Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Post-Doctoral position in brain imaging – University of Geneva {Disarmed}
by Narly Golestani 03 Nov '15

03 Nov '15

?Applications are invited for a Post-Doctoral position in the Brain and Language Lab (www.brainandlanguagelab.org<http://www.brainandlanguagelab.org/>) at the University of Geneva. The position is for 2 years (or more), and will be at the new Biotech Campus (http://www.campusbiotech.ch/en/) Candidates should have a degree in Psychology and/or Cognitive Neuroscience, and should have a solid background in statistics and in the analysis of functional magnetic resonance imaging data. The projects will include brain imaging and behavioural studies on multilingualism and expertise, with a focus on executive skills, attention and statistical/language learning. The salary is competitive, starting salary at ~ 69, 000 CHF/year (~ 81, 000 CHF/year as of August 2016) depending on experience. The position is available immediately, and applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (Narly.Golestani(a)unige.ch) Applications including a CV, a statement of research interests, and the names and full contact details of three referees should be sent to: Narly.Golestani(a)unige.ch<mailto:Narly.Golestani@unige.ch>. ?----------------------------------------------------------------------------------------------------------------------------------------------------------------- Brain and Language Lab Department of Clinical Neuroscience Biotech Campus 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 http://www.brainandlanguagelab.org<https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…> ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

1 0

Freesurfer 6.0
by Hoptman, Matthew 03 Nov '15

03 Nov '15

Hi all, I can see a link for Freesurfer 6.0 on the website, but when I click on it to download, it just blinks at me. I also tried to ftp to your ftp site, and unfortunately, I got the message 421 Proxy is closed (unknown user location). Could you please tell me how I could get the new version of Freesurfer? Thanks, Matt IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

3 2

Re: [Freesurfer] visualizing paths stats by voxel
by Janosch Linkersdörfer 03 Nov '15

03 Nov '15

Hi Anastasia and list, sorry, I just now got around to testing out the new build of dmri_paths you sent me. Sadly, the results look about the same: Here the path stats file for the left SLFt: What could be the problem?! I think I did what you suggested: - install the new version of dmri_paths (https://www.dropbox.com/s/g6i7rcnbegwj5pm/dmri_paths?dl=0) and make it executable - rerun trac-all -path for the subjects with only one time point - rerun trac-all -stat for all subjects Also: Is that problem only a visualization problem, or does it also mean that the values I get for a participant at a specific part of a tract are not aligned and I cannot analyze the data in that way? Thanks for your help!! Best, Janosch > On 20 Aug 2015, at 21:35, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > Hi Janosch - Indeed, someone has to be first. I'll send you a fresh build of dmri_paths tomorrow. You'll have to replace your copy of $FREESURFER_HOME/bin/dmri_paths with it and then rerun "trac-all -path" only for the subjects that have 1 time point. Then rerun "trac-all -stat" with all subjects together. And then tell us what other problem you find :) > > Best, > a.y > > On Thu, 20 Aug 2015, Janosch Linkersdörfer wrote: > >> Hey Anastasia, >> >>> Am 19.08.2015 um 14:03 schrieb Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >>> >>> >>> Hi Janosch - There is a bug in how the output paths are saved when longitudinal TRACULA is run with one time point only. I'm working on a fix. >> >> OK, then I'm relieved that it isn't an error on my side. Thank you very much for looking into it! >> >>> In the meantime, you can try your analysis with the subjects that have multiple time points and you won't be affected by this problem. I can see that the subjects with a single time point are about 1/3 of your sample, and so you may not want to drop them completely. >> >> Yeah, it's children's data, so I'm happy about every measurement we got. I'll be waiting for the fixed script to be able to include all subjects in the analysis... >> >>> >>> Thank you for trying things that nobody else has tried and finding these bugs! >> >> Somebody has to be the first, eh? :) >> >> Thank you very much, >> >> Janosch >> >>> >>> More soon, >>> a.y >>> >>> On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote: >>> >>>> Hey Anastasia, >>>> >>>> thanks for looking into this. >>>> >>>>> Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >>>>> >>>>> >>>>> Hi Janosch - Looking at the stats files of your subjects, just by a quick count of the number of lines, I see that there are some subjects that have only 1 time point and some that have multiple time points, and that the pathstats.byvoxel.txt files have different lengths between those two types of subjects. >>>>> >>>>> I suspect that the strange average path that you get has to do with how this mixing of subjects was done. Did you run the subjects with a single time point through the longitudinal stream as well? >>>> >>>> Yes, I ran the longitudinal stream for all subjects, also for the ones with only one time point. >>>> >>>> Thanks, >>>> >>>> Janosch >>>> >>>>> >>>>> Best, >>>>> a.y >>>>> >>>>> On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote: >>>>> >>>>>> Hi Anastasia, >>>>>> >>>>>> yes, I am. But it looks similar in the distributed version :( >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Janosch >>>>>> >>>>>>> Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: >>>>>>> >>>>>>> >>>>>>> Hi Janosch - Are you by any chance using the dev version of freeview? >>>>>>> >>>>>>> a.y >>>>>>> >>>>>>> On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote: >>>>>>> >>>>>>>> Hi Anastasia and list, >>>>>>>> >>>>>>>> I'm trying to do analyses along the tract with the path_stats_byvoxel files. >>>>>>>> >>>>>>>> When I am visualizing the points using the waypoint functionality of Freeview, it looks a little strange, i.e., the points are not equally spaces on the tract, but clumped together at some parts and spread out on others, see: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> this looks different to your slides: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Also, the most posterior points seem to be strangely located (in the other hemisphere). What could be the reason for this strange behavior? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Janosch >>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the person to whom it is >>>>>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>>>>>> contains patient information, please contact the Partners Compliance HelpLine at >>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in error >>>>>>> but does not contain patient information, please contact the sender and properly >>>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >> >> >>

