Freesurfer November 2008

freesurfer@nmr.mgh.harvard.edu

70 participants
98 discussions

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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mris_volmask.bin: mris_volmask.bin:
by asaf achiron 16 Nov '08

16 Nov '08

dear group, after doing recon-all i get this error: mris_volmask.bin: error while loading shared libraries: /home/fsl/freesurfer/lib/vtk/lib/vtk-5.2/libvtkRendering.so.5.2: cannot restore segment prot after reloc: mris_volmask.bin: i am working on a centos 5. thank you, Asaf

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Hi and for transfer AFNI data to Free Surfer
by Zhang, Xiaochu (NIH/NIDA) [F] 14 Nov '08

14 Nov '08

Hi FreeSurfer experts, I am a beginner of free surfer. Now I am working on my previous dataset with new hypothesis. In this dataset, I found a ROI (located almost in gray matter) showed significant functional difference between groups. I want to test whether the cortical thickness is changed or not in this ROI. I have done "recon-all -autorecon-all" and did some necessary check for data quality. However, I met some problems: 1. The ROI dataset was from AFNI. How will I transfer into free surfer? Which command I can use? 2. After ROI transfered, what will I do to get the averaged cortical thickness from this ROI? Are there some example or manual I can read and learn? Thanks a lot! All the best, 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

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longitudinal processing
by Jared Price 14 Nov '08

14 Nov '08

Hi everybody, 2 quick questions about longitudinal processing. 1) does the longitudinal processing even call the default gca atlas or does it use something else? 2) when processing say 7 time points should all longitudinal scans be processed from baseline or should time 3 be processed from time 2 etc.

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Re: Atlas
by sameer kumar 14 Nov '08

14 Nov '08

Hi all, I am trying to find the sub directory in the Freesurfer directory which contains all the atlases like MNI, JHU, etc. Can you please help me out... Thanks, Regards, Sameer Kumar Gottipati

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Creating a FreeSurfer label/volume
by joel bruss 14 Nov '08

14 Nov '08

Hello- I'm running freesurfer-Linux-centos4-stable-pub-v4.0.5 on Suse 11. I've used the output of FreeSurfer, specifically wmparc.mgz to create a 32-bit volume to which I've applied edits. The two commands I used were: mri_vol2vol --mov mri/wmparc.mgz --targ mri/rawavg.mgz --o wmparc-in-native.mgz --regheader --interp nearest mri_convert --in_type mgz --out_type analyze wmparc-in-native.mgz wmparc_in_native_analyze (The new Analzye set was renamed FSParcel.hdr/img) After making the appropriate edits, I wanted to put this file back into mgz format/freesurfer space so I ran: mri_convert --in_type analyze --out_type mgz FSParcel 3065_FSParcel.mgz mri_vol2vol --mov FSParcel.mgz --targ mri/wmparc.mgz --o FSParcel_FSorient.mgz --regheader --interp nearest (I assumed that a target of wmparc would be most appropriate sinc that's what I started with but I've tried aseg as well) I've been playing around with Slicer and trying load the file as a label file to which I create (I believe) vtk models. If I convert wmparc to an Analyze set and then back to FreeSurfer mgz without any edits, I get an exact copy, as would be expected. If I make any alterations to the file and follow my steps, Slicer gripes that it can't parse the header. No matter what dims I use, I get pixels scattered across the screen and it appears that the volume is scrunched to 1 slice. If I run tkregister (as mri_vol2vol suggests) tkregister2 --mov FSParcel_FSorient.mgz --targ $SUBJECTS_DIR/sub1/mri/aseg.mgz --reg FSParcel_FSorient.mgz.reg everything looks fine. I find the Slicer documentation a bit lacking and don't know who to turn to. Is there something inherently wrong with my commands or is there a way to write header params to the mgz file so that Slicer will just work? -Joel

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X Coordinates signs switched after Qdec
by Alexandru Hanganu 14 Nov '08

14 Nov '08

Dear Freesurfer users, We have made an analysis of 2 groups (i.e. patients, healthy subjects) in order to see the cortical thickness differencies. We have introduced these groups into Qdec. The results showed p-values on a scale from -5 to +5 and the X coordinates of the right hemisphere were negative. Two questions: - are the p-values actually t-values ? - normally the X coordinates of the right hemisphere should be positive. Any ideas why they are negative ? Thank's a lot for any 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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mri_convert
by Alexa Nardelli 14 Nov '08

14 Nov '08

Hi, I have a question regarding converting files to mgz format from siemens (dicom). Per each image I have 144 IMA files (i.e. for one subject I have files from .001.IMA to .144.IMA) and I am wondering how to convert those into 1 mgz file. The only way I seem to find is to use the command: mri_convert filename.001.ima subjectname/mri/orig/001.mgz mri_convert filename.002.ima subjectname/mri/orig/002.mgz ... mri_convert filename.144.ima subjectname/mri/orig/144.mgz While this is painful and time consuming I also worry that in my quest to find the hippocampal volumes, Freesurfer will not read these files as one volume. Is this the correct way to convert these files? Or is there another easier way? Thanks Alexa

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Freesurfer November 2008