Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

Inquiries about the curvature
by Mahtab Farahbakhsh 06 Jul '16

06 Jul '16

Dear FreeSurfer, I am using the mris_anatomical_stats output to calculate the curvature and thickness indices for different brain areas. However, I am not sure what the mean and gaussian curvatures mean. I could not find a complete description on these two. Would you please guide me what principle curvature and mean and gaussian curvatures means exactly? I appreciate your concern in advance. Best Regards, Mahtab.

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Re: [Freesurfer] Freesurfer/Freeview help
by Abbie McNulty 06 Jul '16

06 Jul '16

Hello, Just a couple more questions that would be great if you could answer in explanation form: How do people develop finite element models from brain MRI? How do people learn and implement the software on an example data set? Abbie On Tue, Jul 5, 2016 at 9:42 AM, Abbie McNulty <amcnult1(a)stanford.edu> wrote: > Hello, > > Just a couple more questions that would be great if you could answer in > explanation form: > > How do people develop finite element models from brain MRI? > How do people learn and implement the software on an example data set? > > Abbie > > On Mon, Jun 27, 2016 at 6:37 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > >> Hi Abbie >> >> you just use the recon-all script from the command line: >> >> recon-all \ >> -i <path to 1 file in the correct dicom series> \ >> -sd <path to the directory that you store all your subjects> \ >> -s <identifier to give this subject> \ >> -all >> >> this will take 5-20 hours and at the end will create and populate a >> directory tree with segmented volumes and surfaces >> cheers >> Bruce >> >> On Mon, 27 Jun >> 2016, Abbie McNulty wrote: >> >> > Hi Bruce, >> > I am trying to create a mesh of the MRI scans, eventually with imported >> > scans, but for now just using the information available through the >> > software. How do you work these voxel segmentations? I'm just very new >> with >> > the software. >> > >> > Say I import an MRI scan, and I want to cortically segment it in order >> to >> > create a mesh of the volume. What are the steps to do this and how do I >> > follow through with each step? I tried to watch the youtube tutorials >> on the >> > Freesurfer youtube, but since they are slides informing of what >> Freesurfer >> > can do and not quite a play-by-play interaction of Freeview, I am stuck. >> > >> > Thanks >> > >> > Abbie >> > >> > On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl < >> fischl(a)nmr.mgh.harvard.edu> >> > wrote: >> > Hi Abbie >> > >> > what are you trying to create a mesh of? We supply meshes for >> > the >> > gray/white interface and for the pial surface. We supply voxel >> > segmentations of lots of other things that you could mesh, but >> > we don't >> > by default. >> > >> > cheers >> > Bruce >> > On Mon, 27 Jun 2016, Abbie McNulty wrote: >> > >> > > Hello, >> > > I am trying to segment a MRI brain in order to create a mesh >> > of the image >> > > into finite elements, but I am very new with >> > Freesurfer/Freeview and am not >> > > familiar with the tools. So far, I have only uploaded >> > brain.mgt from the >> > > bert file that comes with the program. If I wanted to mesh >> > this brain, how >> > > should I proceed? The online tutorials have confused me >> > especially since I >> > > am not sure if I am supposed to be using the terminal or the >> > command window >> > > for a lot of the code commands. >> > > >> > > Any help would be appreciated. >> > > >> > > Thanks! >> > > >> > > Abbie McNulty >> > > >> > > -- >> > > Abigail C. McNulty >> > > Stanford University Class of 2018 >> > > B.A. Candidate in Bioengineering >> > > Stanford Women's XC/ Track and Field >> > > >> > > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > The information in this e-mail is intended only for the person to whom >> > it is >> > addressed. If you believe this e-mail was sent to you in error and the >> > e-mail >> > contains patient information, please contact the Partners Compliance >> > HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was sent to you >> > in error >> > but does not contain patient information, please contact the sender >> > and properly >> > dispose of the e-mail. >> > >> > >> > >> > >> > -- >> > Abigail C. McNulty >> > Stanford University Class of 2018 >> > B.A. Candidate in Bioengineering >> > Stanford Women's XC/ Track and Field >> > >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > > -- > Abigail C. McNulty > Stanford University Class of 2018 > B.A. Candidate in Bioengineering > Stanford Women's XC/ Track and Field > -- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field

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FSFAST time series extraction
by curry_sam77＠yahoo.com 06 Jul '16

06 Jul '16

Hi all, I am trying to extract mean time series BOLD data using FSFAST from Cortical ROIs + sub cortical ROIs and cerebellum. preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd mri_segstats --annot fsaverage lh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt mri_segstats --annot fsaverage rh aparc --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt and for cortical time series mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf subCorticalTimeSeries.txt But I am not sure on how exactly to extract time series from cerebellar regions. So if I want to extract time series from regions as described in Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in FreeSurferCololLUT.txt? If not could you please direct me to processes that I can use. Sent from Yahoo Mail. Get the ap

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mri_surfcluster
by tom parker 06 Jul '16

06 Jul '16

Dear Freesurfers, I ran a comparison between different groups using mri_glmfit. Now I would like to correct the results in sig.mgh by multiple comparisons using FDR. I tried using tksurfer but it doesn't work so well on my computer and I read that freeview does not allow to do that yet. I'm now trying to use mri_surfcluster to do it. Is this correct? mri_surfcluster --in sig.mgh --subject fsaverage --surf inflated --hemi lh --fdr 0.05 --sign pos After I run it some thresholds appear in the terminal. Should I use these thresholds to create a FDR corrected sig.mgh map or is there a direct way of getting this using mri_surfcluster or other command? Thank you so much!

