Freesurfer April 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
147 discussions

generating WM parcellation using Destrieux atlas
by Mehul Sampat 11 Apr '10

11 Apr '10

Hi Folks, I was trying to help a colleague generate a wmparc for the Destrieux atlas. That is I am trying to create "wmparc.a2009s.mgz" and "wmparc.a2009s.stats" I used the following two commands: mri_aparc2aseg --s subject_id --labelwm --hypo-as-wm --rip-unknown --new-ribbon --wmparc-dmax 4 --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz mri_segstats --seg mri/wmparc.a2009s.mgz --sum stats/wmparc.a2009s.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject subject_id --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt I was able to run this and I noticed that a number of labels in "wmparc.a2009s.stats" do not have any voxels assigned to them. for examples: 762 4174 0 0.0 wm-rh-S_subcentral_ant 0.0000 0.0000 0.0000 0.0000 0.0000 763 4175 0 0.0 wm-rh-S_subcentral_post 0.0000 0.0000 0.0000 0.0000 0.0000 764 4176 0 0.0 wm-rh-S_suborbital 0.0000 0.0000 0.0000 0.0000 0.0000 765 4177 0 0.0 wm-rh-S_subparietal 0.0000 0.0000 0.0000 0.0000 0.0000 766 4178 0 0.0 wm-rh-S_supracingulate 0.0000 0.0000 0.0000 0.0000 0.0000 768 4180 0 0.0 wm-rh-S_temporal_superior 0.0000 0.0000 0.0000 0.0000 0.0000 769 4181 0 0.0 wm-rh-S_temporal_transverse 0.0000 0.0000 0.0000 0.0000 0.0000 It seems like only labels corresponding to the Desikan atlas have voxels assigned to them in "wmparc.a2009s.stats" ? do you think I made an error while generating "wmparc.a2009s.stats" ? thanks Mehul

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Missing usage for mris_distance_map
by Michael Waskom 11 Apr '10

11 Apr '10

Hi All, I'd like to use mris_distance_map, but it looks like the usage/help info is missing or broken (At least in 4.4.0/4.5.0). When I try it with just the command or -help, it looks like this: mwaskom@ba2:~$ mris_distance_map --help usage: mris_distance_map [options] <input surface file> <output scalar field (.mgz)> This program will compute a distance map of each point on the surface to a reference point (vertex 0 by default) valid options are: mwaskom@ba2:~$ Can someone help me out with these mysterious options? Also, how is it calculating distance? Thanks! Mike

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Analysis of Cortical dysplasia
by Bhavani shankara 10 Apr '10

10 Apr '10

Dear freesurefer experts, I am a freesurfer beginner , e have a MPRAGE image of cortical dysplasia. Is their any way of analysing that single image and to compare with the standard (talairchie or other) template and note the involvement of the cortex. I tried doing recon-all but in autorecon1 command itself it is stopping in the middle and saying that on comparing with the template it is not fitting with the template. Please let me know any methods Thank you in advance expecting a answere. -- Dr. BHAVANI SHANKARA BAGEPALLY PHD STUDENT (CLINICAL NEUROSCIENCES) NIMHANS, BANGALORE, bshankara(a)ymail.com

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Processing of brains with malformations of cortical development
by Diego Herrera 09 Apr '10

09 Apr '10

Hello Do you know how would theorically behave Freesurfer with pathologic brains with malformations like polymicrogiria, schizencephaly, etc. Also, do you have experience with subtle malformations like Focal Cortical Dysplasia (FCD)? Recently, we tried recon-all in a polimicrogiric brain obtaining a very acceptable segmentation. Thanks -- Diego Herrera, M.D. Neuroradiologist Medellin, Colombia

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CEPHES ERROR: fdtrc domain error
by Lars M. Rimol 09 Apr '10

09 Apr '10

Hi, I get this error message when running glm_fit (v.3.02): CEPHES ERROR: fdtrc domain error (I see you've handled this error message before, but there was no solution there: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11602.html) I'm using a model with two groups, and age and ICV as continuous regressors. The error message comes when estimating the 0 0 0 1 contrast, i.e. ICV. Matrix condition = 494.18. The beta for this covariate shows very small numbers, i.e. 0-6*10^-1. And the sig.mgh file for it shows all vertices = 1e+10. yours, Dr. Lars M. Rimol

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Analyze 7.5 hdr into .mat file
by SG KIM 09 Apr '10

