Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Pial and WM edits around the temporal lobes
by Stephanie Otto 14 Jan '19

14 Jan '19

External Email - Use Caution Greetings Freesurfer Team, We are working on quality checking reconstructions and there seems to be a common problem area around the temporal lobes where the white matter surface extends beyond the pial surface, or the pial surface just looks off. We know this is a difficult area to reconstruct and we aren't entirely sure how to correct for this. We want to avoid interfering with the resulting data. Can you instruct us on how we should proceed with this kind of correction (i.e. control points vs fill voxels, etc.)? If we are looking at temporal lobe structures, how much are these areas affected (or something like the grey matter volume)? Is there a standard protocol for dealing with issues such as these? Thanks for all your help and support! Best, Stephanie Otto Academic Advisor, Department of Psychology Graduate Student, Cognitive and Brain Sciences Program Mack Social Science, Room 414 University of Nevada, Reno sotto(a)nevada.unr.edu

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Re: [Freesurfer] -qcache error
by Peters, Douglas G 14 Jan '19

14 Jan '19

External Email - Use Caution I am new to FS, and I am having the same error that Krishna had last year. I don't see a link to the 'lh.white.k' file in my surf folder. Has anyone resolved this problem? I can side step the error with '-qcache -measure thickness' to only process thickness files, but I'd like to be able to process all the files in my subject folders. Thanks, Doug Command line input: recon-all -s <subject> -qcache Command line output: #@# Qdec Cache preproc lh white.K fsaverage /surf mris_preproc --s <subject> --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh nsubjects = 1 ERROR: cannot find /lh.white.K recon-all -s <subject> exited with ERRORS Re: [Freesurfer] -qcache error<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj…> Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Fri, 09 Mar 2018 08:18:34 -0800<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> It was deleted but then it was created as a link. Does the link exist? ________________________________ On 3/7/18 1:33 PM, Krishna Patel wrote: Hi - I would like to do group analysis on freesurfer data that is processed with verson 6. However when I try to run recon-all -s subjid -qcache I get following error after it runs for some time and generates some of the files. ERROR: cannot find surf/lh.white.K When I look at the log file - I see that this file was deleted. See following. total integrated curvature = -1.022*4pi (-12.846) --> 2 handles ICI = 169.4, FI = 1785.3, variation=28139.036 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K Does anyone have any idea of what might be the issue here? Thanks, -Krishna ________________________________ From: Peters, Douglas G Sent: Thursday, January 10, 2019 4:55:31 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: -qcache error I am new to FS, and I am having the same error that Krishna had last year. I don't see a link to the 'lh.white.k' file in my surf folder. Has anyone resolved this problem? I can side step the error with '-qcache -measure thickness' to only process thickness files, but I'd like to be able to process all the files in my subject folders. Thanks, Doug Command line input: recon-all -s <subject> -qcache Command line output: #@# Qdec Cache preproc lh white.K fsaverage /surf mris_preproc --s <subject> --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh nsubjects = 1 ERROR: cannot find /lh.white.K recon-all -s <subject> exited with ERRORS Re: [Freesurfer] -qcache error<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj…> Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Fri, 09 Mar 2018 08:18:34 -0800<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> It was deleted but then it was created as a link. Does the link exist? ________________________________ ________________________________ On 3/7/18 1:33 PM, Krishna Patel wrote: Hi - I would like to do group analysis on freesurfer data that is processed with verson 6. However when I try to run recon-all -s subjid -qcache I get following error after it runs for some time and generates some of the files. ERROR: cannot find surf/lh.white.K When I look at the log file - I see that this file was deleted. See following. total integrated curvature = -1.022*4pi (-12.846) --> 2 handles ICI = 169.4, FI = 1785.3, variation=28139.036 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K Does anyone have any idea of what might be the issue here? Thanks, -Krishna

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Tksurfer and Freeview label visualizations look different
by Anna Mynick 14 Jan '19

14 Jan '19

External Email - Use Caution Hi, I drew a collection of surface labels by hand in Tksurfer, but when I open them in Freeview to visualize them, they look incorrect. In particular, the labels in Tksurfer were drawn without any holes, but the labels in Freeview somehow got odd unintended holes (see attached images). Has anyone else run into this? For what it's worth, I drew the labels with an overlay loaded in Tksurfer, though I didn't think this would have an effect on the labels I saved. Thanks for any help, Anna tksurfer label originally drawn (purple) [cid:775863A3-49CB-4361-A9D7-B5B0745225CE@mit.edu] freeview (below, yellow) [cid:E1BB51C1-561F-4290-9AF9-DA755DAAF3ED@mit.edu]

