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Re: [Freesurfer] Help with MRI segstats
by Greve, Douglas N.,Ph.D. 07 Aug '19

07 Aug '19

You should only pass one of --seg, --annot, or --slabel to mri_segstats. I don't understand how you are trying to use this in the context of your permutation. Is this something that you are running on each iteration? If so, it is probably not what you want to do. Probably you want to run mri_surfcluster to get the cluster sizes out. On 8/7/19 1:31 PM, Daliah Ross wrote: > > External Email - Use Caution > > This is the command line: > mri_segstats --seg F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.mgh > --annot lh.aparc.annot lh parc --slabel fsaverage lh cortex --sum > F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.txt > > We are running the permutations within FS, but because our model is a > linear mixed model, and we didn't think that this would be compatible > with fspalm. So, we are running the permutations "manually" (i.e. we > are generating the random permutations, which in our case is just > switching the subject labels for the thickness data. We are then using > mri_surfcluster to extract the maximum cluster size per permutation > and will use the permutation distribution to determine our the > statistical significance of our results). In addition, our analyses > are a bit out of the ordinary in that the thickness data are an > independent variable in our model, for which we have a repeated > non-imaging measure as the outcome. Effectively, we are using the > thickness maps to generate vertex-wise regressors, with a fixed > outcome measure (fixed in the sense that it doesn't vary across the > brain). > > If you have any thoughts about how we could use fspalm in our case, > your advice would be most appreciated. > > Thanks again, > Daliah > > *Daliah Ross* | dross3(a)mail.yu.edu <mailto:dross3@mail.yu.edu> > > Ph.D. Student, Clinical Psychology with Health Emphasis > Ferkauf Graduate School of Psychology > Yeshiva University > Albert Einstein College of Medicine > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > <freesurfer-bounces(a)nmr.mgh.harvard.edu > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of > Greve, Douglas N.,Ph.D. > Sent: Tuesday, August 6, 2019 12:56 PM > To: freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Help with MRI segstats > > Can you send command lines? Also, are you using the built-in > permutation tool or trying to do something outside of FS? > > On 8/6/19 8:40 AM, Daliah Ross wrote: > > > > External Email - Use Caution > > > > Hi FreeSurfer experts, > > > > I have a couple of questions regarding mri_segstats tool for an > > analysis on vertex-wise cortical thickness data. We are > attempting to > > compare maximum cluster sizes among permutations. We are having > > trouble figuring out how to get the anatomical label for each > cluster > > using the --slabel argument. We are also wondering if the > difference > > between cluster sizes between mri_surfcluster and mri_segstats > is due > > to partial volumes, and if so, how to correctly use the --pv > argument. > > It suggests in the wiki page that mri/norm.mgz volume is usually > used > > but I believe we need something surface-based since we are using > > thickness data. > > > > Thank you in advance for any help you can provide. > > > > Best, > > Daliah > > > > *Daliah Ross* | dross3(a)mail.yu.edu <mailto:dross3@mail.yu.edu> > <mailto:dross3@mail.yu.edu <mailto:dross3@mail.yu.edu>> > > > > Ph.D. Student, Clinical Psychology with Health Emphasis Ferkauf > > Graduate School of Psychology Yeshiva University Albert Einstein > > College of Medicine > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail > > .nmr.mgh.harvard.edu > <http://nmr.mgh.harvard.edu>%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C0 > > 1%7Cmark.wagshul%40einstein.yu.edu > <http://40einstein.yu.edu>%7Cfde693609070412c457808d71a8f16f2% > > > 7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C637007074183066654&sd > > ata=ALndUpHJ%2BYhuMzChviSn9ygf8H112mUKvVmJktGoqB4%3D&reserved=0 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… >

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Re: [Freesurfer] Transform hippocampal/amygdala segmentation to another space
by Jessica Bourgin 07 Aug '19

07 Aug '19

External Email - Use Caution Dear Juan Eugenio, Thanks a lot for your quick response. I don't understand what you mean exactly by "propagate the hard segmentations". And when you say to register the subjects to the Brainnetome, do you mean replace the atlas used by recon-all to do that ? (sorry, I am currently a PhD student with little experience in neuroimaging). You also mention that the transformation is not trivial. But do you think this is "correct" to make it ? Thanks for your help ! Cheers, Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France

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Fwd: Recon-all output space and .annot file registration
by Rachel S 07 Aug '19

