Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30076 discussions

Start a nNew thread

Volume or surface?
by John Anderson 17 Oct '16

17 Oct '16

1 0

FreeSurfer on MP2RAGE
by Daniel Ferreira 16 Oct '16

16 Oct '16

Dear all, We have been working quite extensively with Freesurfer over the years. We are now starting to collect a new large cohort and we are about to decide which T1-weighted sequence to use, MPRAGE or MP2RAGE (Siemens 3T Prisma, headcoil 20 Chanel). When we visually inspect the images we think there is a better contrast between GM and WM in the MP2RAGE over the traditional MPRAGE sequence. Both sequences seem to produce good Freesurfer output, but the cortex tend to be a bit thinner with MP2RAGE, possibly due to the better contrast, but we can of course not be sure of this. Freesurfer have always produced nice results with the MPRAGE sequence and the MPRAGE flag seems to work well. Do you think this flag will work as well on MP2RAGE? Of course it is difficult to say but we wonder if you have any opinion on which sequence to use? Thank you very much, Best regards -- Daniel Ferreira, PhD. Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics (Karolinska Institute, Sweden) daniferp(a)gmail.com | daniel.ferreira.padilla(a)ki.se

1 1

Re: [Freesurfer] Freesurfer Digest, Vol 152, Issue 22
by AKUDJEDU, THEOPHILUS 16 Oct '16

16 Oct '16

Dear All, I want to know the freesurfer anatomical definition for the caudate and the hippocampus. Thank you. Theo ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: 16 October 2016 17:00:01 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 152, Issue 22 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Using "for" to run multiple subjects (Farzaneh keyvanfard) 2. Problem in upload file through ftp (Cong) ---------------------------------------------------------------------- Message: 1 Date: Sat, 15 Oct 2016 18:52:12 +0000 (UTC) From: Farzaneh keyvanfard <f_keivanfard(a)yahoo.com> Subject: [Freesurfer] Using "for" to run multiple subjects To: Freesurfer Support List <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <941247766.328043.1476557532300(a)mail.yahoo.com> Content-Type: text/plain; charset="utf-8" Dear expert, I want to run recon-all for 100 subject simultaneously. I found the following link about it, but as I'm a beginner in this field, I don't understand how to use it. Would you please kindly give an example with a subject names, directory , etc. what should be written instead of * , or how could I define the number of subjects, ...? Thank you very much. https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/Two Best Regards F.Keyvanfard

2 1

Problem in upload file through ftp
by Cong 16 Oct '16

16 Oct '16

Dear freesurfer experts When I use command "put path/to/my/file”, it’s always appear an error "229 Entering Extended Passive Mode (|||37867|). 553 Could not create file”, if I use epsv command before put, then comes an error "227 Entering Passive Mode (132,183,202,158,147,237). 553 Could not create file”. Could you give me some advices? Best Wishes Cong Chen

2 1

group analysis
by charles laidi 14 Oct '16

14 Oct '16

Dear FreeSurfers, I would like to study the interaction between age and cortical thickness in patients and controls. My hypothesis is that there is an interaction and that cortical thickness is decreasing faster with age in patients than in controls. I have both Male and Female included in 6 different centers. I would like to consider also Gender and Site (6 centers) as confounds. My understanding is that I should perform a surface based group analysis with freesurfer. I am not able to find an example for my problem in the documentation https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V Would anyone had some tips to build the Fsgd file and the contrast file ? Thank you very much in advance. Best, Charles

4 4

MRI_segstats for adc.nii from dt recon - increasing decimal digits
by Chung, Yoonho 14 Oct '16

14 Oct '16

Hi! I ran mri_segstats as instructed in the wiki to extract ADC values from adc.nii. And as you can see below in my output, I think the decimal digits are truncated and missing the following decimal values. Is there an option or other way to get around this problem and extract ADC values from the ROIS with greater precision? Thank you! mri_segstats \ --seg $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --id 251 --id 3021 --id 3024 --id 3030 --id 12 --id 4 \ --i adc.nii --sum adc.stat # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 29 3001 344 2752.0 wm-lh-bankssts 0.0007 0.0001 0.0006 0.0009 0.0003 30 3002 450 3600.0 wm-lh-caudalanteriorcingulate 0.0009 0.0003 0.0006 0.0026 0.0020 31 3003 851 6808.0 wm-lh-caudalmiddlefrontal 0.0007 0.0001 0.0005 0.0010 0.0005 32 3005 337 2696.0 wm-lh-cuneus 0.0008 0.0001 0.0006 0.0011 0.0005 33 3006 82 656.0 wm-lh-entorhinal 0.0009 0.0001 0.0008 0.0016 0.0008

2 1

No cluster remains significant after multiple comparisons
by Karamfil Bahchevanov 14 Oct '16