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mris_apply_reg failing for area/volume
by James Michael Roe 14 Jan '19

14 Jan '19

External Email - Use Caution ? Dear freesurfer experts I'm running the following commands to register RH area and volume files per sub to both hemispheres of a symmetrical template following Xhemi routines. The commands have already worked for many subs, but are failing to write the target file for a number of others (and all run fine without the --jac flag) #right to left mris_apply_reg \ --src $SUBJECTS_DIR/$sub/surf/rh.area \ --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \ --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \ --jac #right to right mris_apply_reg \ --src $SUBJECTS_DIR/$sub/surf/rh.area \ --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \ --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \ --jac The error is not template-specific as the output is the same using fsaverage_sym Attached is the log file. Thanks in advance! ?- James

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Grey matter excluded from pial surface
by Borges Pereira Ines Isabel 14 Jan '19

14 Jan '19

External Email - Use Caution Dear FreeSurfer developers, I am trying to obtain adequate pial surface boundaries. Unfortunately, on a few subjects, some grey matter is being excluded from the pial surface, at the temporal pole. I have attempted to solve this problem by adding control points and adding voxels on the wm.gz volume, so as to have FreeSurfer first update the wm boundary and then hopefully the pial surface. As you can see on the attached images, the control points were only partially taken into account and the pial surface was not updated. It would be great to get your support in understanding why this is happening. I am using the following Freesurfer version on Centos: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Thanks! Best regards, Inês Pereira [cid:3140210C-B81A-431D-92FC-E5BD9026A4CE@ethz.ch][cid:36204321-D704-4182-A1A8-B43F8CE27A4F@ethz.ch]

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GLM analysis using own average subject
by Bunting, Emma 14 Jan '19

