Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Can not visualize read_surf.m output with matlab
by ye tian 19 Jun '14

19 Jun '14

Dear Freesurfers, I tried the following in matlab [coords,faces] =read_surf('\subject\surf\rh.orig') Hp = patch('vertices',coords,'faces',faces(:,[1 3 2]),... 'facecolor',[.5 .5 .5],'edgecolor','none') camlight('headlight','infinite') vertnormals = get(Hp,'vertexnormals'); Matlab returns the following error: Error using patch Faces values must be >= 1.0 Indeed, there are 0's in faces. Is this a mistake? Thank you very much! Sincerely, Ye

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GLM: what does "mris_preproc" do?
by ye tian 18 Jun '14

18 Jun '14

Hello Freesurfers, I understand that the output of "mris_preproc" can be the input of "mris_glmfit". In mris_glmfit, a GLM is performed. Does "mris_preproc" give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects? Thank you very much! Sincerely, Ye

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Mouse use for tkmedit
by Caroline Lewis 18 Jun '14

18 Jun '14

Hi, I'm using freesurfer on a mac computer, and therefore my mouse doesn't have a right click or middle button. Is there an alternative way to make edits in tkmedit (such as to correct voxels erroneously classified as white matter in recon-all) without using the mouse buttons? Thanks, Caroline

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GLM: What's the link?
by ye tian 18 Jun '14

18 Jun '14

Hello Freesurfers, I can not tell what the link is from the Mathematical Background in mri_glmfit . Also, why is GLM performed instead of a linear regression (OLS or weighted LS )? I can not see how logistic, probit, etc is better. Thank you very much! Sincerely, Ye

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FreeSurfur Installation problems
by Jonathan Thomas O'Neil 18 Jun '14

18 Jun '14

Hello, I am having issue with running Tkmedit, tksurfer, qdec, and recon-all. Based on the error messages I am receiving, it appears that the program think I have permission issues. I have checked these and that does not appear to be the case. Here are the errors I am getting. Please let me know what I can do tkmedit: mss169:Desktop jto929$ tkmedit bert orig.mgz =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> : : Now exiting... tksurfer: for tksurfer it seems to run, but then stops. a view appears on the screen, but then immediately disappears. s169:Desktop jto929$ tksurfer bert rh pial subject is bert hemi is rh surface is pial surfer: current subjects dir: /Users/jto929/Desktop/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/jto929/Desktop checking for nofix files in 'pial' Reading image info (/Users/jto929/Desktop/freesurfer/subjects/bert) Reading /Users/jto929/Desktop/freesurfer/subjects/bert/mri/orig.mgz surfer: Reading header info from /Users/jto929/Desktop/freesurfer/subjects/bert/mri/orig.mgz surfer: vertices=133299, faces=266594 surfer: single buffered window surfer: tkoInitWindow(bert) mss169:Desktop jto929$ qdec: mss169:Desktop jto929$ qdec Segmentation fault recon-all mss169:Desktop jto929$ recon-all -s bert -autorecon1 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/jto929/Desktop/freesurfer/subjects Actual FREESURFER_HOME /Users/jto929/Desktop/freesurfer rm: /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.cmd: Permission denied mv: rename /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.env to /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.env.bak: Permission denied /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.env: Permission denied. /Users/jto929/Desktop/freesurfer/subjects/bert/scripts/recon-all.env: Permission denied.

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Improving translation of Choi striatal ROIs to original domain
by Paul Beach 18 Jun '14

18 Jun '14

Hi Freesurfers, My processing stream involves moving the parcellated functional networks of Yeo and Choi to original subject domain to do connectivity analyses. While my process works very well for the Yeo networks I'm rather unsatisfied by the results of the Choi translations. I'm hoping someone has some suggestions for improving things so that the Choi ROIs map onto individual subjects nearly as well as the general Freesurfer striatal segmentations. NB - I work with AD patients, so I'm sure part of the problem is atrophy-based. However, I'm sure there are ways to improve things... *My current pipeline involves two steps:* *mri_vol2vol \* *--mov Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \* *--targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader \* *--o FSL_choi_17Net_MNI152_tight_parcellation.nii.gz --no-save-reg --interp nearest* *mri_label2vol \* *--seg FSL_choi_17Net_MNI152_tight_parcellation.nii.gz \* *--reg $SUBJECTS_DIR/{$subj}/mri/transforms/reg.mni152.2mm.dat \* *--invertmtx \* *--o Choi_17Network_tight_striatum_orig.nii.gz \* *--temp $SUBJECTS_DIR/{$subj}/mri/orig.mgz* I suspect one way to improve things would be to do a recon-all based procedure, but I have no clue what commands within the recon-all domain that would involve. Thanks for your suggestions. -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

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Re: [Freesurfer] Linear Mixed Models in FS?
by Lars M. Rimol 18 Jun '14