07 Aug '19

External Email - Use Caution Hello freesurfer developers, I am trying to get the user defined segmentation for a subject generated in here (https://github.com/mattcieslak/easy_lausanne) . After recon-all, I have the pial surface with ~250k vertices. My first question is about the recon-all space. I thought the output of recon-all is already registered with the fsaverage space since it uses bucker40 as the template for segmentation. But some mentioned it is in the individual native space. Which one is true? My second question is about the procedure to generate the segmentation for downsampled surface. I have the .annot file and .label file for that subject and also for fsaverage. Reading the .annot file can give me the region mapping for ~250k matrix. I want to map the subject to fsaverage5 space and also downsample the vertices for the cortical surface to ~20k. And I want to get the region mapping for this ~20k vertices from the ~250k vertice .annot file. I looked into the documentation and email archive, here is a few things I tried. I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 1. Try to map to fsaverage in the recon-all step by using recon-all -i 0000.dcm -s p6_fs5 -all -qcache -target fsaverage5 And here is the error: --------------------------------------------------- #@# 1/1 p6_fs5 Wed 07 Aug 2019 04:49:09 AM EDT -------------- ----------------------- mri_surf2surf --srcsubject p6_fs5 --srchemi lh --srcsurfreg fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.7614/p6_fs5.1.mgh --sval /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness --sfmt curv --noreshape --cortex MRISread(/home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphere.reg): could not open file Source registration surface changed to fsaverage5.sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /home/rachelsun/Software/freesurfer/subjects cd /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf mri_surf2surf --srcsubject p6_fs5 --srchemi lh --srcsurfreg fsaverage5.sphere.reg --trgsubject fsaverage5 --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.7614/p6_fs5.1.mgh --sval /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness --sfmt curv --noreshape --cortex sysname Linux hostname rachel-pc machine x86_64 user rachelsun srcsubject = p6_fs5 srcval = /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.thickness srctype = curv trgsubject = fsaverage5 trgval = ./tmp.mris_preproc.7614/p6_fs5.1.mgh trgtype = srcsurfreg = fsaverage5.sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphere.reg No such file or directory mri_surf2surf: could not read surface /home/rachelsun/Software/freesurfer/subjects/p6_fs5/surf/lh.fsaverage5.sphere.reg No such file or directory Linux rachel-pc 4.19.62-1-MANJARO #1 SMP PREEMPT Sun Jul 28 09:14:58 UTC 2019 x86_64 GNU/Linux 2. Use the basic recon-all step recon-all -i 0000.dcm -s p6 -all, and run mri_surf2surf --srcsubject p6 --sval-xyz pial --trgsubject fsaverage5 --tval-xyz --tval lh.pial.p6 --hemi lh And I can get the surface mapped to fsaverage space, but I am not sure how to get the region segmentation for this new surface. From what I learned, mri_surf2surf is to map .annot between subjects. Sorry for the long email and thank you for your time. I would really appreciate it your input. Best regards, Rachel

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Help us help you learn methods in Advanced Statistics in Neuroimaging and Genetics
by ROBERT CARY WELSH 07 Aug '19

07 Aug '19

External Email - Use Caution Hi, We are in the midst of designing a short course on Advanced Statistics in Neuroimaging and Genetics. We would like to get a sense of the interest. If you don’t mind, please take a moment to fill out this short survey. https://csbsutah.co1.qualtrics.com/jfe/form/SV_eLqjkjI8ikjY0TP Much appreciated, Robert Welsh ------------------------------ Robert Welsh, PhD Associate Professor Department of Psychiatry University of Utah robert.c.welsh(a)utah.edu

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Transform hippocampal/amygdala segmentation to another space
by Jessica Bourgin 07 Aug '19

07 Aug '19

External Email - Use Caution Dear all, I would like to use the Hippocampal Subfields and Nuclei Of Amygdala tool concomitantly with the Brainnetome Atlas for a resting-state analysis. For this purpose, I need the hippocampal/amygdala nuclei to be in the same space as the Brainnetome. Can you advise me on the method to use to transform the segmentation to another space ? Thank you in advance for your help. Best regards, Jessica BOURGIN Laboratoire de Psychologie et Neurocognition CNRS UMR 5105 Université Savoie Mont Blanc (USMB) BP 1104 73011 Chambery Cedex France

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Re: [Freesurfer] need for help
by Greve, Douglas N.,Ph.D. 07 Aug '19