2 2

Adding more than 2 covariates in QDEC
by Deborrah Castillo 03 Nov '15

03 Nov '15

I wanted to ask if it is possible to run analysis in QDEC with more than 2 covariates for examples, instead of Age, I wanted to add depression scores or race? At the moment my qdec table has two groups, two covariates... Class Group1 Class Group2 Variables Age PainMeasure If it is not possible, what is other alternate method would you suggest I could use to run analysis to look at group differences in brain measures with covarying for Age and Race / Depression Score in FreeSurfer? Thank you. Aloha, Deborrah -- -- University of Hawaii John A. Burns School of Medicine Department of Medicine Neuroscience and Magnetic Resonance Research Program Queens Medical Center, 7th Floor UH Tower 1356 Lusitana Street Honolulu, HI 96813 Tel:+1-808-586-7488 Tel: +1808-586-7459 Fax:+1808-586-7465 Web: http://hawaii.edu/mri/home_v6.htm

2 1

cortical thickness - comparing two groups within a ROI
by Eryilmaz, H. Hamdi 03 Nov '15

03 Nov '15

Dear FS experts, I have a question about extracting average cortical thickness from a manually created ROI. I am comparing 2 groups, namely PostFort and PreFort and my fsgd file appears as the following: GroupDescriptorFile 1 Title PostPreFortification Class PostFort Class PreFort Input Subject1 PostFort Input Subject2 PostFort . . . The contrast that I use to compare these groups is [1 -1]. When I display the significance map for this contrast I get the following image on the left hemisphere: [X] My first question is, those blue clusters represent regions, where thickness is greater in the PreFort group, don't they? Assuming this is correct, I created a label for this region (which contains about 3000 vertices) and extracted the thickness value from this region for each subject using the following commands. These commands are part of scripts in which $subject and $label are defined. [X] to make a label for each subject (the original label was created on fsaverage): mri_label2label --srclabel $SUBJECTS_DIR/labels/${label}.label --srcsubject fsaverage --trglabel $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject --regmethod surface --hemi lh to create a stats file of this ROI containing several anatomical measures: mris_anatomical_stats -f $SUBJECTS_DIR/$subject/stats/lh.NP_PostMINUSPre_IPS.label.stats -l $SUBJECTS_DIR/$subject/label/NP_PostMINUSPre_IPS.label $subject lh to compile thickness values from all subjects into one table: aparcstats2table --hemi lh --subjectsfile $SUBJECTS_DIR/Subject_Files/RPDR/214_PrePostFort --parc NP_PostMINUSPre_IPS.label --meas thickness --tablefile $SUBJECTS_DIR/Analyses_Thickness/Tables/LH_NP_PostMINUSPre_IPS_stats.txt This table displays the average thickness value of my ROI for each subject. Based on this table I calculated the mean thickness for each group, which is as the following: PostFort: 3.043 PreFort: 2.842 My question is: If this cluster appears blue in the Post>Pre map, shouldn't the thickness have been greater in the PreFort group? Or am I missing a step? Many thanks in advance! Best, Hamdi