14 Jan '19

External Email - Use Caution Hi, I’ve encountered a few issues when performing GLM using an average subject that I have created (named avgsubject.Controls2), Essentially, the glm_preproc command fails because it is now unable to find the ‘source surface reg’, which it lists as avgsubject.Controls2.sphere.reg in the linux outputs (see below). This already seems odd to me, as I would have thought this would be the target surface reg, as avgsubject.Controls2 is the target. The error occurs because it is trying to find the file within the VIPD_014/surf directory (whereby VIPD_014 is the first subject in our fsgd file). Oddly enough, the file does exist, but within the avgsubject.Controls2/surf directory instead! I was going to copy this file into all the participant’s subject/surf directories that are listed within the fsgd file, but it seems like this is not really the right way of doing it, and there must be a reason why it hasn’t ended up in the expected directories. Is there a way to edit the glm_preproc script so that it directs it to find the avgsubject.sphere.reg file within the avgsubject folder instead, or perhaps to correct the 'source surface reg' to be lh.sphere.reg (which is found within the subject/surf directory)? I’m not sure if this is related, but when looking at the fsaverage folder (where fsaverage is the average subject created by freesurfer) vs the avgsubject.Controls2 folder, I noticed the latter contains ‘reg.template.tif’ files for both hemispheres - which the fsaverage folder lacks. The other fsaverage folders created by freesurfer found within the freesurfer directory (fsaverage3, 4, 5, 6 and freesurfer_sym) do contain these tif files. It’s probably also worth noting that when I created avgsubject, it said “completed with errors” - but when I looked in the error log it didn’t tell us any information on what the errors were. This happens for all the different avgsubjects we have created. Below I describe the commands used for each step: #make_average_subject ebunting@img-140:.../MRI_data/freesurfer$ make_average_subject --out avgsubject.Controls2 --subjects VIPD_007 VIPD_015 VIPD_017 VIPD_028 VIPD_038 VIPD_068 VIPD_069 VIPD_078 VIPD_104 VIPD_105 VIPD_108 VIPD_111 VIPD_115 VIPD_117 VIPD_118 VIPD_119 VIPD_120 VIPD_126 VIPD_142 VIPD_145 VIPD_146 VIPD_160 VIPD_167 VIPD_177 VIPD_180 VIPD_193 VIPD_234 VIPD_257 VIPD_272 VIPD_274 VIPD_275 VIPD_276 VIPD_277 VIPD_280 VIPD_404 VIPD_406 VIPD_601 #n.b. this exited 'with errors'. Details of the recon-all log is attached as “avgsubject.Controls2/scripts/recon-all.log” #The linux outputs when using this command are also attached in a file named “linux outputs for making avgsubject.Controls2” #Preprocessing for GLM analysis ebunting@img-140:.../MRI_data/freesurfer$ mris_preproc --fsgd VIPD_014_SingleSubject.New.fsgd \ > --target avgsubject.Controls2 \ > --hemi lh \ > --meas thickness \ > --out lh.VIPD_014_SingleSubject.New.Controls2.thickness.00.mgh \ > nsubjects = 38 tmpdir is ./tmp.mris_preproc.984 /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer Log file is lh.VIPD_014_SingleSubject.New.Controls2.thickness.00.mris_preproc.log Fri Jan 11 10:47:34 GMT 2019 setenv SUBJECTS_DIR /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer /var/drc/software/64bit/freesurfer/bin/mris_preproc --fsgd VIPD_014_SingleSubject.New.fsgd --target avgsubject.Controls2 --hemi lh --meas thickness --out lh.VIPD_014_SingleSubject.New.Controls2.thickness.00.mgh Linux img-140.drc.ion.ucl.ac.uk<http://drc.ion.ucl.ac.uk> 2.6.32-279.el6.x86_64 #1 SMP Wed Jun 13 18:24:36 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.984 Src lh avgsubject.Controls2.sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/38 VIPD_014 Fri Jan 11 10:47:34 GMT 2019 -------------- ----------------------- mri_surf2surf --srcsubject VIPD_014 --srchemi lh --srcsurfreg avgsubject.Controls2.sphere.reg --trgsubject avgsubject.Controls2 --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.984/VIPD_014.1.mgh --sval /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness --sfmt curv --noreshape --cortex MRISread(/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.avgsubject.Controls2.sphere.reg): could not open file Source registration surface changed to avgsubject.Controls2.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 /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer mri_surf2surf --srcsubject VIPD_014 --srchemi lh --srcsurfreg avgsubject.Controls2.sphere.reg --trgsubject avgsubject.Controls2 --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.984/VIPD_014.1.mgh --sval /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness --sfmt curv --noreshape --cortex sysname Linux hostname img-140.drc.ion.ucl.ac.uk<http://drc.ion.ucl.ac.uk> machine x86_64 user ebunting srcsubject = VIPD_014 srcval = /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness srctype = curv trgsubject = avgsubject.Controls2 trgval = ./tmp.mris_preproc.984/VIPD_014.1.mgh trgtype = srcsurfreg = avgsubject.Controls2.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 /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.avgsubject.Controls2.sphere.reg No such file or directory mri_surf2surf: could not read surface /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.avgsubject.Controls2.sphere.reg No such file or directory #N.b. Outputs when compared to using fsaverage as the target: ebunting@img-140:.../MRI_data/freesurfer$ mris_preproc --fsgd VIPD_014_SingleSubject.New.fsgd \ > --target fsaverage \ > --hemi lh \ > --meas thickness \ > --out lh.VIPD_014_SingleSubject.New.thickness.00.mgh \ > nsubjects = 38 tmpdir is ./tmp.mris_preproc.27392 /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer Log file is lh.VIPD_014_SingleSubject.New.thickness.00.mris_preproc.log Thu Jan 10 16:24:36 GMT 2019 setenv SUBJECTS_DIR /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer /var/drc/software/64bit/freesurfer/bin/mris_preproc --fsgd VIPD_014_SingleSubject.New.fsgd --target fsaverage --hemi lh --meas thickness --out lh.VIPD_014_SingleSubject.New.thickness.00.mgh Linux img-140.drc.ion.ucl.ac.uk<http://drc.ion.ucl.ac.uk> 2.6.32-279.el6.x86_64 #1 SMP Wed Jun 13 18:24:36 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.27392 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/38 VIPD_014 Thu Jan 10 16:24:36 GMT 2019 -------------- ----------------------- mri_surf2surf --srcsubject VIPD_014 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.27392/VIPD_014.1.mgh --sval /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness --sfmt curv --noreshape --cortex Source registration surface changed to 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 /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer mri_surf2surf --srcsubject VIPD_014 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.27392/VIPD_014.1.mgh --sval /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness --sfmt curv --noreshape --cortex sysname Linux hostname img-140.drc.ion.ucl.ac.uk<http://drc.ion.ucl.ac.uk> machine x86_64 user ebunting srcsubject = VIPD_014 srcval = /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.27392/VIPD_014.1.mgh trgtype = srcsurfreg = 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 /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.sphere.reg Loading source data Reading curvature file /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_014/surf/lh.thickness Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (156736) Reverse Loop had 34296 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 138772, nTrgMulti = 25070, MnTrgMultiHits = 2.36801 nSrc121 = 123084, nSrcLost = 0, nSrcMulti = 33652, MnSrcMultiHits = 2.2303 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.27392/VIPD_014.1.mgh #… and this continues for each subject within the fsgd file. #the mris_surf2surf command then works as normal using: mri_surf2surf --hemi lh --s avgsubject.Controls2 --sval lh.VIPD_014_SingleSubject.New.thickness.00.mgh --fwhm 10 --cortex --tval lh.VIPD_014_SingleSubject.New.avgsubject.Controls2.thickness.10B.mgh –> THIS WORKS, BUT IT IS USING lh.VIPD_014_SingleSubject.New.thickness.00.mgh as the input file, which was created using fsaverage – so I am unsure how valid this is to use. #glm_fit command works as normal using: ebunting@img-140:.../MRI_data/freesurfer$ mri_glmfit \ > --y lh.VIPD_014_SingleSubject.New.avgsubject.Controls2.thickness.10B.mgh \ > --fsgd VIPD_014_SingleSubject.New.fsgd \ > --C SingleSubject.1,-1.mtx --C SingleSubject.1,0.mtx --C SingleSubject.0,1.mtx --C SingleSubject.0.5,0.5.mtx \ > --surf avgsubject.Controls2 lh \ > --cortex \ > --glmdir lh.VIPD_014_SingleSubject.avgsubject.Controls2.0 \ > gdfRead(): reading VIPD_014_SingleSubject.New.fsgd #n.b. output logs for both these commands are attached in case you want to examine them too ….So essentially the GLM analysis works fine, as long as the mri_preproc step is skipped. I feel unsure about the surf2surf analysis using an input file that was created using fsaverage as the target in the mri_preproc step – hence I'm trying to figure out why the mri_preproc step won't work. Any help would be greatly appreciated! Many thanks, Emma Bunting