07 Aug '19

The command should be something like tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz Also, tksurfer is also obsolete (but should work). You should be using freeview (or tksurferfv, a freeview front end that takes the same command line args as tksurfer) Also, please remember to respond to the fs list On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote: > > External Email - Use Caution > > I got the mri_vol2surf output with .mgz: > > > my tksurfer command: > > tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of > mri_vol2surf was lh.inflated_MWI.mgz) > > > and the error i got: > > *freadFloat: fread failed** > No such file or directory* > > To me, opening the surfer in tksurfer is only a way to get sure my > vol2surf worked well. the main problem is i got this error for all > mris_smooth, mris_inflate, mris_sphere ... > > > Do you think that means the output of mri_vol2surf is not correct, or > otherwise i could proceed with that , even when tksurfer could not > open it, for GLM in Qdec? > > > Thanks, > > Reza > > ------------------------------------------------------------------------ > *From:* Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> > *Sent:* Tuesday, July 16, 2019 6:01:15 PM > *To:* Reza Rahmanzadeh > *Subject:* Re: need for help > what is your tksurfer command line? Also, the .w file is somewhat > obsolete (it should still work); instead you can use .mgz file (and > don't spec --paint) > > On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote: >> >> External Email - Use Caution >> >> Thanks Doug, >> >> >> I used the one without --inflated also, again the tksurfer could not >> open it and i got the same error. Where is the problem with my cmd.? >> >> >> In addition, i wanted to make the output of mri_vol2surf inflated >> using mris_inflate but i got the same error: >> >> *freadFloat: fread failed >> No such file or directory* >> * >> * >> *could you let me know what is the problem in registering my mwi >> volumes to surface that i getonly such errors.* >> * >> * >> *Thanks,* >> *reza >> * >> >> ------------------------------------------------------------------------ >> *From:* Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> >> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >> *To:* Reza Rahmanzadeh; Freesurfer(a)nmr.mgh.harvard.edu >> *Cc:* greve(a)nmr.mgh.harvard.edu >> *Subject:* Re: need for help >> Don't use --inflated. The inflated surface is not a biological >> surface. The default is the white surface, which is the one you want >> (--projfrac 0.5 will project it to the middle between the white and pial) >> >> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: >>> >>> External Email - Use Caution >>> >>> Dear Freesurfer, >>> >>> I have a batch of myelin water image (MWI) from patients and >>> controls, and trying to have inflated cortex registered on standard >>> surface for GLM (Qdec). >>> >>> With the commandlines below i get my inflated surface of MWI map of >>> my patients and controls. >>> >>> 1-using bbregister to put MWI into FS space and to calculate >>> register.dat: >>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat >>> --o mwf_FS --t1 >>> >>> 2-using mri_vol2surf to extract inflated surface of MWI: >>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5 >>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type >>> paint--inflated (*or*--surf sphere) >>> >>> However the tksurfer could not open the inflated surface and the >>> error message is: >>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices! >>> Probably trying to use a scalar data file as a surface!* >>> >>> I used the commandline below for #2: >>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o >>> mwf-lh.w --out_type paint >>> and i got the error: >>> >>> *ERROR: MRISread: file >>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many >>> more faces than vertices!** >>> Probably trying to use a scalar data file as a surface!* >>> * >>> * >>> As tksurfer could not open my surfaces with errors above, i think >>> perhaps the vol2surf procedure is not done properly. Where is the >>> problem? i need to get the inflated cortex and then putting ob >>> sphere (using mris_sphere) and the registering to standard surface >>> using mris_register for GLM in Qdec, right? >>> >>> >>> It is two weeks i am struggling with these commands, any helps >>> highly appreciated. * >>> * >>> * >>> * >>> * >>> * >>> Best, >>> Reza >>> >> >> 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. >> >

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Re: [Freesurfer] [External] Re: mri_deface fails on pediatric brain
by Soichi Hayashi 06 Aug '19