2 6

Postdoctoral Scholar in Neuroimaging of Epilepsy and Brain Tumors UCSD
by Leyden, Kelly 03 Nov '15

03 Nov '15

Dear Freesurfers, I am writing on behalf of Dr. Carrie McDonald to advertise a Postdoctoral position with our lab at UC San Diego. Location: UCSD Multimodal Imaging Laboratory (MMIL) UCSD Center for Translational Imaging and Precision Medicine (CTIPM) Start date: Flexible, but no later than January 2016 Seeking a full-time postdoctoral scholar to work with a multidisciplinary team of scientists on projects related to the use of multimodal imaging for improving cognitive and health outcomes in patients with epilepsy and primary brain tumors. Our multimodal imaging team includes full-time faculty from Psychiatry, Radiology, Neurosciences, and Radiation Oncology. This group of researchers and clinical investigators are primarily focused on integrating research imaging tools into the clinical work flow to directly and immediately improve patient outcomes. The scholar will work closely with other postdoctoral fellows, medical residents, graduate students, research assistants, and faculty members to help develop methods, analyze structural, diffusion, and functional (fMRI) imaging data, prepare manuscripts and assist with grant applications. The fellow should have strong programming (i.e., MATLAB) and writing skills, experience in neuroimaging or a related field, and a strong interest in pursing an academic career path. Applicants with a strong background in bioengineering, cognitive science, and/or experience working with neurological populations are encouraged to apply. Please send CV and cover letter to Dr. Carrie McDonald (camcdonald(a)ucsd.edu<mailto:camcdonald@ucsd.edu>). Thank you, Kelly Kelly Leyden, MRes Neuroimaging Research Associate Multimodal Imaging Laboratory University of California San Diego kleyden(a)ucsd.edu

1 0

Monte Carlo in mri_glmfit-sim
by smcl＠u.washington.edu 03 Nov '15

03 Nov '15

Hi experts, I am having trouble performing a Monte Carlo correction using mri_glmfit-sim. My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I then ran mri_glmfit on the data. I want to do my analysis/correction only in auditory cortex (AC) so I did my own simulation in AC of each hemisphere using mri_mcsim (as per http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo) So far, so good. But when I try to run: mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it didn't help. Any thoughts? Also, can you clarify which comparison neg vs pos will give me? Thank you, Susan McLaughlin, PhD Research Scientist Laboratory for Auditory Brain Sciences & Neuroengineering Institute for Learning & Brain Sciences (I-LABS) Portage Bay Bldg. Room 204 University of Washington, Box 357988 Seattle, WA 98195-7988 Ph: (206) 616-0102 Fx: (206) 221-6472 Cell: 206-850-8638 E-mail: smcl(a)uw.edu

2 8

First-level analysis (native vs fsaverage)
by Rodriguez-Thompson, Anais 03 Nov '15

03 Nov '15

Hi freesurfer experts, I have a question about how running first-level analyses in either native space or fsaverage space changes activation. My original analysis was a per-session analysis run on native space. The command used to make the analysis was ANALYSIS 1: mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_050514 -TR 2 -paradigm slopepar -event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt -native -fwhm 5 -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 However, my lab was interested in running our analyses -per-run, so I created a new per-run analysis on the fsaverage brain using the command: ANALYSIS 2: mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915_lh -TR 2 -paradigm slopepar -event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt -surface fsaverage lh -fwhm 5 -per-run -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refevendur 2 -fsd bold The group maps for the two looked comparable. However, I covaried those maps with performance on our task. The maps looked significantly different, and while 9 cluster survived MC correction from analysis 1 (3 LH, 6 RH), only 3 survived MC correction from analysis 2 (0 LH, 2 RH). I thought that the difference could have been due to per-run vs. per-session MC, but I created a test analysis (per-session, fsaverage space), and this analysis looked more like the 2nd analysis than the 1st, leading me to believe that the difference in activation was due to running the first-level analysis on fsaverage space rather than native space. The command I used for the test analysis was: mkanalysis-sess -analysis TEST_fsaverage_persession_lh -TR 2 -paradigm slopepar -surface fsaverage lh -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 -fwhm 5 -per-session Do you know why running first-level analyses on fsaverage space rather than native space would decrease activation effects, leading to fewer significant clusters after MC correction? I've attached a pdf file with the maps in question. Thanks, Anais

