Freesurfer

freesurfer@nmr.mgh.harvard.edu

8 participants
30091 discussions

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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subcortseg flag
by A. Yamamoto 15 Mar '13

15 Mar '13

Hi, After upgrading to FreeSurfer 5.2.0, the command with "-subcortseg" flag exited with the following error. MRISread(/usr/local/freesurfer/5.2.0/dist/subjects/test/surf/lh.white): could not open file The "-autorecon1" stage finished without error, so I'm wondering if there is any change in mri_segstats?? FYI, I have attached the last part of recon-all.log file. Thanks for your help. Akio

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mri_cvs_register - use of wmparc instead of aseg
by Güllmar, Daniel 14 Mar '13

14 Mar '13

Dear Lilla, i'm currently applying mri_cvs_register and I'm very happy with the nice results. Congratulation for this very clever approach. However, some data sets which I work on have still aseg.mgz which are not segmented appropriately. As far as I understand aseg.mgz is not redefined after e.g. pial-edits or added control points. Thus, I think it might be better to use aparc+aseg or wmparc instead of aseg within mri_cvs_register. Taking this into account I have the following questions: 1. Do you have experience with mri_cvs_register and --asegfname Option different from aseg? Does it impact the processing time? Are there options, which have to be adopted? 2. Since I think it is better to use aseg instead of wmparc, since it contains fewer IDs and registration will not be overfitted, is there a convenient way to generate a new aseg.mgz, which includes manual corrections like pial edits? 3. The last question regards the norm.mgz ... since it also often contains to much (outer brain) volume .. would it be better to mask norm.mgz with (e.g.) wmparc or a dilated version of wmparc before using it with mri_cvs_register ? Thanks you, Daniel Universitätsklinikum Jena - Bachstrasse 18 - D-07743 Jena Die gesetzlichen Pflichtangaben finden Sie unter http://www.uniklinikum-jena.de/Pflichtangaben.html

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