06 Aug '19

External Email - Use Caution All, I've tried the dev version with FS_HISTO_STD_THRESH set to 20, but I am seeing the same error message. hayashis@xps15-9560:~/test/deface/app-deface(master*) $ export FS_HISTO_STD_THRESH=20 hayashis@xps15-9560:~/test/deface/app-deface(master*) $ ./mri_deface ../t1.nii.gz $FREESURFER_HOME/average/talairach_mixed_with_skull.gca $FREESURFER_HOME/average/face.gca t1.nii.gz logging results to t1.nii.log reading '/home/hayashis/app/freesurfer-dev/average/talairach_mixed_with_skull.gca'... reading '../t1.nii.gz'... changing type of input volume to 8 bits/voxel... MRIchangeType: Building histogram 0 255 1000, flo=0, fhi=0.999, dest_type=0 bounding unknown intensity as < 10.3 or > 1461.6 total sample mean = 111.8 (0 zeros) spacing=8, using 2055 sample points, tol=1.00e-03... resetting wm mean[0]: 143 --> 144 resetting gm mean[0]: 89 --> 89 input volume #1 is the most T1-like using real data threshold=11.0 skull bounding box = (49, 43, 9) --> (207, 213, 219) finding center of left hemi white matter using (102, 100, 114) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 144, using box (83,79,88) --> (121, 120,139) to find MRI wm before smoothing, mri peak at 77 robust fit to distribution - 78 +- 5.8 distribution too broad for accurate scaling - disabling WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=113, mri_peak=144 after smoothing, mri peak at 0, scaling input intensities by inf GCAhistoScaleImageIntensities: could not find wm peak Numerical result out of range I've checked the binary but it doesn't look like this binary contains any reference to FS_HISTO_STD_THRESH parameter. hayashis@xps15-9560:~/Downloads $ strings mri_deface | grep FS_HISTO hayashis@xps15-9560:~/Downloads 1 Did I download the right binary? Soichi On Mon, Aug 5, 2019 at 3:04 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > no, the env variable won't change that. You can try changing the radius > with: > > -radius <n> > > where n=7 by default. Smaller will make it more aggressive. > > cheers > Bruce > On Mon, 5 Aug > 2019, Brian Biekman wrote: > > > External Email - Use Caution > > > > I am also using pediatric brains and am also interesting in using your > defacing algorithm. I downloaded your updated script and changed the > environment variable but it leaves a lot of the jaw and chin. Is this > something that can be fixed by changing the environment variable to some > custom value? > > > > -- > > Brian Biekman > > Graduate Student, University of Houston > > Clinical Psychology, Neuropsychology Concentration > > Laboratory of Early Experience and Development (LEED) > > bdbiekman(a)uh.edu > > Brian.Biekman(a)times.uh.edu > > > > ________________________________________ > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [ > freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Hoopes, Andrew [ > AHOOPES(a)mgh.harvard.edu] > > Sent: Monday, August 05, 2019 12:25 PM > > To: Freesurfer support list > > Subject: Re: [Freesurfer] [External] Re: mri_deface fails on pediatric > brain > > > > Hi Soichi, you can update mri_deface with: > > > > curl > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos7… > -o $FREESURFER_HOME/bin/mri_deface > > chmod +x $FREESURFER_HOME/bin/mri_deface > > > > Then, before running mri_deface, set the env variable: > > > > export FS_HISTO_STD_THRESH=20 > > > > Then, it should print out something like: > > > > mean wm in atlas = 144, using box (79,77,96) --> (120, 132,144) to find > MRI wm before smoothing, mri peak at 76 > > FS_HISTO_STD_THRESH found in the environment resetting from 10 to 20.0 > > robust fit to distribution - 76 +- 6.5 > > after smoothing, mri peak at 76, scaling input intensities by 1.895 > > mean wm in atlas = 144, using box (79,77,96) --> (120, 132,144) to find > MRI wm before smoothing, mri peak at 76 > > FS_HISTO_STD_THRESH found in the environment resetting from 10 to 20.0 > > robust fit to distribution - 76 +- 6.5 > > after smoothing, mri peak at 76, scaling input