09 Apr '10

I want to import anlayze75 with a right direction (still). I have those files: subject.hdr subject.img And got warnings as: -------------------------- INFO: could not find ~/subject.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in ~/subject.mat file -------------------------- I know the orientation info should be provided somehow; but I don't know how to do it. I just tried to make a corresponding MAT file containing header info by simply saving whole header info as >>HRD=analyze75info('subject.hdr'); >>save subject.mat HDR But I got another error as ----------- unsupported matlab format 262149 (unknown) MatrixMultiply: m1 cols 1 does not match m2 rows 4 Segmentation fault ----------- *Does someone who handled Analyze75 format before know how to create a corresponding MAT file?* SG. +I firstly tried import without MAT file, then I worked but with a wrong direction (fig1). I checked the header file. It says 'Transverse unflipped' as default, which is also perplexing because the import was made using the default orientation 'Transverse unflipped' anyway.

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Retinotopy with bow ties
by Peter Jes Kohler 08 Apr '10

08 Apr '10

Hello Everyone, I am a new FreeSurfer user, trying to do retinotopy. My stimulus has the following configurations: - 96 TRs in total per run, including 8 blanks in the beginning and 8 in the end - Polar angle: - bowtie checkerboard wedges - 16 unique positions - 5 repetitions per run - 2 TRs per position per run = 80 stimulus TRs per run. - counterclockwise or clockwise rotation - Eccentricity - checkerboard annuli - 16 unique eccentricities - 5 repetitions per run - 2 TRs per position per run = 80 stimulus TRs per run - expanding on contracting I have 3 runs of CCW wedges, 3 runs of CW wedges, 2 runs of expanding annuli and 2 runs of contracting annuli. I have used this guide by Xu Cui as a template for directory structure and analysis: http://www.alivelearn.net/?p=65 I I have made appropriate .par-files and placed them in the folder for every run. In mk-analysis-sess.new I set ncycles to 5 (because I have 5 repetitions per run). After I paint the results on the flattened map the eccentricity map looks like other maps I've seen, but this the polar map looks awful - like random spray paint on the flattened surfaces, and with a lot of space with no coloring, even close to the calcarine. The field sign maps are completely empty, not even the flattened surface shows up (I don't know how they are supposed to look, but its all black). I have tried several solutions: a) removing the blank TRs from my functional data files, so that only stimulus TRs are included in my analysis. b) setting ncycles to 10 (because we essentially have two polar wedges on the screen at each position). But none of this has helped. I am also somewhat unclear on the settings inside surf-sess. For example, what do I set the values in phase encoded data display at? I would be grateful for any suggestions that might help - if you need to know anything else about my stimulus or analysis, please let me know. Best, Peter K.

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implementation of topology correction
by Jerald Zhao 08 Apr '10

08 Apr '10

Hi freesurfer experts, I have some volumes, which are grey matter surface, to be corrected. So I want to compare the performance of various topology correction methods. Can I only implement the topology correction method in freesurfer? thanks in advance, Jerald

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Covariate for results of cortical parcellation
by Liukarl 08 Apr '10

08 Apr '10

Hello, Freesurfer experts: I noticed for analyzing the results from autorecon2, the intracranial volume are controlled as covariate in some publications. Is there any corresponding covariate for cortical results from autorecon3, cortical thickness, surface, and volume? In my current study, there are two group: one is a group with less optimal developmental environment and the other is control. I noticed that without any covariate, the r square from cortical measure and group variable was really low, only accounting for 2%. Is any standard way to analyze the cortical data? Thanks! Karl _________________________________________________________________ MSN十年回馈，每位用户可免费获得价值25元的卡巴斯基反病毒软件2010激活码，快来领取！ http://kaba.msn.com.cn/?k=1

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tksurfer: Load multiple overlays from command line
by Dickinson, Annelise (NIH/NIMH) [F] 08 Apr '10

08 Apr '10

Hi all, What would be the syntax for loading multiple significance maps into different tksurfer overlay layers from the command line? I tried: tksurfer D14 lh.inflated -overlay lh.Tstat1.mgh -overlay lh.Tstat2.mgh --overlay lh.Tstat3.mgh And tksurfer D14 lh.inflated -overlay lh.Tstat1mgh lh.Tstat2.mgh lh.Tstat3.mgh But neither of those worked. Thanks so much for your consideration! ***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona(a)mail.nih.gov

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Freesurfer April 2010