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Hippocampal Subfields Segmentation
by Permesh Dhillon 06 Jul '16

06 Jul '16

Hello FreeSurfer Developers, I’m having issues with the hippocampal subfields segmentation using OS X Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611. I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting an error message : Error:CTF file '/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' failed to open for 'Read' access. Error message: 'Open a zip file for read/modify failed.’ The segmented hippocampal files as described on free surfer wiki cannot be found under the subject ‘mri’ folder. I understand other users have complained of a similar issue within the last week. I’d ve grateful if you could assist me with the issue above. Many thanks Permesh This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Any updates on recon-all GPU support?
by Derek Pisner 05 Jul '16

05 Jul '16

Anyone manage to successfully configure recon-all to run with -use-gpu for recent cuda toolkit versions? I realize cuda support has ceased over the past few years for Freesurfer, but have there been any successful builds for CUDA toolkit versions 6 and up? I am currently looking to configure cuda support on a Tesla K80 GPU, which is part of a small beowulf cluster, which is working wonderfully with FSL's cuda support. Many moons ago, when gpu support was working, I found the -use-gpu option with recon-all to be significantly faster and more practical (for the user) than the -openmp option (which even on a 150 core cluster has provided limited speedup during batch runs). Curious to hear what others have been doing. -Derek

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Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)
by Lars M. Rimol 05 Jul '16

05 Jul '16

Hi Anastasia, I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the generated bvec file has commas instead of full stop (0,832 instead of 0.832). The input file (attached: "bvec_rows") has full stop. Another thing is that the generated bvals file has an empty space at the end of the row, which is not there in the input file ("bvals_rows"). thank you! LMR Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals and dmri/bvecs files that get generated look fine too? a.y On Sat, 2 Jul 2016, Lars M. Rimol wrote: Hi, Trying to run trac-all -c dmric_file -prep, I get an error message stating that there are different numbers of entries in the bval and bvec files. I don't understand why, since both have the same number of rows (64). OS = Ubuntu 14.04.4 Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated Tracula and FSL (v 5.0.9). Error message: #@# Tensor fit fr. 01. juli 19:20:29 +0200 2016 dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m /media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016 ---------- I also tried flipping the bvec/bval files, but got the same error. I don't know if there's anything wrong with the bval/bvec files, or if this error message is indicative of some other problem. Is the updated Tracula version only compatible with the dev version of FS? I have attached the bval/bvec files and the trac-all.log. ------------------------------------------------------------------- The contents of the dmric file is: setenv SUBJECTS_DIR /media/lmr2/subjects/DTI set dtroot = /media/lmr2/subjects/DTI/tracula_2016_nativerows set subjlist = (4_FS) set dcmroot = /media/lmr2/subjects/DTI set dcmlist = ( 4/5/1.dcm ) set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv Thank you! yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Apply mris_apply_reg for a label
by Alexandre Routier 05 Jul '16

05 Jul '16

Hello everyone, I have a label for the left hemisphere for my subject but I don't understand the syntax to apply mris_apply_reg on this label to obtain the right hemisphere version. mris_left_right_register was performed to get lh.sphere.left_right and lh.sphere.left_right but I don't know how to use this for the mris_apply_reg command. Thanks in advance for your answer. Alexandre

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Registering scans with different voxel sizes/numbers
by zalewk＠u.washington.edu 05 Jul '16

05 Jul '16

Hello Freesurfer team, I have the unfortunate task of performing longitudinal volumetric analysis on subjects collected on three different scanners with different voxel numbers/sizes. I didn't find this out until attempting to run the longitudinal base and receiving this message: WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. By re-registering the original nifti and recreating the norm.mgz/talairach I can correct the geometry, but FSL's Flirt will only work with niftis and not mgz volumes, ergo I can't re-register the manually edited brainmask/wm volumes properly. I was wondering if there were any freesurfer tools I could use to simply re-register the .mgz volumes to the new norm.mgz? If so, how would I go about doing that? Seeing as the brainmask/wm are both registered to 256^3/1mm anyhow, is this something I should even be concerned about? Thanks, KZ

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retinotopic analysis
by Francesca Strappini 05 Jul '16

05 Jul '16

Hello Freesurfers, Where can I find any documentation about how is retinotopic analysis performed in Freesurfer? Thanks. Best -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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