Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

ALE map to surface
by Carla Ammons 01 Aug '16

01 Aug '16

Hi! I am new to freesurfer so this may be a basic question. I have an activation map (.nii) created via ALE meta-analysis in MNI space that I want to visualize on the surface. Do I use bbregister for this? Thanks! Carla

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Creating contrast between two groups, controlling for 2 categorical(gender, scanner) and one continous variable(age)
by Oana Georgiana Rus 01 Aug '16

01 Aug '16

Dear FreeSurfer Experts, I want to compare structural measures(eg. thickness) between patients and controls controling for the effects of age, gender and scanner (parts of sample were scanned in scanner 1 parts in scanner 2). I want to answer the question: *do patients and controls differ significantly in lGI when controlling for age (continous variable), gender(male/female), scanner(scanner1/scanner2)?* *so i have to categorical (gender, scanner) and one continous variable to control for.* *my FSGD file looks like:* /GroupDescriptorFile 1 // //Class PatientFemaleScanner1// //Class PatientFemaleScanner2// //Class PatientMaleScanner1// //Class PatientMaleScanner2// //Class ControlFemaleScanner1// //Class ControlFemaleScanner2// //Class ControlMaleScanner1// //Class ControlMaleScanner2// //Variables Age // //Input subject1 ControlMaleScanner1 23.6// //Input subject2 ControlFemaleScanner2 37.7// //Input subject3 PatientFemaleScanner1 32.6/ ... *Total I would have 16 regressors with following contrasts: * *first conrast:* is there a difference in structural measure(eg. thickness) between *patients and controls* controlling for gender, scanner, age? 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 *second contrast:* is there a difference between the two scanners *scanner 1 and 2* controlling for effects of gender, age and group? 0.25 -0.25 0.25 -0.25 0.25 -0.25 0.25 -0.25 0 0 0 0 0 0 0 0 *Questions:* * Are the Contrasts created ok? * How could I control better for the effect of scanner, as part of the sample was scanned with scanner 1 another part with scanner 2? Thank you very much for your help! Geo -- Oana Georgiana Rus PhD Student Neuroimaging Center TUM-NIC Klinikum rechts der Isar Technische Universität München Einsteinstr.1 81675 München Raum 5.8 Tel. 089 4140 7971

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MNI coordinates of all the vertices of fsaverage
by Sabin Khadka 01 Aug '16

01 Aug '16

Hi Doug, I tried to pick up from the thread below to get MNI coordinates of each destrieux parcellation region. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html I created label files from mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation aparc.a2009s --outdir label_destrieux # which works fine And I tried to get the coordinates of each labels using mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel <label file> --sum <output file> --centroid --thmin 0 --hemi lh --subject fsaverage But, all left labels would produce the same coordinates and so does right labels. (I've attached few example files here with). Also, it says TalX, TalY, TalZ are these coordinates in MNI or Talairach? Thanks for help.

2 3

Long seg for hippo subfields
by Thomas, Adam (NIH/NIMH) [E] 01 Aug '16

01 Aug '16

This look very cool: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields But the flag is not being recognized by recon-all using the most recent build: [adamt@felix scratch]$ cat $FREESURFER_HOME/build-stamp.txt freesurfer-Linux-centos6_x86_64-dev-20160730-bda65ec [adamt@felix scratch]$ recon-all -long-hippocampal-subfields-T1 md105Templ -hsfTP md105-1.long.md105Templ -hsfTP md105-2.long.md105Templ -hsfTP md105-3.long.md105Templ -hsfTP md105-4.long.md105Temp1 -hsfTP md105-5.long.md105Templ ERROR: Flag -long-hippocampal-subfields-T1 unrecognized. -long-hippocampal-subfields-T1 md105Templ -hsfTP md105-1.long.md105Templ -hsfTP md105-2.long.md105Templ -hsfTP md105-3.long.md105Templ -hsfTP md105-4.long.md105Temp1 -hsfTP md105-5.long.md105Templ Linux felix.nimh.nih.gov 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Mon Aug 1 18:42:51 EDT 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [adamt@felix scratch]$ uname -a Linux felix.nimh.nih.gov 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux [adamt@felix scratch]$ which recon-all /data/adamt/Apps/fs6-2016-07-31/bin/recon-all [adamt@felix scratch]$ Is there a newer version of recon-all hiding somewhere? Thanks, -Adam

