Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

TKSurfer - Mean Thickness Overlay Display
by Bramen, Jennifer E. 19 Feb '09

19 Feb '09

Dear Freesurfer List I am trying to make some figures to display mean thickness for my different groups. I have the overlays, but no matter what I do, they look terrible. The only color scale that seems to work is the "hot" scale. Everything else looks completely wrong. Either they look grainy like this or I get a black image. I am attaching screenshot showing what I mean. I am also attaching an example of what I want taken from a paper that also uses Freesurfer. I am studying kids, who have much thicker cortex than adults. I would like to threshold thickness at 1.7, with a max value of 5. Otherwise, I want my figure to look exactly like this one. How can configure the overlay display so that my figures look similar? Thanks Jen Jennifer Bramen, Ph.D. Assistant Research Neuroscientist David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)525-0865 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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mris_divide_parcellation
by Jose Luis Cantero Lorente 19 Feb '09

19 Feb '09

Dear FS Team, I used mris_divide_parcellation to create a new parcelation with smaller regions, but all these regions seem to have a different size. I am interested to get smaller cortical parcellated regions, but all of them with the same area. How can I get it? Could I decide the area size? Thank you in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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volume changes
by Jared Price 19 Feb '09

19 Feb '09

Dear gurus, when running mri_convert -rt nearest -ot nii -rl 001.mgz seg_edited.mgz seg_edited_axial.nii to reslice from coronal to axial space we are seeing some significant volume changes in the segmentation. Anyone know why or how to fix it. Jared

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control points
by Muhammad Ayaz 19 Feb '09

19 Feb '09

Dear All, I am in phase of learning freesurfer. I added control points using tkmedit and ran recon-all -autorecon2-cp <subjid> and i get the following error. " Total Number of Modified Voxels = 854 (out of 716825: 0.119136) sh: wm.mgz: Permission denied Broken pipe Linux eesmith 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:49:06 EST 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Feb 18 14:34:54 EST 2009 " It says permission denied but I have permission to access and make changes to data. Regards Ayaz

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qdec for fMRI using categorical covariate?
by Dave Brohawn 19 Feb '09

19 Feb '09

Hello, I want to generate screenshots of group activation in an anatomical ROI on the left and right hemisphere for two different groups of subjects at a particular contrast and time point of our analysis. We want to use race as a covariate (categorical, with whites and blacks being the two racial groups), and the screenshots to reflect this covariate being taken into account. Many examples I have seen on the wiki and in freesurfer archives describe cortical thickness studies, or use covariates that are continuous (age). Is qdec the program I want to use, and how do I ensure it treats race as

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mris_anatomical_stats segmentation fault
by Diana Wotruba 19 Feb '09

19 Feb '09

Dear FS experts I divided the fsaverage parcellations (aparc.a2005s) with an area threshold of 100mm2. Now I would like to get a stats file, using the following command: mris_anatomical_stats -a aparc.a2005s_100.annot -t ?h.thickness -b -f 001/stats/?h.aparc.a2005s_100.stats 001 ?h I am getting the following error message: "Segmentation fault" (after 1374 entries are read) The same command works just fine with a parcellated .annot file I generated with a lower threshold (p.e. 150mm2). Any help would be appreciated Regards Diana

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- dt_recon and coregistration of DTI to anatomy
by Kjell Inge 19 Feb '09

