Freesurfer April 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
229 discussions

v.5.3 Longitudinal Analysis on v.5.0 processed scans
by Elijah Mak 04 Jun '14

04 Jun '14

Greetings Freesurfer Community, I am running a longitudinal study using Freesurfer v.5.3 to compare rate of cortical thinning between 2 groups of subjects. I hope I can seek some expert advice on the following situation: All data (both the baseline and follow-up) has been processed independently using recon-all. This has been done on Freesurfer 5.0. Since then, I have upgraded to Freesurfer v5.3 to utilize the linear mixed effect capability. For the construction of base and longs, I understand that it is important to add -clean flag to my recon-all strings to overwrite brainmask.mgz etc. When must this be done? I am still new to Freesurer, and I'd greatly appreciate any advice regarding workflow. Many Thanks, Elijah -- Elijah Mak, B.A. Doctoral Candidate *|* Psychiatry University of Cambridge *| *Department of Psychiatry Trinity College, Cambridge, CB2 1TQ

2 4

normalization problem (versions 5.1 and 5.3)
by Maia Pujara 23 May '14

23 May '14

Hi all, After running 200+ subjects through recon-all using version 5.1, all but 30 came back with complete surfaces. The 30 that failed seem to have the same problem with normalization. After re-running these 30 subjects with v5.3, we were able to get a good quality brainmask.mgz output, which was not the case when we ran these subjects through v5.1. See attached for comparisons of v5.1 and v5.3 outputs. Would we need to be adding additional flags to get 5.1 to produce usable results for these subjects? Or might there be some other workaround for this? Thanks in advance! Maia

2 5

Re: [Freesurfer] R: Filipping issue
by Douglas N Greve 21 May '14

21 May '14

Hi Paola, please remember to post to the list and not to us personally. thanks! I would still use the xhemi tools for this. If you have N subjects, you will get 2*N surfaces aligned to the fsaverage_sym atlas. You can then just pick the ones you want to analyze further doug On 04/22/2014 08:34 AM, Paola Valsasina wrote: > Dear Doug, > > We have followed your suggestion and we performed the recon-all analysis for > all study subjects (till autorecon3) on non-flipped images. > > I am now reading the instructions on the wiki about the xhemi tool, but I am > not 100% sure they apply to our case. > > The wiki instructions describe a comparison between LH and RH within > subjects (i.e., an analysis of cortical asymmetry), whereas we would like > simply to L-R flip the final surfaces of patients having a RH damage, so > that all patients have the damage in the LH. > Then, we would like to compare them with control subjects. > > For this purpose, is it sufficient to register the patients lesioned in the > RH to the symmetric template with the --xhemi option? > > (i.e. surfreg --s subject_name --t fsaverage_sym --xhemi --rh --lh) > > Then, how do we perform final statistical analysis? > > Thank you in advance for any suggestion! > Kind regards > Paola > > > > Paola Valsasina, MSc > Research Fellow > Neuroimaging Research Unit (Director Prof. M. Filippi) > Institute of Experimental Neurology, Division of Neuroscience, > Scientific Institute and University "Vita-Salute" San Raffaele > Via Olgettina 60, 20132 Milan, Italy > > -------------------------------------------------------------------------- > IL MIO 5XMILLE VA AL SAN RAFFAELE DI MILANO > PERCHE' QUI LA RICERCA DIVENTA CURA. > CF 07636600962 > SE NON QUI, DOVE? > Info: 5xmille(a)hsr.it - http://www.5xmille.org/ > > > Disclaimer added by CodeTwo Exchange Rules 2007 > http://www.codetwo.com > > -----Messaggio originale----- > Da: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Per conto di Douglas N Greve > Inviato: giovedì 13 febbraio 2014 21.50 > A: freesurfer(a)nmr.mgh.harvard.edu > Oggetto: Re: [Freesurfer] Filipping issue > > > Definitely #2. You should use the xhemi tools > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi > First run them through recon-all as normal, then follow the steps on the > wiki. Contact the list again to get instructions for the final analysis. > > doug > > > On 02/13/2014 08:23 AM, Paola Valsasina wrote: >> Dear List, >> >> we are starting the analysis of cortical thickness for a group of >> patients who have only one side affected. The majority of patients >> have the left hemisphere affected, but some patients have the right >> hemisphere affected. In order to do a group analysis, we would like to >> flip the images of some patients, so that the affected side is left >> for all subjects. >> >> Which is the best way to do this: >> >> 1)flip the 001.mgz volume and perform the entire recon-all pipeline >> with flipped images; >> >> or >> >> 2)perform the recon-all pipeline with the non-flipped volumes and flip >> only the final surfaces for statistical purposes? >> >> Thank you for any suggestion >> >> Kind regards >> >> Paola >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 10

