Freesurfer

freesurfer@nmr.mgh.harvard.edu

10 participants
30093 discussions

running mris_preproc for each glm?
by Laura M. Tully 15 Mar '13

15 Mar '13

Hi freesurfer experts, I'm planning to run a few different glms on surface data using glm_fit e.g. diagnosis * age; diagnosis * age * symptoms; diagnosis * age * somebehavioral variable etc.. Do I have to run mris_preproc using the specific fsgd file for each glm? My data are already qcached, and it seems that there may be an option (-cache--in?) that I can use on just one mris_preproc but I'm not sure if this is correct, or what the -cache--in option does. Thanks! Laura. -- -- Laura M. Tully, MA Social Neuroscience & Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltully(a)mednet.ucla.edu ltully(a)fas.harvard.edu 310-267-0170 -- Follow me on Twitter: @tully_laura

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Re: [Freesurfer] Help with vertices
by Bruce Fischl 15 Mar '13

15 Mar '13

Hi Neha the vertices are indices into the surface file. You can load it in with read_surf, and find the corresponding vertex in the surface (e.g. ?h.white). These are in "surface RAS" or "tkreg RAS" coords, which you will then need to convert to volume coords. I believe Doug has documented this extensively on the wiki. Search for "coordinate systems" and see what you can find Bruce On Fri, 15 Mar 2013, Neha sharma wrote: > Hello freesurfer experts, > I am trying to extract the labels for temporal lobe. This is how i do it, > > i get the vertices > from [vertices,label,colortable]=read_annotation('?h.aparc.annot'); > > The vertices however are indices and if i use matlab's ind2sub to find > corresponding voxel locations in aparc+aseg (256^3 space) I get something > insensible. Am I doing something wrong? I am very new to freesurfer. > > Best, > > Neha > > >

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Definition of temporal lobe
by Akshay 15 Mar '13

15 Mar '13

Hello all, Which labels reside in temporal lobe? Do I look at aseg or aseg+aparc.? I am very new to freesurfer therefore forgive me for my naive questions. Best, Akshay

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Error messages and empty surf files
by Hayley Dorfman 15 Mar '13

15 Mar '13

Hello, I'm having trouble with recon-all. For 1 of 49 subjects, it completes with the following error: mri_watershed Error: GLOBAL region of the brain empty ! Other errors are found in the log which read: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCES This subject's surf files are also empty. I found this thread from two years ago mentioning a similar issue, but a solution was not available: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18863.html Has there been any progress? I've attached my log file. Any help is much appreciated! -Hayley

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Caret to Freesurfer
by Ellspermann, Kara 15 Mar '13

15 Mar '13

I am new to Freesurfer, and I am trying to input/process preterm infant brain data (ultimately attempting longitudinal registration). I already have surfaces generated from Caret, as well as the original T1/T2 images. My question is: Does anything exist to take processed data from Caret into Freesurfer? If not, is there a good way to process the T1/T2 images in Freesurfer despite the differences in contrast and intensity (and anatomy)? Thank you in advance for your advice, Kara

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mri_convert problem
by Valtina Pouegue 15 Mar '13

15 Mar '13

Hi, I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error; -------------[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gzmri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc...mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc[esther@m3012-04 ~]$ --------------------I look up, and the file is at the rith place.... Could you help me..Thanks VP]

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Rejoindre mon réseau sur LinkedIn
by David Chen via LinkedIn 15 Mar '13

15 Mar '13

LinkedIn ------------ David Chen souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de David Chen http://www.linkedin.com/e/-qq80um-hebi3k3g-6j/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de David Chen http://www.linkedin.com/e/-qq80um-hebi3k3g-6j/rso/42105959/HtV3/name/664711… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hebi3k3g-6j/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Correcting CPs and Pial
by Claudia Dacquino 15 Mar '13

15 Mar '13

Hi everyone, I'm a very new fresurfer user and I have to understand the very simple basis of its use yet. So I have some maybe stupid questions about that. I heve to work on cortical thickness, so I suppose I have to complete the segmentation and then correcting CPs and Pial surface. The first question is if I have to edit CPs first and then, after running recon-all -autorecon2-cp -autorecon-3, to edit the Pial surface? The second is in the CPs editing have I to add ctrl pts in white matter areas that are less then 110 in voxel intensity? The last one is how do I have to correct the grey matter? Have I to paint all the None Sgmtn label points, or just the ones incorporating a piece of dura? Thanks a lot, and sorry for the very basic questions. Claudia

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question about autorecon2-cp, autorecon-pial and autorecon-wm flags
by Mehul Sampat 15 Mar '13

15 Mar '13

Hi Folks, I was looking at the autorecon2-cp, autorecon-pial and autorecon-wm flags in recon-all help and also here http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags My interpretation is when I use autorecon-pial, I only need the command: recon-all --autorecon-pial -s subject While for autorecon2-cp and autorecon2-wm we need the command: recon-all -autorecon2-cp -autorecon3 -s subject recon-all -autorecon2-wm -autorecon3 -s subject since for autorecon2-cp and autorecon2-wm only a subset of stages are processed as described in recon-all help: -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg) -autorecon2-wm : process stages 15-23 Thanks Mehul

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"rm:No match." when executing recon-all -qcache
by Yang, Daniel 15 Mar '13

15 Mar '13

Hi all, When I run "recon-all –qcache", there are a lot of Error messages saying "rm: No match." (although just this error message, no others). I'm wondering if this is something of concern, or something I can simply ignore. Thanks! Daniel

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