18 Jun '14

Hi Jorge, Thank you for your reply! Again considering the same model from before intercept(random effect) + centered age + group + group x centered age + sex I think what is confusing me is that I think of the [centered age] covariate as a column vector which will contain the centered age of both the control- and the case group. This is how it would be seen in a GLM using the same design matrix. Therefore it is difficult for me to understand how the contrast [0 1 0 0 0] can inform us about the control group alone. To me it would seem obvious that this contrast tells me something about the effect of [centered age] on the whole of the sample, regardless of the group each subject belongs to. On the other hand, I agree with you that the interaction term could tell us something about the effect of [centered age] on the case-group by considering the contrast vector [0 0 0 1 0]. Just for the sake of argument, please consider the following model intercept(random effect) + (1-group) x centered age + group + group x centered age + sex and compare to the one presented above. Here (1-group) is a column vector which is 1 where the [group] vector is 0, and vice versa. This difference ensures that the second term only includes numbers from the control-group. Applying the contrast [0 1 0 0 0] to this model, would this not be more appropriate for consider the effect of [centered age] on the control-group alone? Given your previous answers I suspect I'm missing something here, but I would greatly appreciate if you could please take the time to explain to me how I've gone wrong. Thanks! LMR ------------------------------------------------------------------- Hi LMR 1) Yes, you should use n-1 (0/1) covariates to model n groups. Eg. (Controls, Case 1 and Case 2) the model would be: intercept(random effect) + centered age?(might be a random effect too)?+ ?Case1 + Case1 x centered age + Case2 + Case2 x centered age + sex 2)In model: intercept(random effect) + centered age + group + group x centered age + sex the fourth coefficient is the interaction term that represents the difference in slope between the patient and control groups. This is easy to see from your Question 1 equations. It's also easy to see from those equations that [0 1 0 0 0] tests the effect of time in the control group since the group-specific slope is only equal to the coefficient of the time covariate (the second covariate) when the group covariate is zero (i.e for the controls). Hope this makes sense. Best -Jorge -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

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Re: [Freesurfer] problem of Label file
by kangchengwang0808＠gmail.com 18 Jun '14

18 Jun '14

Dear Bruce, Thank you very much for your response. The area which I made label could be seen in the figure (below). Is the reason for large number that the line was outside the blue area? Wang Kangcheng

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label from volume on decimated surface
by Kai Schlamp 18 Jun '14

18 Jun '14

Hello Freesurfer experts, I want to project a label from a volume on a decimated surface. Normally I do something like this to generate a label from the volume: mri_vol2surf --src subjects/foobar/mri/aparc+aseg.mgz --regheader foobar --hemi lh --surf pial --out test.mgh mri_cor2label --i test.mgh --id 1024 --surf foobar lh pial --l test.label Unfortunately this does not work if I decimated the lh.pial surface before (for example using mris_decimate). Do you have a suggestion how to accomplish this? Kai

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Researcher/Postdoctoral position: Multimodal Neuroimaging, Twins, Autism and ADHD, Karolinska Institutet
by Elodie Cauvet 18 Jun '14

18 Jun '14

Dear list, One Researcher/postdoc position is available in our group at Karolinska Institutet in Stockholm. Application Deadline is June the 30th 2014. --- Group and Project --- Karolinska Institutet Center of Neurodevelopmental Disorders (KIND) http://ki.se/kind KIND is an excellence center for research, development, education and clinical practice in the area of developmental psychopathology. The Roots of Autism and ADHD Twin Study Sweden (RATSS) is a frontline research project within KIND, focusing on monozygotic twins discordant for autism spectrum disorder and other neurodevelopmental disorders. For the first time ever, twins are examined on multiple levels: behavior, cognition, neurobiology, environment, and genetics to elucidate the etiology of neuropsychiatric disorders. Functional and structural neuroimaging using MRI are an integral part of RATSS. Scanning is performed at the Karolinska Institutet MR Research Center, using a 3 Tesla MR scanner (GE MR750). To date, 80 pairs have been examined. --- Position --- As a neuroimaging researcher (typically, but not necessarily post-doc) in RATSS, while working in a team of scientists, you are mainly responsible for the acquisition and analyses of the multimodal brain imaging data. Diffusion Tensor Imaging (DTI), resting state functional MRI and structural T1 analyses will be integrated into hierarchical network models such as brain connectome. We expect motivation, routine and professionalism in administrative tasks, grant application and article writing. This work will be done in close collaboration with other partners (e.g. Dr. Peter Fransson, the Dept. of Clinical Neuroscience (KI); Institute Pasteur (Paris), EUAIMS project, Mt Sinai (New York)). All details about the position can be found here: https://ki.mynetworkglobal.com/se/what:job/jobID:37590/where:4/ Applications should be submitted here: https://ki.mynetworkglobal.com/en/what:login/jobID:37590/where:4/ Please note that we DO NOT ACCEPT applications being submitted by email. To be considered, your application must be submitted through the application system. Best regards, Elodie Cauvet for KIND Élodie CAUVET | PhD Karolinska Institutet Center of Neurodevelopmental Disorders (KIND) Gävlegatan 22B, floor 8 | 113 30 Stockholm +46 (0)8 51452706 | +46 (0)728 774 058 elodie<mailto:elodie.cauvet@ki.se>.cauvet(a)ki.se<mailto:elodie.cauvet@ki.se> | ki.se/kind<http://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=en&d=130> ___________________________________________________________________________________ Karolinska Institutet – a medical university

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