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FSurf Webinar Announcement
by Suchandra Thapa 07 Apr '17

07 Apr '17

Dear FreeSurfer Community, The Open Science Grid consortium (http://www.opensciencegrid.org) offers a service “FSurf” which allows large scale batch processing of MRI scans using FreeSurfer. FSurf supports the standard FreeSurfer workflow (autorecon-all) or workflows with arbitrary FreeSurfer options. FSurf currently uses FreeSurfer 5.3 but support for FreeSurfer 6.0 will be added in the near future. Note that no proposal for an allocation is required to use the service. We are hosting a 30 minute webinar on Thursday, April 13th, 2pm CDT to cover the basics of batch processing using FSurf. The webinar will be accessible from a PC, Mac, Linux, iOS, or Android device at https://IU.zoom.us/j/644966220. Instructions for getting started with FSurf can be found here: http://bit.ly/freesurferopensciencegrid. We hope to see you there, and best regards. The OSG FSurf support team Suchandra Thapa sthapa(a)ci.uchicago.edu Computation Institute Searle Chemistry Laboratory #201A 5735 South Ellis Avenue Chicago, IL 60637

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PETsurfer output error
by miracle ozzoude 07 Apr '17

07 Apr '17

Hello Freesurfer, I am trying to concat my surface pet file using mris_preproc but I get this error with no output folder or files " mris_preproc --fsgd Pet.fsgd --target fsaverage --hemi lh --is C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --is C6_01_003_140908/lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --o all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz nsubjects = 2 INFO: output detected as nifti, turning on reshaping tmpdir is ./tmp.mris_preproc.20623 /net/synapse/nt/mozzoude/Analysis Log file is all.lh.mgx.ctxgm.fsaverage.sm00.mris_preproc.log Fri Apr 7 10:03:48 UTC 2017 setenv SUBJECTS_DIR /net/synapse/nt/mozzoude/Analysis cd /net/synapse/nt/mozzoude/Analysis /opt/freesurfer-6.0.0/freesurfer/bin/mris_preproc --fsgd Pet.fsgd --target fsaverage --hemi lh --is C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --is C6_01_003_140908/lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --o all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz Linux neuron2.sri.utoronto.ca 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.20623 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/2 C6_01_001_140813 Fri Apr 7 10:03:48 UTC 2017 -------------- ----------------------- mri_surf2surf --srcsubject C6_01_001_140813 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.20623/C6_01_001_140813.1.mgh --sval C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --reshape --cortex ERROR: dimension inconsistency in source data Number of surface vertices = 125993 Number of value vertices = 163842 Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /net/synapse/nt/mozzoude/Analysis cd /net/synapse/nt/mozzoude/Analysis mri_surf2surf --srcsubject C6_01_001_140813 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.20623/C6_01_001_140813.1.mgh --sval C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --reshape --cortex sysname Linux hostname neuron2.sri.utoronto.ca machine x86_64 user mozzoude srcsubject = C6_01_001_140813 srcval = C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz srctype = trgsubject = fsaverage trgval = ./tmp.mris_preproc.20623/C6_01_001_140813.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /net/synapse/nt/mozzoude/Analysis/C6_01_001_140813/surf/lh.sphere.reg Loading source data" Below are the scripts i ran prior to mris_preproc and the mris_preproc command line: 1) mri_vol2surf --mov C6_01_001_140813.gtmpvc.output/mgx.ctxgm.nii.gz --reg C6_01_001_140813.gtmpvc.output/aux/bbpet2anat.lta --hemi lh --projfrac 0.5 --o lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --cortex --trgsubject fsaverage 2) mri_vol2surf --mov C6_01_003_140908.gtmpvc.output/mgx.ctxgm.nii.gz --reg C6_01_003_140908.gtmpvc.output/aux/bbpet2anat.lta --hemi lh --projfrac 0.5 --o lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --cortex --trgsubject fsaverage 3) mris_preproc --fsgd Pet.fsgd --target fsaverage --hemi lh --is C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --is C6_01_003_140908/lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --o all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz Thanks. Best, Paul

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help
by Dilip Puri 07 Apr '17

07 Apr '17

Hi everyone, I am working on Hippocampus segmentation using Neural Networks for that I need labeled images of Hippocampus corresponding to original images. I am using OASIS Dataset for this. I want to generate labeled images using FREESURFER. Is there any way to label each 3D co-ordinate HippoCampus -1 Otherwise - 0 Here are sample files link <https://drive.google.com/drive/folders/0B6rH1c6LupG_b3I4WUJ1RWZCbnM?usp=sha…> Kindly help me! Dilip Puri <http://dilippuri.github.io> IIIT Vadodara <http://www.iiitvadodara.ac.in>

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QDEC-Cortical Thickness
by Limachia, Gaurang (NIH/NINDS) [F] 07 Apr '17

07 Apr '17

Hello Freesurfer Experts, I want to compare the cortical thickness between the groups (HC & Patients), and wanted to know where qdec shows this information. Once the design tab is loaded, I am seeing the question in the analysis results – does the correlation between thickness and Age differ from zero? Do I need to a run the command for GLM in order to see if there is a cortical difference between the two populations? I would greatly appreciate your help. Thanks, Gaurang

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MRIread (load_nifti)- Out of memory
by Ilaria Sani 07 Apr '17