2 1

mris_label2annot
by Caroline Beelen 01 Aug '16

01 Aug '16

Dear FS, Sorry to bother again, but I'm currently in need for some quick help. Today, I also ran into another problem. I tried to display only few ROI's in Freeview instead of the whole brain. Therefore, I tried to create a new annotation file consisting of only few labels (from regions of DK-atlas) and I used the mri_annotation2label on my own created fsaverage to get these labels. This worked fine. Then I used the command of mris_label2annot to create the annotation file, but part of the command, --ctab aparc.annotation.ctab, is not recognized. Replacing it by -ctab fsaverage/label/lh.aparc.annot (file exists in the label folder of fsaverage) gives me the following error: CTABreadASCII: badly formed file. ERROR: reading fsaverage/label/lh.aparc.annot. I couldn't find, or create, any other aparc.annot file. What would be the right command (for the part of ctab) to get mris_label2annot working? Or is there perhaps a better way to only display certain ROI's in Freeview? (the latter I could still explore but assistance is certainly appreciated) Thanks a lot! Caroline

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freesurfer 6.0 release date
by Fengji Geng 01 Aug '16

01 Aug '16

Hi fs developers, I am wondering if you have any estimation when fs 6.0 will come out. The reason that I ask this is because we are running some analysis using fs 5.1 and planning to switch to a more recent version of fs. If fs 6.0 will come out soon, we will probably hold and wait for it. If not, we will just switch to fs 5.3. Thanks! -- Fengji Geng

2 1

Freesurfer dev version
by Liu, Daniel 01 Aug '16

01 Aug '16

Hi, I wanted to follow up on the error that came up in the freesurfer dev version this past week. Has it been fixed yet? If so, has the link to the download page been changed? The one I booked marked does not lead me to the page anymore and I would appreciate it if you could direct me to the correct location. Thanks, Daniel

3 3

Cannot launch freeview
by Da, Xiao 01 Aug '16

01 Aug '16

Hi Freesurfer Developers, I tried to run freeview but got this following error message. freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux version: NAME="Red Hat Enterprise Linux Workstation" VERSION="7.2 (Maipo)" ID="rhel" ID_LIKE="fedora" VERSION_ID="7.2" PRETTY_NAME="Red Hat Enterprise Linux" I tried "locate libXss.so.1", but returned nothing. Please let me know if you have the solution to fix this error. Thanks and best regards, Xiao Da Biomedical Engineer - Programmer Analyst II Functional Neuroimaging Laboratory Brigham and Women's Hospital 221 Longwood Avenue, Braunwald Building, Room LM116 Boston, MA 02115 xda(a)bwh.harvard.edu

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mri_label2label error
by Aquino Domenico 01 Aug '16

01 Aug '16

Dear Freesurfer team, I'm trying to segment a pre-processed 3D PSIR volume. Everything seems to work correctly, however at the end of recon-all something goes wrong. The command "mri_label2label" returns the ERROR "No such file or directory\ mri_label2label: could not open label file...". Actually the file has not been created but I don't understand why. I checked the path for special characters, I checked the permissions and so on and it seems all ok. Which could be the issue? In attachment you'll find the recon-all.log file. Thanks a lot, Domenico ___________________________________________ Eng. Domenico Aquino Department of Neuroradiology IRCCS Foundation Neurological Institute "Carlo Besta" Via Celoria,11-20133 Milano Phone: +39 02 23942472 Fax +39 02 23942543 [1463859753944_LogoWhite.jpg]

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significance overlay Freeview
by Caroline Beelen 01 Aug '16

01 Aug '16

Dear FS, Yes, I'm running FS 5.3. :) How can I visualize the significance overlay (correctly)? Which command should I use to view a significance overlay in freeview in FS 5.3? See also my email below. Thank you very much in advance! Best, Caroline Hi Caroline, Are you running FS 5.3? The command on the webpage is based on the upcoming 6.0, I believe. So some of the command line options are not available in 5.3. Best, Ruopeng > On Jul 29, 2016, at 9:11 AM, Caroline Beelen <caroline.beelen(a)kuleuven.be<mailto:caroline.beelen@kuleuven.be>> wrote: > > Dear FS team, > > Apologies in advance for perhaps again a rather basic question. I attempted to load the aparc overlay in freeview by using the written command from the group analysis page, however it failed to load correctly. > > I used the following command: > freeview -f fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5 -viewport 3d > ? roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis and dyslect is the contrast folder within this file (main effect of dyslexia), containing a sig.mgh file (all seems fine) > > Unfortunately, I got an error that it does not recognize overlay_treshold=4,5. I used freeview ?h and tried certain commands alike, but they didnt work. When leaving out this part, I got another error that it failed to recognize annot_outline=1. Again, leaving this out too, freeview loads itself and the DK-regions become visible. However, nothing else seems to get activated, and even not when putting configure overlay (which is set to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens. > When looking at the command line it says that it implemented the colortable of DK-atlas (even twice), but it tells me nothing else. Also, after closing and reloading Freeview by using the similar command and then clicking on configure overlay the screen sometimes gets stuck, giving me the impression that something must be wrong with the command. > > Could you please help me out and provide me the right command-line for loading the overlay of the significance map of roi.lh.area.dyslect_basic.glmdir/dyslect? > > Thanks in advance! > > Kind regards, Caroline

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