19 Feb '09

I am using Freesurfer and I am having difficulties in coregistration of a DTI volume to the anatomy image. I have been running recon-all -i <anatomy1.nii> -i <anatomy2.nii> -s 2005_anatomy followed by recon-all -autorecon1 -s 2005_anatomy and then dt_recon --i dti/subj_539_dti.nii --b dti/aging_hds_2005_dti.bval dti/aging_hds_2005_dti.bvec --s 2005_anatomy --o outputdti where "dti/subj_539_dti.nii" is my DTI volume, "aging_hds_2005_dti.bval" and "dti/aging_hds_2005_dti.bvec" are my bval and bvec files and "2005_anatomy" is my subject folder. I have made an output folder inside "2005_anatomy" named "outputdti" My bval and bvec files are attached below. Everything runs smoothly with no error messages, and there is a bunch of files created in "outputdti". Now, my questions are as follow: 1. How do I see the registered DTI (for instance the FA) visualized on the anatomy? Is the finally registered FA image inside the file "FA.nii" or do you have to run a transformation on that? If so, which transformation and how is that done? There are several files containing rigid transformations, the .reg files and the register.dat file. When I check FA.nii it does NOT seem to be coregistered with my anatomical input image. What went wrong? 2. When I open the image "mask.nii" it is like a white box, no structures, is this really correct? Does this mean that the BET has not succeeded? However, when I open "brainmask.mgz" by "tkmedit" it is certainly skullstripped. 3. Does dt_recon really do a nonlinear registration? When looking through the script, I can only see that dt_recon uses flirt (inside "eddy_correct" on the "dwi.nii", producing "dwi-ec.nii" and inside "fslregister", applied to "lowb.nii") which is an affine registration tool. I hope someone can solve my problems. Erlend bvec: 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 bval: 0 0 0 0 0 -0.532213 -0.25014 0.633507 0.218922 0.41315 -0.734236 -0.93647 0.333112 -0.103315 0.92654 -0.801489 0.916837 0.537756 0.213559 0.124139 -0.27398 0.443315 -0.024171 -0.568365 -0.93093 0.825459 -0.472598 -0.504263 -0.149336 0.694717 0 0 0 0 0 0.104013 -0.721834 -0.753136 0.850393 -0.780294 -0.661804 0.054189 -0.242859 -0.991677 0.372983 0.543143 -0.261948 0.438028 -0.664684 -0.051816 0.960273 0.878048 0.368772 0.637098 -0.168158 -0.182178 -0.629557 -0.129265 0.688743 0.344412 0 0 0 0 0 -0.840197 0.64528 -0.177358 0.478441 0.469519 0.151371 0.346537 0.911074 -0.076828 -0.04907 -0.250221 0.30132 -0.720382 -0.715952 -0.990911 -0.053015 -0.180284 0.929206 0.520641 -0.324178 -0.534255 -0.616692 0.85382 -0.709459 0.631465 _________________________________________________________________ Connect to the next generation of MSN Messenger http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=…

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qdec for fMRI analysis with categorical covariate? (continued)
by Dave Brohawn 19 Feb '09

19 Feb '09

as a categorical covariate? Thank you, Dave Brohawn

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recon-all error: libexpat.so.0
by Narly A Golestani 19 Feb '09

19 Feb '09

Dear all, I installed freesurfer_Linux_centos4_x86_64-stable-pub-v4.2.0-full on SuSE Enterprise (SLED 10.2), and ran recon-all. The process ran until near the end, and then terminated with the following error: ***************** ..... Reporting on 49 segmentations #-------------------------------------------- #@# Cortical ribbon mask Fri Feb 13 15:31:16 CET 2009 /home/narly/data/freesurfer/subjects/2_Lena/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 2_Lena mris_volmask.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory ************************** but I'm able to visualise the labels on the 3D volume using tksurfer (i.e. the output looks ok). Do I still need to install libexpat.so.0, and if so, how? thanks in advance, Narly.

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getting vertex numbers
by Lars M. Rimol 19 Feb '09

19 Feb '09

Hi, I've done a glm model fit comparing cortical thickness between two groups, and have certain areas ("blobs") on the cortical surface that are above sig. threshold. I'd like to get a list of the vertex numbers for each of these significant areas, which do not correspond to the parcellations in FS. In other words, I'm not trying to combine the already excisting ROI's. I've tried drawing labels (on fsaverage) and saving them, but without success. I clicked on 'Make path' and tried to mark vertices around the area, then I tried 'Custom fill' with various options, and 'Mark label', 'New label from marked' and 'save label'. But I only manage to save one or at most 3-4 vertices. I'm using FS v 4.0.5. Any tip on how to do this would be appreciated! Thank you! -- yours, LMR

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