2 5

R: Re: average z-score of each subject from a common cluster
by stdp82＠virgilio.it 03 Nov '15

03 Nov '15

Thanks.I have obtained: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh aparc --i z.nii.gz --sum summaryfile sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano UseRobust 0 Loading z.nii.gz Loading z.nii.gz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 22 segmentations Computing statistics for each segmentation 0 -7 2 2.000 1 -6 110 110.000 2 -5 255 255.000 3 -4 518 518.000 4 -3 1190 1190.000 5 -2 1692 1692.000 6 -1 4104 4104.000 7 0 61577 61577.000 8 1 42598 42598.000 9 2 28146 28146.000 10 3 14859 14859.000 11 4 5845 5845.000 12 5 1899 1899.000 13 6 485 485.000 14 7 116 116.000 15 8 75 75.000 16 9 74 74.000 17 10 78 78.000 18 11 65 65.000 19 12 104 104.000 20 13 45 45.000 21 14 5 5.000 How I can know the meaning of this number? Where is z? I have tried also with:mri_segstats --seg z.nii.gz --annot Control_21 rh aparc --i z.nii.gz --sum summaryfile --mask .../fc.ramgseed.surf.rh/R_Amygdala/my-glm.wls/group.diff/cache.th13.neg.sig.masked.nii.gz --avgwfvol mrivol but I have problem with interpretation. Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 30-ott-2015 16.17 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] average z-score of each subject from a common cluster On 10/30/15 7:16 AM, stdp82(a)virgilio.it wrote: Hi list, I have two queries, please. I'd like to have the z-score from my rsfMRI data (seed-analyis). 1) I have extract the z-score from the Vtx Max In details, after groups comparison analysis, I have opened the cache.th13.pos.sig.cluster.summary contained in group.diff folder and I have read the Vtx Max coordinates. Next, I have open the z.nii.gz of each subject and I have expected the z-score from the vertex which have the Vtx Max coordinates. Is this procedure corrected? Yes 2) z-score of each subject from a common cluster I would like to use the cluster which shows the group difference (cache.th13.pos.sig.cluster.nii.gz) as ROI mask. Thus, I would extract from it the average of the z-score which is contained in each subject. How should I do? Use mri_segstats passing the z map as the input (--i) and the cluster map as the seg. The output will be --sum. Run with --help for more info Thanks. Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

R: Re: error vcsf.config
by stdp82＠virgilio.it 03 Nov '15

03 Nov '15

Yes, the ventricle is very small. The segmentation in aparc and aseg is nice.How can I do to analyze this subject? I need to include it in the analysis.Many thanks, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 30-ott-2015 16.03 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] error vcsf.config That means it could not find any CSF voxels. Try checking the registration. It could also be that this is a subject with really small ventricles. On 10/30/15 3:57 AM, stdp82(a)virgilio.it wrote: Hi list, During fcseed-sess -s subj -cfg vcsf.config a subject produces the follow error. I have rerun recon-all, cheched aparc+aseg with tkmedit. They seem to be ok. Why this error is produced? Thanks Stefano Creating output directory /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm Loading y from /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz Saving design matrix to /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/Xg.dat Normalized matrix condition is 61.5872 Matrix condition is 1e+08 Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/mask.mgh search space = 0.000000 DOF = 297 Starting fit and test Fit completed in 0.0008 minutes Computing temporal AR1 Writing results Computing FSNR mean maxvox sig=0 F=0 at index 0 0 0 seed=1446518089 linear maxvox sig=0 F=0 at index 0 0 0 seed=1446518089 quad maxvox sig=0 F=0 at index 0 0 0 seed=1446518089 Computing PCA (300) ERROR: no voxels in mask _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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