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Problem with checking registration quality using tkregister-sess: if: Expression Syntax.
by Keri Woods 14 Jan '19

14 Jan '19

External Email - Use Caution Hi I’m having a problem that I’m hoping someone could help me with. I’m trying to check the quality of the alignment of structural and functional data, using the command: tkregister-sess -s 20_1 -fsd bold -per-run where 20_1 is the subject ID. Nothing opens, and I get the following error: -------------------------------------------------------------- tkregister-sess logfile is /home/keri/audio2/log/tkregister-sess.log -------------------------------------------------------------- Session: 20_1 ---------------- if: Expression Syntax. I’ve opened the log file, which doesn’t shed much light on the problem. Its contents are: tkregister-sess log file $Id: tkregister-sess,v 1.42 2015/12/10 22:51:31 zkaufman Exp $ setenv SUBJECTS_DIR /home/keri/recon_all/subjects cd /home/keri/audio /usr/local/freesurfer/fsfast/bin/tkregister-sess -s 20_1 -fsd bold -per-run buddha /usr/local/freesurfer/bin/tkregister2 Session: 20_1 ---------------- The SUBJECTS_DIR show here is correct. I’ve been looking through the archives, and someone suggested checking whether tkmedit works when having problems with tkregister. I’ve done this, and it works fine. On a side note, when checking the quality of registration using the command in the format of: tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum I get very poor results for many of the subjects (some of them are even > 1, which I didn’t think was possible). Could this be part of the problem? The subject 20_1 I used as a example did have a fairly good result (eg 0.5090 for one run). Thanks in advance. Best wishes, Keri

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Custom templates and longitudinal processing
by Jason Tourville 11 Jan '19

