in all within and between regression analysis? Many thanks in in advance. Best regards, Jose

2 3

dt_recon error
by Daniel Davidson Callow 18 Feb '19

18 Feb '19

External Email - Use Caution Hello, I am still trying to run dt_recon and am having issues. The code I am running is attached...and an abbreviated version is below. foreach subj (`ls -d /Volumes/DANIEL/AES101 | sed 's/\// /g' | awk '{print $3}'`) foreach cond (Ex Rest) echo "subj = " ${subj} ", cond = " ${cond} cd /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/ mri_convert image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/dwi.nii.gz dt_recon --sd /Volumes/DANIEL/tutorial_data/diffusion_recons/ --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/tutorial_data/dtrecon/${subj}.${cond}. and the following is the output and errors I am getting from running the above code. I have also attached a screenshot of the path and folder with the various file inputs and outputs. subj = AES101 , cond = Ex mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File exists mri_convert.bin image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from image000001.dcm... Getting Series No Scanning Directory INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex INFO: Scanning for Series Number 171 INFO: found 65 files in series INFO: loading series header info. INFO: sorting. RunNo = 170 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName AES101 Date and time StudyDate 20170409 StudyTime 105710.343000 SeriesTime 120657.984000 AcqTime 120650.230000 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 170 SeriesNo 171 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 630.8714 646.6747 -31.8394 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 35 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: (128 128 35), nframes = 65, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 6300, TR = 6300 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName AES101 Date and time StudyDate 20170409 StudyTime 105710.343000 SeriesTime 120657.984000 AcqTime 120650.230000 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 170 SeriesNo 171 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 105.8714 121.6747 -31.8394 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 35 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.8714 16.6747 31.1606 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz... Saving bvals and bvecs -rwxrwxrwx 1 administrator staff 1276058 Feb 18 10:18 /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm INFO: SUBJECTS_DIR is /Volumes/DANIEL/tutorial_data/diffusion_recons/ dt_recon logfile Mon Feb 18 10:19:18 EST 2019 VERSION $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ setenv SUBJECTS_DIR /Volumes/DANIEL/tutorial_data/diffusion_recons/ cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex /Applications/freesurfer//bin/dt_recon --sd /Volumes/DANIEL/tutorial_data/diffusion_recons/ --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm --s AES101.Ex --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. hlhp-105.umd.edu administrator /usr/local/fsl/bin/eddy_correct ECRefTP 0 #@#------------------------------- Converting input Mon Feb 18 10:19:18 EST 2019 cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii mri_convert.bin /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm... Getting Series No INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex INFO: Scanning for Series Number 171 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 170 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName AES101 Date and time StudyDate 20170409 StudyTime 105710.343000 SeriesTime 120657.984000 AcqTime 120650.230000 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 170 SeriesNo 171 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 630.8714 646.6747 -31.8394 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 35 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (128 128 35), nframes = 65, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 6300, TR = 6300 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName AES101 Date and time StudyDate 20170409 StudyTime 105710.343000 SeriesTime 120657.984000 AcqTime 120650.230000 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 170 SeriesNo 171 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 105.8714 121.6747 -31.8394 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 35 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 0.8714 16.6747 31.1606 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii... Saving bvals and bvecs #@#------------------------------- Eddy/Motion Correct Mon Feb 18 10:19:30 EST 2019 cd /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0 Image Exception : #61 :: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi Image Exception : #61 :: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi /usr/local/fsl/bin/eddy_correct: line 94: 64175 Abort trap: 6 fslsplit $input ${output}_tmp Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value rm: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp????.*: No such file or directory rm: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_ref*: No such file or directory Any help you could provide for trouble shooting the issue would be greatly appreciated! Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow(a)umd.edu <dcallow(a)gmail.com> 443-254-6298

1 1

midbrain mask for LGI
by Sanfelici, Rachele 18 Feb '19

18 Feb '19

1 0

Excluding Specific Regions from a Volumetric File
by Maedeh Khalilian 18 Feb '19

18 Feb '19

External Email - Use Caution Dear FreeSurfer experts, I have used "mri_aparc2aseg" in order to map my parcellation file to a volumetric file, but in the end I wanna exclude some regions which I know their labels. I think it must be opposite of what "mri_binarize" does. I wonder how to do that. I would be grateful if u could help me with that. Best regards, Maedeh

2 1

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