Freesurfer March 2018

freesurfer@nmr.mgh.harvard.edu

115 participants
161 discussions

Freesurfer and crypt
by Bennet Fauber 19 Apr '18

19 Apr '18

I have a couple of users here who are reporting that on machines with FIPS enabled, which in turn disables certain cryptographic functions, FreeSurfer core dumps with a call to the crypt() function, which FIPS disables. Someone speculated based on output from strace that this is FreeSurfer possibly attempting to validate its license. Is this a known problem? Is there a solution? We have a university compliance office and possibly similar people from our local VA who are insisting that FIPS be enabled. If you need more information, please let me know and I will try to obtain it for you. Thanks, -- bennet

2 4

LME univariate data
by lanbo Wang 17 Apr '18

17 Apr '18

Dear Experts, Hi, There is no example detail on website of LME tutorial. I have some question about it. Could you send me the table of ADNI univariate example data? Thanks, Lanbo

2 8

Longitudinal strean including more than an image per time point
by Maria Paternina Die 16 Apr '18

16 Apr '18

Dear all, We want to run the longitudinal FS processing pipeline for our study, which has 4 time points. The 1st one was acquired with a radiofrequency head coil of 8 channels. Then, due to unexpected problems, some subjects at the 2nd time point were acquired with a different head coil of 16 channels. At time points 3 and 4, all subjects were scanned with the first head coil and only the subjects with different head coil at time point two were acquired twice (using both head coils). My question is: is there a way to do the longitudinal processing pipeline including more than an image per time point (one with the 16ch and the other with the 8ch)? If so, which will be the best procedure to follow? Thanks in advance for your time, Maria

2 1

ASEG and APARCSTATS2TABLE on longitudinal data
by Lisa Delalande 16 Apr '18

16 Apr '18

Hi FreeSurfer experts, I would like to use the asegstats2table and the aparcstats2table commands on my longitudinal data, which have been processing following the longitudinal pipeline (recon-all -cross, - base and finally -long). And I have two questions : 1) Am I obliged to do the ''long_stats_slopes --qdec ./qdec/longi_presentacio.qdec.table.dat --stats aseg.stats --meas volume --do-avg --do-rate --do-pc1 --time months'' command before using the aseg/aparc commands ? 2) And I would like to know which subjectsID I have to choose for the command line, example : asegstats2table --subjects *001_tp1 002_tp1*...etc. (cross)? OR *template_001 template_002*...etc (base)? OR *001_tp1.long.template_001 002_tp1.long.template_002*...etc (long)? Knowing that it's for a comparison test-retest (microlongitudinal : 1 month). Thanks you in advance for your precious help, Best regards, Lisa

3 2

Re: [Freesurfer] Longitudinal analysis using SLURM {Disarmed} (Martin Reuter)
by Backhausen, Lea 16 Apr '18

