Freesurfer December 2014

freesurfer@nmr.mgh.harvard.edu

15 participants
20 discussions

mri_surfcluster problem
by wangzhiwei3233 02 Dec '14

02 Dec '14

Hi Freesurfer experts, I just want to try cluster level threshold by cluster size, but not by mc simulation. So I tried the command like : mri_surfcluster --in sig.nii.gz --subject fsaverage --hemi lh --annot aparc --sign pos --minarea 50 --sum area50.pos.cluster.summary --o area50.pos.cluster.nii.gz --thmin 1.3 However, I found that the command did not set the non-cluster vertices to zero. The help of mri_surfcluster says that this command currently only supports paint (or w) format for input and output. I converted the sig.nii.gz to sig.w using mri_surf2surf --s fsaverage --hemi lh --sval sig.nii.gz --tval sig.w --trg_type paint. But command mri_surfcluster could not read the paint file. Could anyone help me? Thanks! Zhiwei

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relationship between cortical thickness and gyrification index
by elisa veronese 02 Dec '14

02 Dec '14

Dear FreeSurfer users, I have a question regarding the link between cortical thickness and gyrification index: suppose I have a general decrease of cortical thickness in a lobe of the brain. Is it correct to suppose that consiquentely the gyrification index will decrease in the sulci (because of the decreased curvature) and that it will increase in the gyri (because of the increased curvature)? So that probably I would not be able to measure any difference in the gyrification index of that lobe? Thank you. Best, elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php <http://icbn.uniud.it/tiki-index.php>*

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incorrectly labeled vertices in fsaverage lh labels
by Vincent Beliveau 02 Dec '14

02 Dec '14

Hi everyone, In the lh labels of fsaverage (FS 5.3 stable), vertices 102162 and 102163 seem to be incorrectly labeled in lh.cortex.label rather than lh.Medial_wall.label. Anyone noticed this before? I didn't check rh yet. Regards, Vincent.

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TRACULA with Philips par-rec format
by Woo-Suk Tae 01 Dec '14

01 Dec '14

Dear TRACULA exports I've successfully processed with Philips DICOM DTI data. But, I have Philips 32 directional DTI data with par-rec format. How can I process par-rec data in TRACUAL? Best regards! ------------------------------------------------------------ Woo-Suk, Tae Ph.D. Research Professor, Neuroimaging Lab. Neuroscience Research Institute, Clinical Research Institute, Kangwon National University Hospital Chuncheon, Korea office: 82-33-258-9164 mobile: 82-10-9120-4629 email: wstae(a)kangwon.ac.kr woostae(a)gmail.com -------------------------------------------------------------

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Using the -seg-wlo option
by Marx, Gabe 01 Dec '14

01 Dec '14

Hello freesurfers, I wanted to get your opinion on altering the white matter low limit in the mri_segment command through attaching the "-seg-wlo" flag onto -autorecon2. I am working on a Frontotemporal Dementia cohort. In patients with severe atrophy, there always tends to be a great deal of both white matter and pial surface underestimation in the anterior temporal and dorsal frontal areas. I have found that lowering the white matter low limit does a fantastic job of fixing the surface underestimations in those regions-saving the numerous hours of labor required to manually fix these problem areas with control points. I was hoping someone could provide insight into what exactly changing this value is doing to the data. Does changing this value lead to inaccuracies that I am not seeing? Most importantly, is it safe to mix cases where I set the white matter low limit to 60 (or 40 in some severe cases) with other cases that retain their default value of 90 in the same dataset? Thank you! Gabe Gabe Marx Clinical Research Coordinator UCSF Memory & Aging Center 675 Nelson Rising Lane, Suite 190 San Francisco, CA 94158 T: (415) 476-3861

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Neuroinformatics Database cloud storage version available
by Greg Book 01 Dec '14

01 Dec '14

Neuroinformatics Database is an all purpose storage and retrieval system for imaging data. NiDB is geared toward neuroimaging research, but can store any modality of data. NiDB is released in an open-source format: http://nidb.sourceforge.net, but now offers a cloud based storage option to make it even easier to setup and use. Here are some of the features of the cloud based NiDB system: * DICOM receiver * perfect for multi-site studies * longitudinal storage * import and retrieve data from any where * project based permissions * cross-project sharing of subject demographics * automated QC metrics for MR data, add your own QC modules * store any modality of data (MR, CT, US, EEG, etc) from any species (human, non-human primates,etc) * create data packages for export to NDAR and RDoCs * store basic demographic data and assessment metrics * share data directly with other NiDB instances * download data in multiple formats and directory structures * affordable, pay by the GB Sign up for an account on the demo instance: http://neuroinfodb.com or ask about setting up your own trial instance to which you can upload data.

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Creat ROI from annotation file
by wangzhiwei3233 01 Dec '14

01 Dec '14

Hi Freesurfer experts, I want creat some ROI masks or parcellation from Caret PALS_B12_Visuotopic.annot file in fsaverage's label folder. I used the command mri_label2vol, mri_label2vol --annot $Dir/label/lh.PALS_B12_Visuotopic.annot --temp $Dir/mri/T1.nii --fillthresh .5 --o PALS_B12_Visuotopic.nii --subject fsaverage --hemi lh --identity The parcellation in output volume were like some lines located at the boundry of white matter , and did not cover the gray matter (see picture). Then, I used another methods as follows. Firstly, I converted the annotation file into some label files using mri_annotation2label command; Secondly, I created ROIs using these labels by mri_vol2roi. However, the masks also couldn't cover the gray matter. Could anyone help me creat good masks? Thanks a lot! Zhiwei

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mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08
by lindsay hanford 01 Dec '14

01 Dec '14

Hello Freesurfer Experts! I am encountering the dreaded mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08. I have tried to troubleshoot how to solve this problem from other inquiries, however, I still have had no luck. I am trying to run a 4 group 1 variable analysis: with diagnosis being my variable of interest and trying to regress out the effects of sex and age. 1. Command line: mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh 2. The FSGD file (if using one) (see attached) 3. And the design matrix: 0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached) To the best of my knowledge, all my files are the right format and I believe I have adequate number of participants per group? I also tried mean centering my age variable. I had success when I ran just a two group analysis (diagnosis) not controlling for sex or age, however, as soon as I try to run four groups, I encounter this error. I have no idea how to proceed. I am looking forward to your response! Thanks, Lindsay -- Lindsay Hanford, BSc, PhD Candidate McMaster Integrative Neuroscience Discovery & Study | *Department of Psychology, Neuroscience & Behaviour * McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|* Hamilton, ON, L8S 4L8 905 525 9140 x24784 *|* lindsay.hanford(a)gmail.com

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Number of slices generated in the brainmask.mgz
by Gunjan Gautam 01 Dec '14

01 Dec '14

Hi FreeSurfers, brainmask.mgz is generating 256 slides per volume. How can I have control over it, in terms of generating less number of slides (say 181) per volume? Gunjan

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ALLvsFIX contrast
by Reza Rajimehr 01 Dec '14

01 Dec '14

Hi, In an fMRI experiment, I have 60 conditions. I want to make ALLvsFIX contrast to select vertices that are visually responsive, by finding vertices that have ces values greater than zero in this contrast. For this, I can run: mkcontrast-sess -analysis analysisname -contrast allvsfix -a 1 -a 2 -a 3 ... -c 0 Since this is a very long command, is there a smarter way to make such contrast? Thanks, Reza

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Freesurfer December 2014