Freesurfer February 2016

freesurfer@nmr.mgh.harvard.edu

123 participants
179 discussions

Regarding: T2w and HcV analysis
by Dr Sampada Sinha 03 Feb '16

03 Feb '16

Dear freesurefr experts, Hope this mail finds you all doing well. I want to calculate hippocampal subfield volume using T2w mages. Is the recon-all command same as we do for the T1images (recon-all -i input to T1.nii.gz -s 001 -all)? I was not able to understand the recon-all command for the T2w images. if you can please explain it to me: recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume -T2pial -all what is -i here (which input volume)? Since, -T2 is the T2 images (dcm or nifti) I am going to feed for processing. Appreciate all you help! Best wishes and regards, Sampada -- Sampada Sinha

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Question about mri convert
by Edward Su 03 Feb '16

03 Feb '16

Dear colleagesI am trying to convert my dicom files to .mgz from Freesurfer by using the mri_convert command, but it provides me the following error:edward-virtual-machine:~/freesurfer/subjects/Artists/Controls/C1> mri_convert /home/edward/freesurfer/subjects/Artists/Controls/C1/mprage grappa2x_i0001.dcm mri/orig/001.mgz mri_convert /home/edward/freesurfer/subjects/Artists/Controls/C1/mprage grappa2x_i0001.dcm mri/orig/001.mgz mri_convert: extra argument ("mri/orig/001.mgz") type mri_convert -u for usageCould anybody help me with this problem? Thanks in advance -Edward

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FreeSurfer 6.0 hippocampal subfields error
by Rosanna Olsen 03 Feb '16

03 Feb '16

Dear Eugenio, I am writing because I am getting a mkdir error when I try to run the FreeSurfer 6.0 hippocampal subfields segmentation. I tried moving my installation of freesurfer to a local directory where I have write permission and I also made sure I had write permission in my subject's directory. Do you have any idea what might be causing the error? Thanks in advance! Command and error pasted below: recon-all -s 1001 -sd . -hippocampal-subfields-T1 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 INFO: SUBJECTS_DIR is /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0 Actual FREESURFER_HOME /opt/freesurfer6 -rw-rw-r-- 1 rolsen buchsbaum_lab 549732 Feb 3 09:35 /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0/1001/scripts/recon-all.log Linux gateway.neuroinfo.rri 2.6.32-279.9.1.el6.x86_64 #1 SMP Tue Sep 25 21:43:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Wed Feb 3 09:35:59 EST 2016 /opt/freesurfer6/bin/segmentSF_T1.sh /opt/freesurfer6/MCRv80 /opt/freesurfer6 1001 /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0 left See log file: /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0/1001/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/freesurfer6/MCRv80/runtime/glnxa64:/opt/freesurfer6/MCRv80/bin/glnxa64:/opt/freesurfer6/MCRv80/sys/os/glnxa64:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/opt/lib.exported Warning: application is running on a locale different from the original platform locale. Error using mkdir Permission denied Error in segmentSubjectT1_autoEstimateAlveusML (line 113) MATLAB:MKDIR:OSError #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Wed Feb 3 09:36:07 EST 2016 /opt/freesurfer6/bin/segmentSF_T1.sh /opt/freesurfer6/MCRv80 /opt/freesurfer6 1001 /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0 right See log file: /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0/1001/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/freesurfer6/MCRv80/runtime/glnxa64:/opt/freesurfer6/MCRv80/bin/glnxa64:/opt/freesurfer6/MCRv80/sys/os/glnxa64:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/opt/lib.exported Warning: application is running on a locale different from the original platform locale. Error using mkdir Permission denied Error in segmentSubjectT1_autoEstimateAlveusML (line 113) MATLAB:MKDIR:OSError #------------------------------------------ Started at Wed Feb 3 09:35:56 EST 2016 Ended at Wed Feb 3 09:36:14 EST 2016 #@#%# recon-all-run-time-hours 0.005 recon-all -s 1001 finished without error at Wed Feb 3 09:36:15 EST 2016 done -- Rosanna Olsen, Ph.D. Scientist, Rotman Research Institute, Baycrest rolsen(a)research.baycrest.org http://research.baycrest.org/rolsen