16 Apr '18

Hi Martin, thank you so much for your detailed answer. I will see how we can implement these modifications. Just two quick follow up questions: 1) I have half of the data already processed with the CROSS step using FS 5.3.0. Is it possible to use this data when running the TEMPLATE and LONG steps with FS 6.0.0 or would this corrupt results? 2) Our HPC system is known to have problems from time to time and jobs end up being killed. If the long_submit_jobs job gets killed prematurely would it just resume processing the data that hasn't been processed yet if I submit this job/script again? Thanks again for your help! Best, Lea Backhausen Research assistant Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Thursday, February 22, 2018 5:33 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 168, Issue 34 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. Re: Search angle limitation in the flirt registration (Douglas N Greve) 2. Re: Extracting the centroids from Desikan-Killiany atlas (zuxfoucault Wong) 3. Unsubscribe Mailing List (Duy Nguyen) 4. Unknown Label in following postprocessing with mne-python (Daniel van de Velden) 5. Re: Surface Errors (Emily Schwartz) 6. Re: Problem with cortical parcellation of rh but not lh (Amal Achaibou) 7. Re: Longitudinal analysis using SLURM {Disarmed} (Martin Reuter) 8. Re: Longitudinal analysis using SLURM {Disarmed} (Satrajit Ghosh) 9. Re: Longitudinal analysis using SLURM {Disarmed} (Martin Reuter) 10. Re: Freesurfer equivalent to fslmaths? (Bruce Fischl) 11. asymmetric parcellation error (Dijkshoorn, A.B.C. (Aicha)) ---------------------------------------------------------------------- Message: 1 Date: Wed, 21 Feb 2018 18:26:32 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Search angle limitation in the flirt registration To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <1e86b3d8-54c6-c9ad-54b3-7cc8df81c5ed(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed you should post your question to the FSL list (they developed and support flirt) On 02/21/2018 05:34 PM, Yixin Ma wrote: > Hi freesurfer developers and users, > > I'm writing to ask about the search angle limitation (--searchrx, -- > searchry and --searchrz) in the flirt function. I use the search angle > option a lot for limited angle search, which usually generate a better > registration result compared with the broad angle search. But I still > don't quite understand how rx,ry and rz are defined and how negative > and positive angles affect the result. Because sometimes I find the > result after the angle limitation does not align well with my > expectation of rotation angle. > > Thank you for your help, > > Yixin Ma > > Brain Image and Analysis Center > > Duke university > > > > _______________________________________________ > 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/ ------------------------------ Message: 2 Date: Thu, 22 Feb 2018 02:23:36 +0000 From: zuxfoucault Wong <zuxfoucault(a)gmail.com> Subject: Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAEUEyJPM6mZ5dSqN6ObDTuBgrEgALr6_USReiwQSHg8K3bW+9g(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Yes! I got better results now! Thanks!! On Thu, Feb 22, 2018 at 12:57 AM Kirstie Whitaker <kw401(a)cam.ac.uk> wrote: > Hi Foucalt, > > I think you need to set the threshold to slightly larger than 0 otherwise > you're taking the center of mass of the whole image (including the 0s) when > really you want to exclude the 0s and only look at the individual regions. > > I changed --thmin 0 to --thmin 0.1 and the results looked good. > > Kx > > On 21 February 2018 at 09:28, zuxfoucault Wong <zuxfoucault(a)gmail.com> > wrote: > >> Attach name file and result file. >> >> Thank you for your time! >> >> Best, >> Foucault >> >> On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong <zuxfoucault(a)gmail.com> >> wrote: >> >>> Hi Kirstie, >>> >>> Thank you very much for the suggestions! >>> I modified my snippet to prevent it from looping the same value and >>> still got the same results? >>> >>> ###### >>> input=($(cat ./names_68parc.txt)) >>> labels=() >>> hemis=() >>> j=0 >>> for i in "${input[@]}"; do >>> if [[ $i == lh_* ]]; then >>> hemis[j]="lh" >>> i=$(echo $i | sed 's/^lh_//g') >>> labels[j]="$i" >>> (( j++ )) >>> elif [[ $i == rh_* ]]; then >>> hemis[j]="rh" >>> i=$(echo $i | sed 's/^rh_//g') >>> labels[j]="$i" >>> (( j++ )) >>> fi >>> done >>> >>> nlabel=68 >>> if [[ ${#labels[@]} != $nlabel ]] && [[ ${#hemi[@]} != $nlabel ]]; then >>> echo " number of label not match " >>> fi >>> >>> >>> for hemi in lh rh; do >>> mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels >>> done >>> >>> for ((i=0;i<${#labels[@]};i++)); do >>> mri_surfcluster --in >>> /usr/local/freesurfer_orig/subjects/fsaverage/surf/${hemis[i]}.thickness >>> --clabel ./labels/${hemis[i]}.