14 Oct '16

Hello Freesurfer experts, I'm really struggling with my study. I have a 27 scans that I analyze in QDEC. Scans are from Siemens machine, mprage protocol, TR1620, TE 4.3, FOV 240*256, acq. matrix 232*256, slice thickness 0,9mm. After I enter model and have some initial significant clusters (threshold 2 - 5) I run multiple comparisons, and none have survived the procedures, no matter method or significance - FDR (0.1-0.05-0.01) or Monte-Carlo(0.05-0.01-0.01). This repeats no matter of the tested variables and the initial significancy and size of the clusters. I'm really confused of that and could not find an explanation, except that my study is really non-significant. However, the significant results I get are in the regions that I expect to be, that are reported previously and they also explain my results. If they happen to survive, but that never is the case (In fact one survived, but I entered wrong variables and model was wrong). What could be the reason? Outliers? Really non-significant results (which I doubt as I said already)? Should I recheck the quality of the processed scans? I also made my own average, hoping to improve things somehow, but QDEC doesn't allow me to run multiple comparisons with it. Anyway, is it mistake to discuss the results when they don't survive simulation, as they fit with initial hipothesis and what I'm testing. I have to point that there are only few significant clusters, that could not be explained with what I'm testing and tested population, so in fact the "noise" is very small. Any help will be of great value, Thanks

2 1

Warping an ROI from one subject to another
by Joel Bruss 14 Oct '16

14 Oct '16

I have two subjects, subA and subB. subA has a binary ROI mask, native space, that I'd like to place in subB's native space. Both subjects have been run through all stages of recon, edited, etc. Is there a better or easier way to achieve this than what I've run?: #Resample the native space binary ROI file into "brainmask" space mri_convert -rl /subA/mri/brainmask.mgz -rt nearest --no_scale 1 ROI.nii.gz /subA/mri/ROI.mgz #Convert ROI file into a label mri_cor2label --id 1 --c /subA/mri --i ROI.mgz --l ROI.label #Move label from subA to subB mri_label2label --srcsubject subA --srclabel /subA/mri/ROI.label --trgsubject subB --trglabel /subB/mri/ROI_to_subB.label --regmethod volume #Convert warped ROI label to a volume mri_label2vol --label /subB/mri/ROI_to_subB.label \ --subject subB \ --temp brainmask.mgz \ --regheader brainmask.mgz \ --o /subB/mri/ROI_to_subB.mgz #Convert the volume back to native subB space mri_convert -rl subB_native.nii.gz -rt nearest --no_scale 1 /subB/mri/ROI_to_subB.mgz ROI_to_subB_native.nii.gz A few follow-up questions: 1) When running mri_label2label, is better to use surface or volume for the "regmethod"? Which method will give me a better fit for my output? 2) The output I'm getting looks striped (there are holes in the binary mask) and doesn't quite fit the anatomy (the final file is shifted up and away from where I would expect it to be although in the general vicinity of what I would expect). It's almost as if I've chosen a wrong target or file along the way. I don't expect the fit to be perfect, but did I do something wrong? Thanks in advance to any and all replies. ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

5 17

GLM in groups with unequal size
by Eelco van Duinkerken 14 Oct '16

14 Oct '16

Hi all, I am using FS with data from 2 different studies that were acquired on the same MRI-machine with the same T1 and FLAIR sequences. Unfortunately, the group sizes are not very balanced, with 31 controls, 16 obese and 32 diabetes patients. Is the GLM for thickness used in FS very sensitive to this unequal group size? Thanks for the help, Eelco

4 8

issue with unpacksdcmdir
by Marco Loggia 14 Oct '16

14 Oct '16

Hello Doug and Freesurfers, We are having trouble unpacking DTI data collected in Bay7. Data are here: cd /autofs/eris/marco/tmp/seun The error I get is this one, which prevents the nii file from being created: ERROR: mri_convert child killed: segmentation violation It looks like the problem doesn’t occur for other data (E.g., BOLD, MPRAGE), so could it be only DTI-specific? More details are below, and the infodump.dat file is attached. Thanks! Marco ################## olaf:marco[195] cd /autofs/eris/marco/tmp/seun olaf:marco[196] unpacksdcmdir -src DTI_sevoEEG_006/ -targ . -generic -run 10 dti nii dti.nii -unpackerr $Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $ /autofs/eris/marco/tmp/seun -src DTI_sevoEEG_006/ -targ . -generic -run 10 dti nii dti.nii -unpackerr Thu Oct 13 17:13:49 EDT 2016 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/13-21:13:49-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: marco Machine: olaf Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 olaf Linux olaf 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Thu Oct 13 17:13:49 EDT 2016 Log File is ./unpack.log INFO: Logfile is ./unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is ./dicomdir.sumfile INFO: status file is ./parse.status Scanning directory Thu Oct 13 17:13:49 EDT 2016 mri_parse_sdcmdir --sortbyrun --d DTI_sevoEEG_006/ --o ./dicomdir.sumfile --status ./parse.status 0 2 4 6 8 10 12 15 17 19 21 23 26 28 30 32 34 36 38 41 43 45 47 49 52 54 56 58 60 63 65 67 69 71 73 75 78 80 82 84 86 89 91 93 95 97 100 Done scanning Thu Oct 13 17:14:01 EDT 2016 ------------------------------------------ 10 ep2d_diff_mgh_30dir_b1000_2000_10b0_tensor err 128 128 64 70 MR.1.3.12.2.1107.5.2.38.51006.2015051409122443188606899 unpacking config ------------------ {10 dti nii dti.nii} ----------------------------------- --------------------------------------------------------- Run 10 ----------------------------------------- Thu Oct 13 17:14:01 EDT 2016 10 dti nii dti.nii INFO: this run has an error, but trying anyway mri_convert DTI_sevoEEG_006//MR.1.3.12.2.1107.5.2.38.51006.2015051409122443188606899 ./dti/dti.nii --sdcmlist ./dti/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child killed: segmentation violation

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