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Re: [Freesurfer] Freesurfer Digest, Vol 143, Issue 54
by Shady El Damaty 02 Feb '16

02 Feb '16

Thank you ZK! On Thu, Jan 28, 2016 at 4:32 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > On 01/28/2016 01:11 PM, Shady El Damaty wrote: > > Hi, > > > > I was curious to know what the tentative release date for FreeSurfer 6 > is. I?m currently running FreeSurfer on multiple machines with El > Capitan installed and I?m wondering whether it?s worth installing the beta > distribution or rather uninstalling SIP on each of these many machines. > > > > The release date for FreeSurfer 6 has been hard to nail down but we are > in the final stages. I hesitate to give a solid date but I would say a > month is a fair estimate. > > > > Also is there any documentation on any specific bugs to watch out for > with El Capitan and FreeSurfer 5.3? I?ve been running some functions and > haven?t found any errors yet. > > > > I would only expect you to encounter errors if you were calling scripts > which call freesurfer binaries (e.g. recon-all). If your just calling > the binaries themselves then those should run successfully. > > > > > PS - how does FreeSurfer 6 plan to get around SIP? > > We plan on getting around it using two methods. 1) creating wrapper > scripts for some binaries. 2) Adding a source file in existing scripts > to recreate the library path that were stripped by SIP. >

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Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)
by will brown 02 Feb '16

02 Feb '16

Hi Bruce, I've attached a shot of the misalignment as seen in freeview. Yes the original images were DICOM created in Siemens machine T1, 0.8 slice thickness, can provide all DICOM tags if needed. Thanks, Will On Tue, Jan 26, 2016 at 6:00 AM, <freesurfer-request(a)nmr.mgh.harvard.edu > wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: mritotal failed - help with manual registration (Bruce Fischl) 2. recon -all errors (Jasmin Alves) 3. Re: Processing .mnc files (Ankita Chatterjee) 4. Re: Processing .mnc files (Bruce Fischl) 5. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg) 6. hippocampal subfields - multispectral segmentation with FLAIR (Luigi Antelmi) 7. Re: hippocampal subfields - multispectral segmentation with FLAIR (Eugenio Iglesias) 8. Re: recon -all errors (Bruce Fischl) 9. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl) 10. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg) 11. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl) 12. FDR map: hide very little cluster (stdp82(a)virgilio.it) 13. [All] position available immediately (Bruce Fischl) 14. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) (Douglas Greve) 15. Re: FDR map: hide very little cluster (Douglas Greve) 16. R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) 17. R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) 18. Re: R: Re: FDR map: hide very little cluster (Douglas N Greve) 19. R: R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) 20. Re: R: R: Re: FDR map: hide very little cluster (Douglas N Greve) 21. R: Re: R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) ---------------------------------------------------------------------- Message: 1 Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mritotal failed - help with manual registration To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1601241858240.29174(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Will can you take the same images with freeview and send them along? Also: tell us a bit about your images. What format did they start in? Were they dicoms? Bruce On Mon, 25 Jan 2016, will brown wrote: > Hi all, > After attempting recon-all I received the error "mritotal failed, see > transforms/talairach.log" etc which I understand may have something to do > with bad output from registration. I've checked orig.mgz which does look out > of line - the orientation is off so that it appears the subject has their > head tilted off to one side (see Image1.jpg). > > I have tried to fix this manually with the help of this tutorial: > > http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview > > Hovever, the "movable" blurry image that I'm trying to line up with my > subjects image does not match the coronal, sagittal or horizontal views, > e.g. when I click "coronal" my subject is displayed correctly but the > movable image is displayed horizontally (see Image2.jpg and Image3.jpg). > > Am I missing something obvious? (and am I even on the right track given this > error?) > > Thanks in advance for any help. > > Cheers, > Will

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getting vertex-wise correspondences across subjects
by John Griffiths 02 Feb '16