11 Jan '19

External Email - Use Caution Hi Freesurfers, We are collaborating with a group at Michigan that planss to use Freesurfer's longitudinal pipeline to process T1 data collected from children (see brief project summary below) at multiple time points. Our role is to oversee recon QA and application of a custom cortical parcellation labeling system. As we move to longitudinal processing, we have a couple questions about when/how/if to apply various custom templates that we're using. In preparing the cross-sectional recons, we used a custom tal atlas generated from our sample with help from Avi Snyder. Question 1: When creating the base or running longitudinal processing, should this atlas be specified in some manner? We also generated a custom pediatric surface template and cortical classifier; we co-register each subject to this template and apply the classifier (we actually just use surf2surf to map the labeled template to the individual subject surfaces) to generate cortical labels. Question 2: how should we do this in the longitudinal stream? would we register the subject's base to the pediatric surface template then use the the resulting sphere.reg in the call to mris_ca_label? In the longitudinal work flow, it looks like cortical labeling is done in the longitudinal stream. Question 3: If we notice a labeling error and correct it, is there a means of propagating that correction across all the time points? Question 4: If we've labeled and reviewed all the cross-sectional time-point-one data, is there a way to map those labels to the longitudinal stream time points that doesn't compromise the resulting labels? Question 5: Given the project summary below, are there any other concerns that we should be aware of when applying the longitudinal pipeline? *Brief summary of the longitudinal study of childhood stuttering at University of Michigan (Soo-Eun Chang)* Over the last few years, we have collected yearly structural and functional MRI scans from around 300 children who do and do not stutter. These are children between the ages of 3-10 at initial scan. Scans were acquired each year for up to 4 years (some children do not have all 4 years, but many do). Data from year 1 has been published (Garnett et al., 2018) using a custom labeling system and atlas. We have just finished manual editing of the scans from years 2 – 4 and are preparing to conduct a longitudinal analysis with all 4 years of scans in FreeSurfer. We plan to extract cortical and subcortical measures of thickness, area, volume, LGI, etc. and compare developmental trajectories of these measures in the stuttering group vs. the control group. Also, because of the longitudinal design, we have information on whether children in the stuttering group went on to recover or if their stuttering persisted. All children were considered stuttering at their initial visit, and based on evaluations each year, we are able to retrospectively assign them to the persistent group or the recovered group. In this way, in addition to comparing morphometric measures between children who stutter and controls, we also hope to find neural markers that help predict persistence vs. recovery in childhood stuttering. Many thanks for your input. Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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DKT vs. DK Freesurfer atlases
by Gabor Perlaki 11 Jan '19

11 Jan '19

Dear all, I've found an article comparing DK and DKT atlas based automatic segmentations to manual labels (Klein and Tourville, Front Neurosci. 2012; 6:171, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514540/) It seems that using DKT40 works better than DK in most of the cortical regions (based on Dice). Does anybody know that the DKTatlas related results created by Freesurfer (e.g. aparc.DKTatlas+aseg.mgz, lh.aparc.DKTatlas.stats) are based on the same DKT40 atlas used in the article and whether the DKT40 atlas related results were also created by Freesurfer in the article by Klein and Tourville? Are the Freesurfer created results in lh.aparc.DKTatlas.stats generally more reliable than the results in lh.aparc.stats? -- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-2084367 E-mail: petzinger.gabor(a)gmail.com

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Position Available in Neuroimaging of PTSD at VA Boston
by Emma Brown 11 Jan '19

11 Jan '19

External Email - Use Caution The Behavioral Science Division (Boston) of the National Center for Postraumatic Stress Disorder is strongly tied to the Neuroimaging Research for Veterans (NeRVe) Center at VA Boston. Imaging candidates with interest in military-associated traumatic stress are strongly encouraged to apply for this position with duties beginning in 2019. The National Center for PTSD is a multi-site consortium within the Department of Veteran Affairs. The Behavioral Science Division is nationally recognized for developing model research and clinical programs in stress and trauma. The Division has outstanding resources for research, training, and clinical activities. Exceptional opportunities exist for professional collaboration with a wide array of researchers locally and at six other National Center divisions, as well as with investigators in other academic, VA, and military settings. A major focus of National Center research is adjustment following military service, but candidates who have background in related areas or with other types of trauma are welcomed. Requirements for a position are a doctoral degree plus demonstrated skills in research, scientific publication, and grant writing. Clinical psychologists must have graduate training and clinical internship from APA-accredited programs, as well as existing professional licensure or eligibility for licensure. Division investigators participate in the training and supervision of postdoctoral fellows and predoctoral interns. Faculty appointment at the Boston University School of Medicine is anticipated. Salary and benefits are competitive. Please send a curriculum vitae with a cover letter, reprints, and the names of anticipated professional references to Brian Marx, Ph.D., National Center for PTSD (116B-4), VA Boston Healthcare System, 150 S. Huntington Ave., Boston, MA 02130-4817 or via email to brian.marx(a)va.gov. Materials will be reviewed on a first-come basis until available positions are filled. Formal position posting and the application process will follow federal procedures via the USAjobs.gov website. U.S. citizenship is required. The Department of Veteran Affairs is an Equal Opportunity Employer.

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