Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

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

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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

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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. >

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Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)
by Anna Daniels 15 Apr '18

15 Apr '18

Hi Andrew, hi Bruce, thanks for the tip! Unfortunately, the dev version of mri_normalize did not work (resulted in the same error log) but simply manually checking the control points in the respective cross runs and deleting the ones outside the brain before rerunning worked! Best, Anna 2018-04-11 23:22 GMT+02:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > p.s. you probably want to grab a new freeview also, as it lets you jump to > the voxel coords of each control point so you can see them > > On Wed, 11 Apr 2018, Hoopes, Andrew wrote: > > >> Hi Anna, >> >> >> >> You can download the new mri_normalize from this link - >> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_ >> binaries/centos6_x86_64/mri_normalize >> >> >> >> To get it into your FS installation, first set executable permissions and >> then move it into your >> $FREESURFER_HOME/bin directory (sudo might be required): >> >> >> >> chmod +x /path/to/downloaded/mri_normalize >> >> mv /path/to/downloaded/mri_normalize ${FREESURFER_HOME}/bin/ >> >> >> >> best >> >> Andrew >> >> >> >> From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Anna Daniels >> <anna.daniels(a)fu-berlin.de> >> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> >> Date: Monday, April 9, 2018 at 1:10 PM >> To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter >> peak at 110, cannot allocate >> memory) >> >> >> >> Hi Bruce, >> >> thank you for the quick reply! >> >> Ubuntu 16.04 LTS 64-bit >> >> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c >> >> Please let me know how to incorporate the new version into the >> installation. >> >> Thank you very much and best, >> >> Anna >> >> >> >> Hi Anna >> >> no attachments :< >> >> Srishti's issue stemmed from control points outside of the head. The >> current (dev) version of mri_normalize detects and removes them. Can you >> grab a new version of mri_normalize and see if it fixes your problem? Let >> us know your hardware/software environment and we will get it to you >> >> cheers >> Bruce >> >> >> On Fri, 6 Apr 2018, Anna Daniels wrote: >> >> > Hi Bruce, hi Srishti, >> > >> > I have exactly the same problem with several subjects rerunning >> recon-all >> > and there was sufficient memory available. I also tried out the last >> command >> > directly which resulted in the same error log. >> > >> > ?mri_normalize -f/home/anna/FREESURFER/00_DAT >> A_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer >> > uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg >> > aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz >> > >> > Attached you can find the input file. >> > >> > Thank you and best, >> > Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE] >> >> >> >> > > 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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segmentation and parcellation advances
by John Absher 14 Apr '18

14 Apr '18

During the last lectures of the recent 4/2-5 course, Dr. Fischl referenced code that would properly segment/parcellate sub-par images. If we don't have a good 3D MPRAGE or SPGR T1 image, is there a specific command I need to use for these alternate/sub-par inputs into recon-all ? If not, when might this code be available? I'm looking at archival images and often only a sagittal T1 volume is available. Also, can I just change this to 1mm voxels and leave it as a sagittal for recon-all, or should I reformat as axials first? Great course, by the way. Thanks, John John R. Absher, MD, FAAN GHS Neurosciences jabsher(a)ghs.org<mailto:jabsher@ghs.org> 864-350-6655 (mobile)

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Segmentation of anterior and posterior commissures
by Antonin Skoch 14 Apr '18

14 Apr '18

Dear experts, a question was raised whether it is possible to automatically segment anterior and posterior commissures. Do you think that it is achievable with reasonable accuracy, using in-vivo data of 0.7 mm3 resolution? I was thinking what would be the best way: a) Is it possible to customize Hippocampal subfields segmentation framework to achieve this goal? b) I considered the most straightforward option to extend current RB_all_2016-05-10.vc700.gca atlas to include also labels of anterior and posterior commisure. However, this would need to have labeled source subjects for this atlas. Is it publicly available? If yes, do you think that it makes sense to do it this way? c) In case of source subjects for RB_all_2016-05-10.vc700.gca are not available, then there would be option to create the atlas from scratch. Does it make sense to do it like following: Take let's say 10 representative subjects, run them through recon-all, take their aseg.mgz, manually label their commissures (only, other stuff in aseg.mgz leave as is) and run rebuild_gca_atlas.sh on relabeled aseg.mgz? This (in contrast to do the manual labeling of whole brain) seems doable to me. I do not know how the resolution of subjects constituting RB_all_2016-05-10.vc700.gca was, so maybe doing labeling on our 0.7mm3 subjects could lead to even more accurate results, than option b)? Could you please comment on? Regards, Antonin Skoch

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Visualizing Single anatomical ROI on FreeView
by Srinivasan, Dhivya 13 Apr '18

13 Apr '18

Hi, I am attempting to view single anatomical ROI (say Right-Hippocampus) overlaid on MRI image using freeview.How can I achieve this?

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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

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mri_vol2surf: issue with registration
by srishti goel 13 Apr '18

13 Apr '18

Hi , I am facing an issue when I try to compare two network-based maps, one of which has been registered on a surface while the other one has not. If anyone has tried doing something similar and has any thoughts about it please share your suggestions, I highly appreciate it. I have two sets of network based maps (both generated from meta-analysis), one set is ours' and one set is our collaborators'. We want to compare the two sets of maps. Our collaborators maps are on the surface in freesurfer. We wanted to project our volume based maps on that surface. Our collaborators' maps are: SN_like_cortical_lh.nii SN_like_cortical_rh.nii SN_like_subcortical.nii Our maps are: negative_allsocial_proportion.nii negative_somesocial_proportion.nii Etc. In order to compare their volume map (SN_like_subcortical.nii) to our (negative_allsocial_proportion.nii) we just used the MNI152 template from freesurfer wiki and viewed it in Freeview and it worked fine. The issue is when we try to project our maps on the surface that they used. The gave us the template brain (mni152_subject) folder that had been recon-all already and I just used that with the following steps: mri_vol2surf --src negative_allsocial_proportion.nii --regheader mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 To view it: tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 When I view it, our map doesn't show up on the surface and that is because our map didn't register with --regheader. I checked the registration by using: tkregisterfv --mov negative_allsocial_proportion.nii --reg register.lta --surfs The registration is definitely off, we used bbregister to register our maps on the mni152_subject but that didn't work either. Does anyone has thoughts about this? Thanks!

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Import tract files from other programs
by samanthabaldi145＠gmail.com 13 Apr '18

13 Apr '18

Good morning, For our project, we are studying tracts that from two deep brain nuclei spread to the cortex. Our aim is to find the coordinates of the cortical targets and compare them across individuals to assess the variability of these projections. We used the recon-all command for preprocessing of the T1-weighted anatomical scan and for cortical parcellation. We then switched to the program ExploreDTI, and we registered the DWI images to the brain.mgz file obtained as output of recon-all. We performed brain tractography using ROI masks (from fsl atlases) and obtained tracts files (*.mat, can be converted to *.trk, *.vtk, *.wrl) and tract masks (*.nii). Is it possible to import these tract files in Freesurferview? I would like to obtain one image which shows both the cortical parcellation and the tract of interest, in order to identify the cortical target based on the labeled model obtained from Freesurfer. I first loaded the brain volume brain.mgz (converted to *.nii). Then I selected “File > Load Tract” (converted to *.trk), but I can only visualize the tract separately from the brain volume, meaning that it’s not warped into the subject’s brain. I attach a picture of what I obtain. I wonder whether it is possible to obtain one image as I described above by importing tracts not obtained with Freesurfer? Thanks in advance, Regards Samantha Baldi

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