${labels[i]}.label --sum >>> ./labels/sum.${hemis[i]}.${labels[i]} --centroid --thmin 0 --hemi >>> ${hemis[i]} --subject fsaverage >>> tail -1 ./labels/sum.${hemis[i]}.${labels[i]} | sed 's/ */ /g' | cut >>> -d' ' -f6-8 >> ./labels/68parc.centroids.txt >>> done >>> ###### >>> >>> >>> The output message of mri_surfcluster: >>> ###### >>> thsign = abs, id = 0 >>> version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman >>> Exp $ >>> hemi = rh >>> srcid = >>> /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.thickness >>> srcsubjid = fsaverage >>> srcsurf = white >>> srcframe = 0 >>> thsign = abs >>> thmin = 0 >>> thmax = -1 >>> fdr = -1 >>> minarea = 0 >>> xfmfile = talairach.xfm >>> clabelfile = ./labels/rh.lateraloccipital.label >>> clabelinv = 0 >>> nth = -1 >>> sumfile = ./labels/sum.rh.lateraloccipital >>> subjectsdir = /usr/local/freesurfer_orig/subjects >>> FixMNI = 1 >>> Loading clabel ./labels/rh.lateraloccipital.label. >>> Found 5963 points in clabel. >>> ------------- XFM matrix (RAS2RAS) --------------- >>> >>> /usr/local/freesurfer_orig/subjects/fsaverage/mri/transforms/talairach.xfm >>> 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; >>> ---------------------------------------------------- >>> Reading source surface >>> /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.white >>> Done reading source surface >>> Computing metric properties >>> Loading source values >>> number of voxels in search space = 5963 >>> Done loading source values (nvtxs = 163842) >>> overall max = 3.19752 at vertex 122846 >>> overall min = 0 at vertex 0 >>> surface nvertices 163842 >>> metric props tot surface area 65020.839844 >>> group_avg_vtxarea_loaded 1 >>> masked surface area 4459.747559 >>> NOT Adjusting threshold for 1-tailed test >>> thminadj = 0 >>> Searching for Clusters ... >>> thmin=0.000000 (0.000000), thmax=-1.000000 (-1), thsignid=0, >>> minarea=0.000000 >>> Found 1 clusters >>> Max cluster size 82167.000000 >>> INFO: fixing MNI talairach coordinates >>> >>> >>> On Wed, Feb 21, 2018 at 3:15 PM, Kirstie Whitaker <kw401(a)cam.ac.uk> >>> wrote: >>> >>>> Hi Foucault, >>>> >>>> In the snippet you added you don?t define the labels variable (which >>>> you subsequently loop over in for label in ${labels}). >>>> >>>> There are two possible mistakes that are easy to fix. One may be that >>>> you forgot to read in the labels! And the other is that to get all the >>>> values in an array you need ${labels[@]}. >>>> >>>> I don?t think you need greater precision than you have. The regions are >>>> pretty far apart in mm terms :) >>>> >>>> Kirstie >>>> >>>> Sent from my iPhone, please excuse any typos or excessive brevity >>>> >>>> On 21 Feb 2018, at 03:44, zuxfoucault Wong <zuxfoucault(a)gmail.com> >>>> wrote: >>>> >>>> Dear Freesurfer experts, >>>> >>>> Based on this >>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/03333… , I >>>> wrote a short script to extract the centroids from Desikan-Killiany >>>> atlas. >>>> >>>> ###### >>>> for hemi in lh rh; do >>>> mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir >>>> ./labels >>>> for label in ${labels}; do >>>> mri_surfcluster --in >>>> /usr/local/freesurfer/subjects/fsaverage/surf/${hemi}.thickness --clabel >>>> ./labels/${label}.label --sum ./labels/sum.${label} --centroid --thmin 0 >>>> --hemi ${hemi} --subject fsaverage >>>> tail -1 ./labels/sum.${label} | sed 's/ */ /g' | cut -d' ' -f6-8 >> >>>> ./labels/68parc.centroids.txt >>>> done >>>> done >>>> ####### >>>> >>>> However, 1) the value is not precise enough, it is only one digit after >>>> decimal point. And 2) I kept getting the same value for each hemisphere. >>>> Eg,. >>>> 29.8 -20.7 18.0 >>>> 29.8 -20.7 18.0 >>>> 29.8 -20.7 18.0 >>>> 29.8 -20.7 18.0 >>>> 29.8 -20.7 18.0 >>>> 29.8 -20.7 18.0 >>>> 29.8 -20.7 18.0 >>>> >>>> I would appreciate if you have any suggestions regarding extracting >>>> centroids and the aforementioned issues! >>>> Thank you for your time! >>>> >>>> Best, >>>> Foucault >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> 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. >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> 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. >>>> >>>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> 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. >> >> > > > -- > Kirstie Whitaker, PhD > > Research Fellow, Alan Turing Institute > Research Associate, University of Cambridge > > *Mailing Address* > Brain Mapping Unit > Department of Psychiatry > Sir William Hardy Building > Downing Street > Cambridge CB2 3EB > > *Phone: *+44 7583 535 307 <+44%207583%20535307> > *Website:* https://whitakerlab.github.io > *Twitter:* @kirstie_j <https://twitter.com/kirstie_j> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 1