intensities by 1.895 > > > > > > ________________________________________ > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu < > freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Soichi Hayashi < > hayashis(a)iu.edu> > > Sent: Monday, August 5, 2019 11:32 AM > > To: Freesurfer support list > > Subject: Re: [Freesurfer] [External] Re: mri_deface fails on pediatric > brain > > > > External Email - Use Caution > > > > We run on our freesurfer through singularity/docker container, and we > are currently using Centos7 as the base image to build our freesurfer > container, but we can run it on any other Linux based OSes. As far as our > hardware goes, we run on variety of hardware including HPC system, public > and private cloud platforms and a few dedicated desktop machines at our > labs. > > > > Thanks! > > Soichi > > > > On Sun, Aug 4, 2019 at 10:55 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > > Hi Soichi > > > > I have a fix for you. Can you let us know what kind of hardware/software > > env you are running in and we will send it to you? > > > > cheers > > Bruce > > > > > > On Sun, 4 Aug 2019, Soichi Hayashi wrote: > > > >> > >> External Email - Use Caution > >> > >> Bruce, > >> I've uploaded one of the failed subject to surfer.nmr.mgh.harvard.edu< > http://surfer.nmr.mgh.harvard.edu> ftp > >> server (named t1.nii.gz).Thank you for looking into this problem. > >> > >> Soichi > >> > >> On Sun, Aug 4, 2019 at 10:35 AM Bruce Fischl < > fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> > >> wrote: > >> This message was sent from a non-IU address. Please exercise > >> caution when clicking links or opening attachments from > >> external sources. > >> ------- > >> > >> Hi Soichi > >> > >> mri_deface isn't really supported anymore, but if you upload a > >> subject > >> that fails I'll take a look. I would have thought in the ABCD > >> subject age > >> range it would work > >> > >> cheers > >> Bruce > >> On Sat, 3 Aug 2019, Soichi Hayashi wrote: > >> > >> > > >> > External Email - Use Caution > >> > > >> > Hello. > >> > > >> > We are running mri_deface on subjects from ABCD (Adolescent > >> Brain Cognitive > >> > Development) study and many of the subjects are failing on > >> mri_deface. > >> > > >> > $ mri_deface t1.nii.gz > >> > $FREESURFER_HOME/average/talairach_mixed_with_skull.gca > >> > $FREESURFER_HOME/average/face.gca defaced.nii.gz > >> > logging results to defaced.nii.log > >> > reading > >> > > >> '/usr/local/freesurfer/average/talairach_mixed_with_skull.gca'... > >> > reading 't1.nii.gz'... > >> > changing type of input volume to 8 bits/voxel... > >> > MRIchangeType: Building histogram > >> > bounding unknown intensity as < 10.3 or > 1461.6 > >> > total sample mean = 111.8 (0 zeros) > >> > spacing=8, using 2055 sample points, tol=1.00e-03... > >> > resetting wm mean[0]: 143 --> 144 > >> > resetting gm mean[0]: 89 --> 89 > >> > input volume #1 is the most T1-like > >> > using real data threshold=11.0 > >> > skull bounding box = (54, 38, 18) --> (205, 255, 220) > >> > using (104, 110, 119) as brain centroid... > >> > mean wm in atlas = 144, using box (85,83,94) --> (122, > >> 136,143) > >> > to find MRI wm > >> > before smoothing, mri peak at 79 > >> > robust fit to distribution - 80 +- 8.7 > >> > distribution too broad for accurate scaling - disabling > >> > WARNING2: gca.c::GCAhistoScaleImageIntensities: > >> > h_mri->nbins=111, mri_peak=140 > >> > after smoothing, mri peak at 0, scaling input > >> intensities by > >> > inf > >> > GCAhistoScaleImageIntensities: could not find wm peak > >> > Numerical result out of range > >> > > >> > > >> > Should talairach_mixed_with_skull.gca template work with > >> pediatric > >> > subjects? Or is there a different template we must choose? Or > >> maybe any > >> > parameters that we could tweak to get it work better? > >> > > >> > Thanks! > >> > Soichi > >> > > >> > > >> > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Help with MRI segstats
by Daliah Ross 06 Aug '19