A newbie to fMRI analysis
by Dr Sampada Sinha 20 May '14

20 May '14

Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file as well into the Applications/freesurfer directory. I have run into the first problem and that is of data conversion. My file is in dcm format and I have 11,000 dcm files to convert. However, before I was using Jamaan Alghamadi created gui and it is not able to convert the mri dcm files. Then I shifted to UNIX and again it is saying error. My file is on the desktop and I have given it subject id as Grace. My directory to the dcm file is '/Users/sampada/desktop/Grace. My terminal look like this before I proceed with the file conversion Last login: Mon Apr 28 15:10:13 on ttys001 dhcp020-223-179:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Will anyone please let me know what I am doing wrong? I will be very grateful for any input. Thanks and regards, Sampada Senior research support specialist Molecular and neuroimaging department Department of Psychiatry 451, biomedical research building University at Buffalo (south campus) Buffalo, NY-14216

5 19

TRACULA preprocessing error, FreeSurfer 5.2.0
by McGinnity, Colm 16 May '14

16 May '14

Dear Experts, I am very new to TRACULA, I apologise for what is probably a silly question. I've got the following error on running trac-all -prep (FreeSurfer 5.2.0): awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or directory) mri_concat --i /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz --mean --o /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz niiRead(): error opening file /home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz Can anyone tell me what this means and how to fix this, please? I'm guessing I've set up my configuration wrong or have the files in the wrong place? Many thanks! Best wishes, Colm. King's College London

3 7

Re: [Freesurfer] NHP surface reconstruction in FS5.3
by S.V.Shepherd [work] 13 May '14

13 May '14

I believe ventricles and callosum are correctly labeled. I've been viewing with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs '''. I've uploaded ( as per the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file contents of my Otis's mri/ directory, as SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. I hope this will be enough? Ares of concern are * ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow grey from CC? * OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too bright. * Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual overpaint. stephen Hi Stephen Are the ventricles and callosum correctly labeled? If you upload a subject I'll try to take a look Cheers Bruce > On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]" > <stephen.v.sheph...(a)gmail.com> wrote: > > Greetings, > > I've been reconstructing a surface in an NHP using a Kolster T1 scan and > FS5.3. It went very well, at first, but I've hit a wall. I have trouble in > occipital (due to poor signal strength/constrast) and some typical-with-NHP > problems in ACC and OFC. I think there are three related questions. > > 1) I lose parts of the ACC near the genu of the corpus callosum. I have > attached a screen shot -- the white matter and gray matter both look decent. > I wondered if the corpus callosum might be handled specially, and if > differences between human and nhp callosi might prevent the ACC from growing > normally? > > 2) In trying to deal with this, I greyed out the ACA, which was bright and > potentially confounding. I wasn't sure how to do this in > brain.finalsurfs.manedit, since my understanding is that only 1s (nonbrain) > and 255s (wm) were preserved. I tried brain, which got overwritten, but > ultimately succeeded by editing brainmask and rerunning -autorecon2-wm. Is > there a way to repain gray matter in brain.finalsurfs.manedit? Alternately, > if I continue editing brainmask (or equivalent) directly, should I be > darkening or lightening the gray matter in the excluded section of the ACC? > I would assume lighten -- but in the OFC, some gray matter (not shown) > appears to be excluded for being too bright. > > 3) In some places I've specified wm (e.g. in the ACC, here) but it hasn't > stuck. I assume this is because autorecon isn't convinced by the wm > specification after looking at brain.finalsurfs -- how might I (gently!) > override this? > > Thanks very much for your time and patience. > > stephen > > <Capture1.PNG><Capture2.PNG>

