Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

tksurfer display question II
by j janssen 19 Nov '08

19 Nov '08

i´ll rephrase my question: can one display "filled" labels and other "outlined" labels at the same time in tksurfer? see my current attachment (made with help from Gimp..): surface+curvature+aparc (outlined)+some label (filled)+some label (filled). mri_annotation2label will give me labels, fine, but it won´t solve my rephrased question, i think. appreciate your help! -joost Or do you want the separate units to have separate colors? If that's your > goal you can use mri_annotation2label to turn all the parcellation units > into labels and only use the 2 (or more) that you want. > > > cheers, > Bruce > > On Wed, 19 Nov 2008, j janssen wrote: > > Hi Bruce, >> >> to be 100% sure that you guys understand what i want, i have attached the >> same attachment as before but now i quickly manually-painted in some >> regions >> using Gimp. Now, obviously i would like to do this not-manually and within >> FreeSurfer. is this possible? >> >> >> you can use the "custom fill" tool to fill up to other labels. >> >> >> how can i use "custom fill" to fill up a specific label, making it visible >> in tksurfer while keeping the other labels in 'outlined' status? >> >> >> >> You can also start with "all marked vertices" and click in a number of >>> regions, then save them as a label (you can change its color with the >>> "change label color" button on the 2nd row of icons near the right). >>> >> >> >> with "its" you refer to 1 label representing "all marked vertices" for >> which >> the color can be customized. look at the attachment, this is not what i >> would want. maybe i´m missing something obvious, apologies. >> >> -joost >> >> >> >>> >>> On Wed, 19 Nov 2008, j janssen wrote: >>> >>> Hi, >>> >>>> >>>> using version 4.0.5 >>>> >>>> look at the attached picture. its the result of: >>>> >>>> tksurfer code lh inflated -aparc aparc -gray >>>> >>>> i have selected one region (yellow outline). i would like to >>>> - fill this region and some other regions, *but not all regions*! >>>> - give the filled regions different color-labelings >>>> - i would like to display them (outlined and filled regions) at the >>>> *same* >>>> time. >>>> >>>> i have tried numerous ways, without result. any suggestions? >>>> >>>> thanks, >>>> -joost >>>> >>>> >>>>

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tksurfer display question
by j janssen 19 Nov '08

19 Nov '08

Hi, using version 4.0.5 look at the attached picture. its the result of: tksurfer code lh inflated -aparc aparc -gray i have selected one region (yellow outline). i would like to - fill this region and some other regions, *but not all regions*! - give the filled regions different color-labelings - i would like to display them (outlined and filled regions) at the *same* time. i have tried numerous ways, without result. any suggestions? thanks, -joost

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mri_surf2surf - Error
by Alexandru Hanganu 19 Nov '08

19 Nov '08

Dear Freesurfer Users, We have a little problem with mri_surf2surf. Our goal is to determine the statistical data - t-test, ANOVA, for a group of subjects. So initially we made the recon-all, autorecon1,2,3 and -qcache for all subjects. After that we created the FSGD file and mris_preproc - in order to create ?h.thickness.mgh file. Now in order to initiate the mri_glmfit step we have to create the ?h.thickness.sm10.mgh file with the mri_surf2surf command. We used this command line: mri_surf2surf --hemi lh \ --s average \ --sval lh.thickness.mgh \ --fwhm 10 \ --tval lh.thickness.sm10.mgh and we receive the Error: – /usr/local/freesurfer/subjects/average/surf/lh.sphere.reg – could not open file Could you please tell us where might be the mistake ? What step is needed to create the lh.sphere.reg file. Thank you very much for your help. Best regards, Dr. Alexandru Hanganu ___________________________________ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.