07 Apr '17

Dear All, I'm trying to load a pretty big diffusion MRI dataset (320x320x260x122). I'm running matlab 2015a 64bit on a linux machine. I'm using MRIread, which in turn calls load_nifti. I'm getting the following error: Error using + Out of memory. Type HELP MEMORY for your options. Error in load_nifti (line 158) hdr.vol = hdr.vol * hdr.scl_slope + hdr.scl_inter; Error in MRIread (line 158) hdr = load_nifti(fspec,headeronly); When I load half dataset (320x320x260x61) it works ok. I tried to increase the Maximum array size in Matalb (default 1,000 - now 10,000), but I'm still getting the error. I tried to change machine (which runs matlab 2013a on linux) and it worked fine. I think this is due to some matlab settings. Can anyone help? Thanks a lot, Ilaria ------------------------------------------- Ilaria Sani, PhD Postdoctoral Fellow, Freiwald Lab The Rockefeller University 1230 York Ave., New York, NY 10065. Phone: (212) 327 7699 Fax: (212) 327 7698 Email: isani01(a)rockefeller.edu<https://rumail.rockefeller.edu/owa/redir.aspx?C=Kqhy3ohui0OLc6NBHS0gx_jC9yH…>

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Analyzing xhemi results
by Marissa Pifer 07 Apr '17

07 Apr '17

Hi free surfers, I have run the xhemi process on the subjects for my study. The study is on stroke patients and their lesions are a mix of left and right hemispheres. In analyzing the results, we want to look at correlations between fmri activation in M1 and the cortical thickness of M1 ipsilesional and contralesional. To do so, I followed instructions written out in response to a question about xhemi on the mailing list: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-December/026823.… My question, is there a way when running the analysis step: *# Analyze *>* mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir *>* glm.lh.lh-rh.thickness.sm05 \ *>* --osgm --surf fsaverage_sym lh *> Can I modify this command line to include my fmri data and run that correlation also? Thank you, Marissa

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How to segment subnuclei of thalamus?
by Shane S 07 Apr '17

07 Apr '17

Hello Experts, I am interested to do a segmentation of the thalamus subnuclei based on T1 data. Is there any atlas that I could use for this? Best Wishes, S

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Hippocampal subfield segmentation, file content
by Nina Jacobsen 07 Apr '17

07 Apr '17

Hi All, I have made a hippocampal subfield segmentation using FreeSurfer version 6.0 with multispectral segmentation settings, and have both labels for the right and left hippocampus. The segmentations look very nice when viewed with freeview, so all good. Now, my problem is the file content. I would like a segmentation file, which labels all subfields with a single value (all voxels in CA1 would for example be with value 1, all voxels in CA2 would be with value 2 and so on). Does anyone know how i can gain this file? Is it in some way possible to convert the label files (lh.hippoSfLabel.v10.mgz) into such a "simple" segmentation file? Currently, the content of the label files (lh.hippoSfLabel.v10.mgz) is values in the range 0-226, which I guess origin from the RGB encoding - I opened the file with matlab. Hope my question is clear. Thanks, Nina Jacobsen.

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Multiple Comparisons Correction thresh error
by teodora petrova 07 Apr '17

07 Apr '17

Hello, I would like to correct my glm_fit results for multiple comparisons. I am using the following commands, similar to the one in the group analysis tutorial: mri_glmfit-sim --glmdir lh.index.glmdir --cache 1.3 abs --cwp 0.05 --2spacesmri_glmfit-sim --glmdir lh.index.glmdir --cache 2.0 pos --cwp 0.05 --2spaces And receive the following errors: ERROR:thresh=1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 ERROR:thresh=2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 I am sure I am typing a point, but it is read as a comma. Any ideas why? Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Platform: Ubuntu MATE 16.04 Thank you very much! Regards,Teodora

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QA Tools v1.2 and future release
by Yong Li 07 Apr '17

07 Apr '17

Dear Freesurfer Experts, As one of the new freesurfers, I really appreciate the excellent work of authors as well as great support of users' forum. A good guess of mine is that authors, e.g., Vasanth or Louis etc., are busy updating QA tools after the FSv6 release since the QA Tools v1.2 was written for FSv5.3. If so, is it possible to provide an estimated release date please so as to adjust my plan? Thanks for understanding! In case, it might take a while to release the next QA Tool, may I dare to provide my attempts of code updating of some functions in QA Tools? The following are the brief list of code adapting steps: 1. modified codes for generating file order list in recon_checker; 2. modified codes for matching segment names for instance from DefaultAsegMeans.txt in gparcmean_from_table; 3. adapted default_FOF and default_status_log for FSv6. After these adaptation, QA Tools ran through and I only encountered some 'syntax error' in terminal for 2 segments, 5th-Ventricle and WM-hypointensities, that I have to ask the experts to guide me through this point if it's of your interests. To ensure the QA Tools functioning well, I tested 116 elderly patients and detected reasonable outliers per patient. Therefore, I would like to double that my code updating based on my general understanding of QA Tool still fit to the basic purpose of authors by asking the following theoretical questions: 1. SNR and segments outliers detection are measures of quality assessment in QA Tools. Have other factors such as subject's motion, image bias, resolution etc. been considered in QA Tools or future release? The default SNR threshold is 16 based on any reference? The max SNR of my patients so far is 32. Any idea of scores of healthy elderly controls? 2. The QA Tools v1.2 analyzes aseg.stats output. Is it possible to include output of brainstem substructures and HippocampalSubfields of FSv6? If yes, I would like to adapt the codes and provide you some feedback if you think that I can help bit. 3. Future directions mentioned in QA Tools wiki site are interesting and thoughtful. Are other features like 'Detect outliers in aparc and aparc2009 volumes' on the way? 4. Is there a function to summarize all QA measures to csv files, like the quantifyBrainstemStructures.sh in brainstem substructures? Thank you in advance! Kind regards, Yong Li, PhD _________________________ Department of Neurology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany

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