06 Aug '19

External Email - Use Caution Hi FreeSurfer experts, I have a couple of questions regarding mri_segstats tool for an analysis on vertex-wise cortical thickness data. We are attempting to compare maximum cluster sizes among permutations. We are having trouble figuring out how to get the anatomical label for each cluster using the --slabel argument. We are also wondering if the difference between cluster sizes between mri_surfcluster and mri_segstats is due to partial volumes, and if so, how to correctly use the --pv argument. It suggests in the wiki page that mri/norm.mgz volume is usually used but I believe we need something surface-based since we are using thickness data. Thank you in advance for any help you can provide. Best, Daliah *Daliah Ross* | dross3(a)mail.yu.edu Ph.D. Student, Clinical Psychology with Health Emphasis Ferkauf Graduate School of Psychology Yeshiva University Albert Einstein College of Medicine

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Neuroimaging Data Analyst Position at MGH, Harvard Medical School (Boston, MA)
by Camprodon, Joan A.,M.D.,M.P.H.,Ph.D. 06 Aug '19

06 Aug '19

RESEARCH AND DATA ANALYST LABORATORY FOR NEUROPSYCHIATRY AND NEUROMODULATION MASSACHUSETTS GENERAL HOSPITAL, HARVARD MEDICAL SCHOOL Background: The Laboratory for Neuropsychiatry and Neuromodulation at the Massachusetts General Hospital, Harvard Medical School, is seeking a full time Research and Data Analyst for a series of exciting large-scale projects aimed at understanding circuit dynamics underlying neuropsychiatric disorders and their treatments. The laboratory is a multidisciplinary group conducting clinical, translational and basic human neuroscience research with healthy and neuropsychiatric populations, using device-based neuromodulation interventions (TMS, tDCS, ECT, DBS, etc.), neuroimaging, EEG, behavioral and clinical methods. The program includes the Transcranial Magnetic Stimulation (TMS) clinical service, tightly integrated with our research mission, where we provide individualized treatments for neuropsychiatric patients. Duties and Responsibilities: The Scientific and Data Analyst responsibilities will include, but are not limited to: 1. Implement and support statistical analyses and processing pipelines/scripts for behavioral, EEG and multimodal neuroimaging analysis, including resting‐state and task-based fMRI, DTI and volumetric data. 2. Assist in the creation of databases, query tools for data mining, and documentation on their effective use. Behavioral (RedCap, etc.) and neuroimaging databases (XNAT, etc.) are emphasized. 3. Maintain quality control and integrity of neuroimaging and behavioral data by developing, implementing and overseeing data entry and QC protocols. 4. Implement web-based behavioral questionnaires (e.g. RedCap) and program behavioral tasks with presentation software (e.g. Psychophysics Toolbox, PsychoPy, Presentation). 5. Provide programming and analysis support for lab members. 6. Coordinate general lab computer/network administration (including data management and archiving). 7. Assist with the preparation of scientific reports and publications. Qualifications: 1. B.A., B.S. or equivalent with background in neuroscience, computer science, engineering or related fields. Masters or PhD degree preferred but not required. 2+ years of prior technical experience. 2. Quantitative and extremely proficient with multiple neuroimaging analysis platforms (e.g. HCP Pipeline and Workbench, FreeSurfer, SPM, FSL, AFNI, etc.). 3. Strong programming skills and comfort with diverse computing environments required. 4. Strong background in statistics and statistical software scripting (R preferred). 5. Strong background creating scientific figures and writing technical scientific reports. 6. Strong interpersonal skills and a high level of organization with careful attention to detail are absolutely required. This position requires a high degree of motivation and self‐sufficiency, although extensive training and supervision will be provided. Additional Qualifications: 1. Experience with neuroimaging and behavioral databases. 2. Experience with graph analyses, machine learning and modeling confer a significant advantage. 3. Experience with EEG analysis is preferred. 4. Graphic or Web design skills are considered a plus. Additional Information: Applications must be sent by email to Dr. Joan Camprodon (jcamprodon(a)mgh.harvard.edu<mailto:jcamprodon@mgh.harvard.edu>) CCing Dr. Kristen Ellard (kellard(a)mgh.harvard.edu) and include a CV, cover letter and names of three references. Expected start date: Fall 2019

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WM surface including too much gray matter
by Brian Biekman 05 Aug '19

05 Aug '19

External Email - Use Caution To whom it may concern: I'm dealing with an issue in my subjects' recon-all output where the white matter surface extends into the gray matter, especially in the parietal and posterior temporal regions. This is caused by the wm.mgz including too much gray matter. This issue occurs to some degree in every subject's scans. This can be fixed with extensive wm volume edits but since this appears to be a systematic problem, I wanted to find a solution that could be applied to every subject, possibly in the recon-all pipeline. I've tried using an expert parameters 2 different ways to no avail. I've changed the -wlo values in mri_segment but it removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried adding the -prune and -gentle flags to mri_normalize but that appears to make the problem worse. Is there a better approach to try? If necessary, I can send a subject's recon-all output. -- Brian Biekman Graduate Student, University of Houston Clinical Psychology, Neuropsychology Concentration Laboratory of Early Experience and Development (LEED) bdbiekman(a)uh.edu Brian.Biekman(a)times.uh.edu

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