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recon-all -long questions
by Mishkin Derakhshan 18 Nov '08

18 Nov '08

Hi, I have a couple questions regarding the -long option. 1) The longitudinal instructions listed in recon-all -help all use recon-all -all -long. If I am only interested in the subcortical segmentation, will the longitudinal processing still work if I only use recon-all -subcortseg ? 2) How long does the longitudinal pipeline take for a) tp1, which has already had the cross-sectional workflow run b) tp2, which gets compared to tp1. I suspect a) and b) are the same, but do they take the same amount of time as a conventional cross sectional run? thanks, mishkin

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Configure thresholds in overlay options
by Juranek, Jenifer 18 Nov '08

18 Nov '08

Hi, Running FSv405 on RHEL5. Is any descriptive information available for threshold options in the configure overlay display gui? Specifically the bases for linear, linear opaque, and piecewise thresholds? Visually, the three options appear dramatically different. Are there specific datatypes each overlay option is designed to handle? Many thanks for any information you can provide, Jenifer

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(no subject)
by Al-Radaideh Ali 17 Nov '08

17 Nov '08

Dear FreeSurfer expert, Any way that I can convert the mgz back to any analyze format so that different softwares can open it?. if not, any software that can open the mgz other than freesurfer? Many thanks Ali This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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RE: [Freesurfer] RE: for cortical thickness
by Zhang, Xiaochu (NIH/NIDA) [F] 17 Nov '08

17 Nov '08

This mask is from functional group analysis. Before I did do group analysis, I have to transfer all individual data into standard space. Therefore, there is no special reference for this mask. The only reference whole brain data is the standard talarich dataset in AFNI. I know if I want to get a perfect anatomical ROI mask, I should draw it based on the subject's own T1 data. However, because I want to run a functional and anatomical combined study, I prefer to use one exactly standard ROI from funcitonal result although it has high variability. Usually, in this case when I do a ROI analysis, I will transfer the ROI from the standard space back to the individual space. Please feel free to contact me if you still have some questions about the ROI mask. Thanks a lot! Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch National Institute on Drug Abuse - IRP Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619 -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Monday, November 17, 2008 2:37 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Subject: RE: [Freesurfer] RE: for cortical thickness can you send the file from which ROI5.nii was created? we would need something, even if it is a functional scan, that shows the whole brain, so that we have a reference of just where the mask voxels are located in the brain. our surface tools do not work directly with talairach coords because those coords have such high variability (that can off by as much as 2cm, or more). On Mon, 2008-11-17 at 14:02 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > Thank you so much for your response, Nick! > I uploaded "ROI5.nii" (i.e., abc.nii) just now. This ROI has been in > Talarich space. > Actually, it is from my group functional data. So I did not have > corresponding T1-data. > > BTW: when can I read the web page describing the steps taken to get > cortical thickness from an ROI defined by a volume mask? I hope I can > read it ASAP. If it is possible, could you please do me a favor and > send the draft to me? > Thanks, again! > > > Xiaochu Zhang PhD > > Visiting Research Fellow > > Neuroimaging Research Branch > > National Institute on Drug Abuse - IRP > > Biomedical Research Center > > 251 Bayview Blvd. > > Suite 200 (NIDA) > > Baltimore MD > > 21224 > > Tel: 443-740-2619 > > > -----Original Message----- > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Monday, November 17, 2008 12:59 PM > To: Zhang, Xiaochu (NIH/NIDA) [F] > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] RE: for cortical thickness > > Xiaochu, > > I'm putting together a web page describing the steps taken to get > cortical thickness from an ROI defined by a volume mask. Can you send > me these two files so that I can make sure the steps work correctly? > > 1) the ROI mask file (what you are calling 'abc.nii') > 2) the T1-weighted anatomical volume of the subject from which abc.nii > was created. i need this file to register to a template volume. > > You can post those files (available only to me) by uploading to our > file > drop: > > https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Nick > > > On Sat, 2008-11-15 at 00:48 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > > Hi, FreeSurfer export, > > > > Thank you very much for response! > > Now, under some export's help, I used to the mri_surf2vol to > > transfer > cortex thickness into nifti. > > The below line is what I used. > > mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon > > --template orig.mgz --volregidentity ${subid} --outvol lh.ribbon.nii > > > > I checked the result and found the voxel outside the gray matter is > always zero and in the gray matter is about 0-3. Could you please do > me a favor and tell me whether these data is cortex thickness or not? > > If they are cortex thickness, why are they always different. In my > mind, it should be same in one direction because we calculate the > distance between the white matter line and the gray matter line. > > > > Thanks a lot! > > All the best, > > Xiaochu > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > >

