Freesurfer

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Re: [Freesurfer] niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii
by Anastasia Yendiki 01 Oct '15

01 Oct '15

It's trying to find a file called SUBJECTS_DIR/Enzo_recon1/dti.nii. This is a relative path, i.e., it's trying to find it under the directory where you are currently cd'd. This seems like a problem with defining paths properly for unix, rather than a tracula problem per se. On Wed, 30 Sep 2015, andrea cristina Lima wrote: > I got the error below. Could you help me? I've already check the dti file and it seems Ok. Tks > > macprolim446:Antonio_recon1 LIM44$ trac-all -prep -c > /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer/Enzo_recon1/conf_tracula1_fls.txt > > INFO: SUBJECTS_DIR is /Users/LIM44/Desktop/Freesurfer/subjects_freesurfer > > INFO: Diffusion root is SUBJECTS_DIR/Enzo_recon1 > > Actual FREESURFER_HOME /Applications/freesurfer > > trac-preproc -c SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/dmrirc.local -log > SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.log -cmd SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/scripts/trac-all.cmd > > #------------------------------------- > > /Applications/freesurfer/bin/trac-preproc > > #------------------------------------- > > #@# Image corrections Wed Sep 30 11:27:28 BRT 2015 > > mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz > > mri_convert SUBJECTS_DIR/Enzo_recon1/dti.nii SUBJECTS_DIR/Enzo_recon1/Enzo_recon1/dmri/dwi_orig.nii.gz > > niiRead(): error opening file SUBJECTS_DIR/Enzo_recon1/dti.nii > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from SUBJECTS_DIR/Enzo_recon1/dti.nii... > > Darwin macprolim446.local 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; > root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 > > > trac-preproc exited with ERRORS at Wed Sep 30 11:27:28 BRT 2015 > > > -- > Andrea Cristina de Lima PardiniCV: http://lattes.cnpq.br/0921194840474573 > >

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Re: [Freesurfer] Calculating local gyrification using CIVET's surface file ('.obj')
by Bruce Fischl 01 Oct '15

01 Oct '15

Hi Kie Woo can you run mris_euler_number on those surfaces to see if they are topologically correct? cheers Bruce On Thu, 1 Oct 2015, Nam, Kie Woo wrote: > > Dear experts, > > > > I’m trying to calculate local gyrifcation index using CIVET’s surface file > (‘.obj’). > > > > > > > > > > First, I’ve successfully done ‘CIVET --> FreeSurfer’ conversion and created > a ‘.pial’ file - below are the commands that worked for ‘CIVET --> > FreeSurfer’ and ‘FreeSurfer --> CIVET’ conversions. > > CIVET (MNI obj) --> FreeSurfer (ASCII) --> FreeSurfer (BINARY_BE (Big > Endian)): “ConvertSurface -i_mni CIVET_2.0_icbm_avg_mid_sym_mc_left.obj > -o_fs lh.pial; mris_convert lh.pial.asc lh.pial” > > FreeSurfer (BINARY_BE (Big Endian)) --> CIVET (MNI obj): “ConvertSurface > -i_fs lh.pial -o_mni lh.pial” > > > > > > > > > > Then, I ran “recon-all -s Subject -localGI”, but it keeps crashing with the > following message. > > ************************************************************************ > > lGI for vertex number 5501 of the outer mesh is 4.1122 > > lGI for vertex number 5601 of the outer mesh is 0.86156 > > lGI for vertex number 5701 of the outer mesh is 3.8343 > > ... remeasuring lGI value for vertex iV = 5801. It may take a few minutes. > > WARNING -- Problem for vertex iV = 5801, lGI value is aberrantly high > (lGI=62.3205)... > > ...lGI computation will be stopped. This may be caused by topological > defects, check mris_euler_number on the pial surface. > > ************************************************************************ > > > > The link below suggests rerunning “recon-all -autorecon2-wm -randomness”, > but it’s not an option for me because I have no other FreeSurfer compatible > files except “.pial”. > > http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg18228.html > > > > > > > > So, could there be any solution for this? > > > > > > > > Best wishes, > > > > Kie Woo > > >

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Hippocampal subfields
by von Polier, Georg Ferdinand Anto 02 Dec '14

02 Dec '14

Dear FreeSurfers, I am just finishing a paper using output from Hippocampal subfields and recognized that the current version has been deprecated. I am interested in volumes of the whole hippocampus. Are these volumes still valid and can you estimate when a new version will be available? Can you provide maybe a brief comment on the decision to deprecate the current version? Best regards, Georg

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error from selxavg3-sess: matlab:commond not found, ERROR:fast_selxavg3() failed\n
by zhang mingxia 02 Dec '14

02 Dec '14

Dear freesurfer experts, I got this error when I analysis the retinotopic data by this code: selxavg3-sess -a rtopy.self.lh -sf sessid The version of freesurfer is v5.1.0. What does this error mean? What should I do? Thank you for your support! Mingxia

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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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