2 14

Coordinate transformation to average surface space
by ISAAC PEDISICH 05 May '14

05 May '14

Hi All, I am attempting to transform sets of coordinates from subject CRS space into the surfaceRAS space of an average subject, made with make_average_subject. By our current method, we register the individual CT to the average surface using mri_robust_register with the command: mri_robust_register --mov [subj_CT].img --dst average_orig.mgz --lta reg_avg.lta --iscale --satit and then check and adjust the registration with: tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average These steps work fine, and when I load the average brain in freeview, then load the subject CT with with the registration file reg_avg.lta applied, the two overlap just as they should. However, when I attempt to do the same thing in matlab, some (though not all) of the subjects present a problem. I do the coordinate transformation (as suggested on http://freesurfer.net/fswiki/CoordinateSystems) by applying: inv(Reg_avg) * Tmov * CT_coords with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as reg_avg.lta, and CT_coords as the relevant coordinates in CRS space from the CT (with a vector of ones appended). As I said, some of the scans come out fine, with the coordinates in the correct place on the average surface, while others are very far removed from their correct location. How can I fix this? Thanks, Isaac

3 9

brain.finalsurfs.mgz editing
by Khadka, Sankalpa 02 May '14

02 May '14

Dear freesurfer community, My question is directed to those who have experience with editing brain.finalsurfs.mgz. According to the tutorials, after making edits on brainmask.finalsurfs.mgz (which is normally done when the pial surface is not accurate), we can run, recon-all -autorecon-pial -subjid subj" However, I found an anomaly when I looked at the steps that -autorecon-pial flag goes through. The very first step of autorecon-pial flag is "mri_mask" command. This takes brain.mgz and brainmask.mgz as inputs and gives brain.finalsurfs.mgz as output. Now, if we have made edits on brain.finalsurfs.mgz, it will be overwritten by the new one and hence our edits won't take an effect. I ran few experiments too. First, I made edits on brain.finalsurfs.mgz and ran recon-all with autorecon-pial flag. I ended up with a new brain.finalsurfs.mgz and my edits did not make any changes. Second, I made edits on brain.finalsurfs.mgz and ran with white, smooth2, inflate2, autorecon3 flag (basically starting from mri_make_surfaces command). On doing so, the edits made desirable changes and brain.finalsurfs.mgz remained intact. Third, I made changes on brainmask.mgz and brain.mgz (inputs for mri_mask). It also works as expected. Finally, I also followed the recommended steps from the tutorial by creating brainmask.finalsurfs.manedit.mgz, however, the edits from "manedit" were not carried on to brainmask.finalsurfs.mgz Could anyone please shed some light on this? What would be the best strategy to follow? Thank you, Sankalpa

2 1

per voxel regressor in LME toolbox?
by Marnie Shaw 02 May '14

02 May '14

Dear Freesurfers, Is there a way to include a per voxel regressor in an LME model within the matlab LME toolbox? Just like you can do with mri_glmfit? Cheers, Marnie

3 4

Multi-echo FLASH
by Jon Houck 02 May '14

02 May '14

Hi all, I'm building a scan protocol for what is primarily a MEG study, which needs T1 information for co-registration and T1/T2 information to construct an accurate BEM from the inner skull surface. It seems like the two multi-echo FLASH sequences at 5 and 30 degrees would give me all of the information that I need without an MPRAGE, but I'm not sure how well the two MEFs work in the standard Freesurfer pipeline. Would it be reasonable to acquire no MPRAGE but two MEF sequences at 5 and 30 degrees, combine them following the method from https://surfer.nmr.mgh.harvard.edu/fswiki/MEF, and send the resulting T1 to recon-all? With my scan time constraints, the alternative would be to acquire a multi-echo MPRAGE and a single 5-degree MEF. Thanks for any help on what is probably a naïve question. Jon Houck

2 2

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 April 2014