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FreeSurfer
by Bruce Fischl 17 Nov '08

17 Nov '08

Dear FreeSurfer users, We wanted to make you aware of a paper recently published in Neuron by Makris et al. (Neuron, 2008, volume 60 issue 1 pp.174 - 188) that may prompt questions by reviewers of studies employing FreeSurfer. Please find attached the figure that the authors published in this paper depicting some inaccurate FreeSurfer surfaces (the top image labeled "CV-FS" uses manual segmentations carried out by some of the authors followed by a surface-deformation that we provided for them, and "FS" on the bottom is the automated FreeSurfer result). Since publication the authors provided us access to the original data. Unfortunately it seems that many of the inaccuracies were probably a consequence of sub-optimal motion correction as well as averaging of multiple T1 volumes in the presence of substantial between-scan subject motion. Obviously it would have been better if this problem had been identified and communicated to us prior to publication, as we are always happy to help improve the results with any users of our tools. We also feel that this kind of comparison is best done systematically and quantitatively rather than using arbitrary slices that may illustrate a desired point. We have already been told that in some quarters this paper is being taken to show that automated methods such as FreeSurfer should be used very cautiously. Because of this, we communicated with the authors, and after some discussion they agree that these results are not representative of a widespread inaccuracy of our tools, but rather a localized incident indicative of poor motion correction. We have contributed a joint comment to Neuron to this effect that includes a re-analysis of the data using only a single acquisition per subject to remove motion-correction artifacts, the results of which can be found at: http://surfer.nmr.mgh.harvard.edu/fswiki/NeuronMakris We think that it is important to communicate this to a wider audience of FreeSurfer users and readers of relevant journals. Certainly all software has failure modes and users are always encouraged to carefully examine their data. However, if anyone feels that in their experience FreeSurfer surfaces are significantly more accurate than those shown in the attached figure, we encourage you to contribute a comment at neuroncomments(a)cell.com via email. Feel free to email us if you have any questions. The FreeSurfer Team

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Talairach space yes or no?
by Marieke Langen 17 Nov '08

17 Nov '08

Dear FreeSurfer people, I have got a very basic question. I would like to (or better: have to) do some manual tracing on my data. For this, I want my brains to be motion- and nu-corrected and in Talairach. Therefore, I apply the -autorecon1 step to my dataset. I always assumed that the T1.mgz output is in Talairach space, but 1) when I compare it to the original scan and 2) when I look at the processing flow in the ReconAllDevTable, I doubt this. Do I still need to apply the talairach.xfm to the T1.mgz or something like that? 1) Could you please let me know whether the T1.mgz is indeed the scan I need (thus: is T1.mgz the result of all the autorecon1-steps, accept for skullstripping)? 2) If not: how do I process my scans so that they are motion- and nu- corrected and in Talairach space? THANK YOU! Marieke

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volume in freesurfer
by Lúcia Garrido 16 Nov '08

16 Nov '08

Hello, I've run recon-all in two groups of subjects using FS version 4.0.2. I want to compare cortical thickness between the two groups, but I'd like to also compare volume maps between groups. I'd like to see how results in FS compare with results from VBM. In the 'measures' available in design I can't see the option to compare volume, though the tutorial on the website says it's available. Is this a feature that is not available in my version? Can I use a more recent version to run stats on the results from recon-all in v4.0.2? If this is not possible, is there any other possible way to compare volume maps? Thank you very much. And I'm sorry if this info is already available in the mailing list, but I couldn't find it. Best regards, Lucia

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