Running Linear Mixed Effects (LME) Model
by Kaushal, Mayank 13 Apr '18

13 Apr '18

Dear Freesurfer Community, Running lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex); gives the following error, Starting parallel pool (parpool) using the 'local' profile ... Error using parpool (line 104) You requested a minimum of 8 workers, but the cluster "local" has the NumWorkers property set to allow a maximum of 2 workers. To run a communicating job on more workers than this (up to a maximum of 512 for the Local cluster), increase the value of the NumWorkers property for the cluster. The default value of NumWorkers for a Local cluster is the number of cores on the local machine. Error in lme_mass_fit (line 137) parpool(prs); Error in lme_mass_fit_vw (line 73) [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e); I am running Matlab on a personal MacBook Pro, 2.4 GHz Intel Core i5, 8 GB 1600 MHz DDR3. I have researched the forum on how to stop the function from trying to initiate parallel processing but so far haven’t been able figure out how to overcome this. Any help would be much appreciated. Mayank Kaushal MD MBA Postdoctoral Fellow Department of Neurosurgery Medical College of Wisconsin

2 24

"preproc-sess" with intermediate volume
by David Sánchez Bestué 12 Apr '18

12 Apr '18

Dear all, I have a problem with the command: "preproc-sess" I wanted to use the Registration option to add an intermediate volume. The only documentation I could find about it was the one that appears with the command: "preproc-sess --help" Registration options -init-fsl : use fsl to initialize bbr registration -init-spm : use spm to initialize bbr registration (needs matlab) -init-header : use geometry to initialize bbr registration -bbr-int ifsd istem : use intermediate volume in sess/ifsd/RRR/istem I used the last flag in my line as follows: preproc-sess -s session_1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run -bbr-int ifsd istem I got this error: ERROR: could not determine file for ifsd/001/istem It seems that the path is not working but I do not why. The relevant paths are this: session_1/bold/001/f.nii session_1/ifsd/001/istem/orig.mgz Any help would be really appreciated! Thank you all Bests, David

2 3

[FSFAST]
by Walid Yassin 09 Apr '18

09 Apr '18

Hi Doug, Is it possible to run retinotopy-like analysis to reveal areas in the brain responsible for a certain phase of a presented stimuli? Say, instead of presenting 0 - 360 degrees of rotating wedge per cycle, we would like to present arbitrary scale of 0 - 100 of a particular stimulus feature, that does not necessarily differ in their retinotopic locations. We thought, if we pretend that scale-0 is equivalent to a wedge of 0 degree, and scale-50 is equivalent to a wedge of 180 degrees, and so on, we would be able to map the cortical area corresponding to each value of the scale. However, the retinotopy protocol of freesurfer requires the input of a stimulus type “e.g. polar or eccen” and direction “e.g. pos or neg”, so our analysis won’t work as we intend. Running Freesurfer v5.3.0 Thank you Walid

3 5

mri_glmfi-sim multi-thread
by Dowling, Kevin Francis 08 Apr '18

08 Apr '18

Dear Freesurfer Experts, My apologies for what might be a very simple question, but I have been unable to locate an answer in the archives/wiki. Our group is trying to cut down on our mri_glmfit-sim time (as we are hoping to run mri_glmfit-sim -sim mc-full, rather than -sim mc-z). I know that --bg will split up the larger number of simulations into n background jobs, but I also noted the warning that this option is not to be used on the Martinos launchpad computational cluster. As we are hoping to find a way to use launchpad, I was wondering if mri_glmfit-sim is multi-threaded (or can be multi-threaded similar to -parallel flag in recon-all)? We are currently running Freesurfer 5.3, but can move up to 6.0 if needed. (Our specific command is: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../glmdir --sim mc-full 2.3 1000 mcfull1000_2.3 --sim-sign abs --cwpvalthresh .05) Thank you in advance for your help! Kind regards, Kevin Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.3215

2 1

which dev version for amygdala segmentation
by Anik Dar 04 Apr '18

04 Apr '18

Hi All, How do I download reqd. files / FS developmental version to run hippocampal/amygdala pipeline as described in the wiki https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… I tried downloading the el capitan version of the development version of freesurfer from the https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall and I cant find any code segmentHA_T1.sh Can anyone help, Thanks Ani

2 1

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Freesurfer March 2018