02 Feb '16

Dear surfers, Could you please help me with the following analysis workflow: I am doing an analysis where I identify patterns on the ?h.orig surfaces. What I want to do now is to resample these patterns over vertices, such that I have vertex-wise correspondence across subjects. I believe this essentially requires the construction of and projection to a group template (although I'm aware this could be done with e.g. fsaverage). Here is where I'm at: cd(freesurfer dir) 1. Read ?h.orig surfaces; compute patterns (...some in-house stuff...) 2. Write patterns out to .mgh file Matlab save_mgh(pat,outfile,eye(4)); Python nibabel.MGHImage(pat[:,numpy.newaxis,numpy.newaxis].astype(np.float32),numpy.eye(4)).to_filename(outfile) 3. Generate group template make_average_subject --out avgsub --sd <fs dir> -subjects subj1 subj2 subj3 .... 4. Register a single example subject to the new group template mris_register -curv subj1/surf/lh.sphere avgsub/lh.reg.template.tif subj1/surf/lh.sphere.reg.avgsub 5. Project the surface patterns identified above on to the new group template, so that the vertex values correspond across subjects, and can be averaged, statistically compared. etc. mri_surf2surf --srcsubject subj1 --srcsurfreg sphere.reg.avg_sub --trgsubject avg_sub --trgsurfreg sphere.reg --hemi lh --sval <pattern mgh file> --tval /tmp/test_avgsub.mgh However this breaks down at mri_surf2surf, and I'm not particularly confident that the earlier parts are exactly right either. Could you please show me what commands I should be using for the aims as described above? Many thanks, John -- Dr. John Griffiths Post-Doctoral Research Fellow Rotman Research Institute, Baycrest Toronto, Canada and Honorary Associate School of Physics University of Sydney

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PostDoc at UC San Diego - Epilepsy and Brain Tumor Research {Disarmed}
by Leyden, Kelly 01 Feb '16

01 Feb '16

Hello FreeSurfers, I am writing on behalf of Dr. Carrie McDonald to advertise a Postdoctoral position with our lab at UC San Diego. Location: UCSD Multimodal Imaging Laboratory (MMIL) UCSD Center for Translational Imaging and Precision Medicine (CTIPM) Start date: As soon as possible Seeking a full-time postdoctoral scholar to work with a multidisciplinary team of scientists on projects related to the use of multimodal imaging for improving cognitive and health outcomes in patients with epilepsy and primary brain tumors. Our multimodal imaging team includes full-time faculty from Psychiatry, Radiology, Neurosciences, and Radiation Oncology. This group of researchers and clinical investigators are primarily focused on integrating research imaging tools into the clinical work flow to directly and immediately improve patient outcomes. The scholar will work closely with other postdoctoral fellows, medical residents, graduate students, research assistants, and faculty members to help develop methods, analyze structural, diffusion, and functional (fMRI) imaging data, prepare manuscripts and assist with grant applications. The fellow should have strong programming (i.e., MATLAB) and writing skills, experience in neuroimaging or a related field, and a strong interest in pursuing an academic career path. Applicants with a strong background in bioengineering, cognitive science, and/or experience working with neurological populations are encouraged to apply. For any addition questions or to apply for the position, please send CV and cover letter to Dr. Carrie McDonald (camcdonald(a)ucsd.edu) Thank you, Kelly Neuroimaging Research Associate Multimodal Imaging Laboratory University of California San Diego

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Recon for Rhesus Macaque
by Casas, Rafael (NIH/CC/DRD) [F] 01 Feb '16

01 Feb '16

Hello, I'm wondering what is the first step in reconstruction when working with rhesus macaque. script 01.05 requires files to be in mgh format initially ? I understand that the recon-all scipt is not setp to work with monkey data [cid:image003.jpg@01D15CF6.FFDB5710] Thanks, Rafael

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recon_checker error
by LIEWALD David 01 Feb '16

01 Feb '16

Opensuse 11.4 : Freesurfer 5.3 :QAtools_v1.1 I am trying to generate QC data from data generated using Freesurfer ver 5.3 and I'm getting the following error " Checking if all files exist...PASSED Checking actual file order...FAILED (read ../1006454_20216_2_0/scripts/recon_checker.log) ERROR: Actual file order disagrees with common file order for subject 1006454_20216_2_0" On checking the recon_checker.log it states This subject may have been processed with a different version of FreeSurfer other than the version used to create the common file order file (based on v5.1 by default if not specified by the user). Consider generating an output file order file for your specific dataset using the 'genoutputorderfile' flag. See the '-help' flag for details. I cannot find any details of this flag in any help file or any online help as to how to correct his problem Dave Liewald The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Freesurfer February 2016