Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

Re: [Freesurfer] Caret to Freesurfer
by Nick Schmansky 15 Mar '13

15 Mar '13

Kara, the gifti format is used to convert between caret and freesurfer surfaces. use mris_convert (see --help). Nick > Matt, > > Yes, I think the plan is to discuss this and other potential options. I > had a feeling you may know the most, but I thought I would send out the > question in case anyone else has tried. As it stands, it sounds like no > method currently exists for a Caret surface-to-Freesurfer transition? > > I am still trying to understand Freesurfer basics, but it sounds like the > longitudinal pipeline generally requires the same input data as > across-subject. My hope is that, since the surfaces are already > constructed, I can avoid the need for an (infant) atlas, but I am still > figuring out what that means in terms of files I need/conversion/etc. > > Thanks for your help, and I look forward to further discussion this > afternoon. > > Kara > > > ________________________________________ > From: Matt Glasser [matt(a)ma-tea.com] > Sent: Thursday, March 14, 2013 7:14 PM > To: Bruce Fischl; Ellspermann, Kara > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Caret to Freesurfer > > She wants to go from Caret to FreeSurfer, rather than from FreeSurfer to > Caret, which is what I do. > > Kara, I believe we are meeting tomorrow to discuss the options for this? > > I don't know anything about the FreeSurfer longitudinal pipeline, but it > would take going through the pipeline and finding all of the inputs needed > and converting them or generating them. I think the main goal here is to > use the longitudinal surface registration. > > Matt. > > On 3/14/13 8:04 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >>Hi Kara >> >>I think the answer is yes as there are people at Wash U that do this >>routinely. Maybe Matt Glasser or someone else can chime in? >> >>cheers >>Bruce >> >> >>On Thu, 14 Mar 2013, Ellspermann, Kara wrote: >> >>> 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 >>> >>>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>The information in this e-mail is intended only for the person to whom it >>is >>addressed. If you believe this e-mail was sent to you in error and the >>e-mail >>contains patient information, please contact the Partners Compliance >>HelpLine at >>http://www.partners.org/complianceline . If the e-mail was sent to you in >>error >>but does not contain patient information, please contact the sender and >>properly >>dispose of the e-mail. > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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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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Freesurfer March 2013