Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Watershed
by SOURAV RANJAN KOLE 16 Jul '14

16 Jul '14

Hello everyone, This is the FreeSurfer version that I am using: freesurfer-Darwin-leopard-i686-stable-pub-v4.4.0 1. I am using watershed to perform more aggressive skull stripping but it seems to be not working for me. Below, I have provided every command I am running to identify the problem: setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh cd to correct directory setenv SUBJECTS_DIR ${PWD} Before Watershed: tkmedit 1203/1203 brainmask.mgz -aux T1.mgz –surfs See attachment- Before_Watershed.png After Watershed: recon-all -subjid 1203 -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -no-isrunning tkmedit 1203 brainmask.mgz -aux T1.mgz -surfs See attachment- After_Watershed.png After watershed, skull stripping seems almost worse and it is not respecting the manual edits that I have done either. You can see the manual edits in the Before_Watershed.png file if you zoom in. 2. Which version of FreeSurfer do I need to have to use gcut as it is giving me the following error- recon-all -skullstrip -clean-bm -gcut -subjid 10 ERROR: Flag -gcut unrecognized.

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mri_glmfit-sim question
by Govindarajan, Koushik Athreya 16 Jul '14

16 Jul '14

Dear FS experts, I am trying to do a paired analysis between 2 time points obtained from the longitudinal pipeline and had some trouble interpreting the results. I have 2 different treatment groups I and II. I ran the paired analysis at p = 0.05, p = 0.01 and p = 0.001 vertex-wise thresholds. For p = 0.05, group I shows greater differences between the 2 time points whereas at p = 0.01 and p = 0.001, group II shows greater differences between the 2 time points. Is there any reason that might explain this discrepancy? If not, which result do I trust? The sample size in both groups is comparable (approximately 120 subjects in each group). Thanks Koushik

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mri_surfcluster --centroid
by Jockwitz, Christiane 16 Jul '14

16 Jul '14

Dear experts, in one of the earlier posts there was a discussion about mri_surfcluster and the -centroid option. I'am using Freesurfer 5.1 (Linux) so I don't have the --centroid option implemented. Is there a possibility to use it anyway (via a script)??? Thank you advance. Best. Christiane ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Position available at Hospital San Raffaele
by Zonca Lucia 16 Jul '14

16 Jul '14

The Neuroimaging Research Unit, Division of Neuroscience at Hospital San Raffaele is looking for a highly motivated junior researcher or postdoctoral fellow with previous experience in analysis of structural and functional MR scans in multiple sclerosis and other white matter conditions. He/she will work on projects aimed at improving the understanding of the mechanisms leading to the accumulation of irreversible physical disability and cognitive impairment in adult and pediatric patients with multiple sclerosis and other white matter diseases, including vasculitides, neuromyelitis optica, migraine and trauma. The Neuroimaging Research Unit (NRU) is an international research centre, part of the Institute of Experimental Neurology, operating since 15 years. NRU mission is to foster state-of-the-art neuroimaging research directed at understanding the structural and functional correlates of central nervous system (CNS) changes in healthy subjects and damage in diseased individuals. The NRU currently comprises a multidisciplinary team including physicians, post-Docs, bioengineers, PhD students, residents in neurology, technicians and data-managers (http://www.hsr.it/research/organization/divisions-centers/division-of-neuro…) The ideal candidate should have expertise in the acquisition and analysis of advanced MRI techniques (volumetric, diffusion tensor MRI and functional MRI). Expertise in voxel-based morphometry, tract-based spatial statistics, resting state and active fMRI analyses would be an advantage. The job requires the analysis and acquisition of MRI data sets and implementation of novel analytic tools, contributing to the design and programming of MRI experiments, assisting in analyzing the results, and participating in the writing up of the results. Good social skills are important as the candidate is expected to actively collaborate with other members of the laboratory. Applicants should be able to demonstrate a consistently good academic record, including publications in international journals. Starting date: October 2014 for up to 3 years. Salary will vary based on previous experience. CVs, including name of two references, should be sent to: Prof. Massimo Filippi at filippi.massimo(a)hsr.it<mailto:filippi.massimo@hsr.it>. Thank you. Please feel free to advertize it to whoever you think might be interested. [cid:5x100osr201472d5.jpg] <http://www.5xmille.org/> Disclaimer added by CodeTwo Exchange Rules 2007 www.codetwo.com<http://www.codetwo.com>

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watershed error
by Janosch Linkersdörfer 16 Jul '14

16 Jul '14

Hi all, recon-all runs smoothly for all my subjects but one. It throws the error "mri_watershed Error: indices out of bounds" and finishes (see https://www.dropbox.com/s/4del0uy8g1qw5az/recon-all.log) The image quality does not seem to be different... The error has been discussed on the list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021896.…) but I don't know where in the brain and in which image space I should add control points or what else I can do to prevent this from happening. Thanks for your help, Janosch

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recon-all exits after mri_nu_correct
by ISAAC PEDISICH 15 Jul '14

15 Jul '14

Hi All, I'm trying to reconstruct surfaces using recon-all. Though many of the subjects have succeeded, a few are failing at the mri_nu_correct stage. The error file (posted below) provides little detail as to why the error is occurring. Even if it is not fixable, it would be nice to know what caused this error. I can provide data if requested. Thank you for your help, Isaac The following is the contents of the reocn-all.error file: ------------------------------ SUBJECT UP044 DATE Thu Jun 26 11:19:36 EDT 2014 USER analy HOST rhino.psych.upenn.edu PROCESSOR x86_64 OS Linux Linux rhino.psych.upenn.edu 2.6.18-371.4.1.el5 #1 SMP Thu Jan 30 06:08:24 EST 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/global/freesurfer/bin/recon-all PWD /data3/eeg/freesurfer/subjects/UP044/mri CMD mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

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sulcal depth
by Aleksandar Ristic 15 Jul '14

15 Jul '14

Hi Freesurfer experts, I did thickness group analysis in pts and healthy subject groups in qdec (age corrected( and got thicker cortex in left insula and thinner precentral gyrus bilaterally that survived FDR 0.01 Surface area and curvature analysis found no difference. However, sulcal depth analysis reveled striking difference (positive) in bilateral insula (survived FDR 0.001). As this finding can attribute significantly to understanding of the background of investgated disorder, I kindly ask for representative references covering sulcal depth method (as the variability of the folding patterns is still largely not understood, and different methods have been employed already to best of my knowledge). Second, do I have to correct sulcal depth for age? thanks, Alex Aleksandar J. Ristić, MD, PhD Epilepsy Center Neurology Clinic, Clinical Center of Serbia University of Belgrade, Belgrade - Serbia --- avast! antivirus zaštita je aktivna stoga ova e-pošta nema virusa i zlonamjernih programa. http://www.avast.com

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Is there any saving a brain from this type of error?
by Jonathan Holt 15 Jul '14

15 Jul '14

Attached is an image of wm.mgz after a routine recon-all...

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Re: [Freesurfer] Fw: Re: Problem with uploading Cluster Simulation data
by Douglas N Greve 15 Jul '14

15 Jul '14

You have to load a surface and then load the overlay on top of that. See the freeview tutorial doug ps. Please post to the list! On 07/15/2014 09:03 AM, carina(a)van-vlodrop.de wrote: > I have opened freeview with the commands 'freesurfer' and 'freeview'. > I thought that I could upload the data directly in freeview. Or which > command do I need? > *Gesendet:* Montag, 14. Juli 2014 um 19:38 Uhr > *Von:* "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > *An:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de>, > "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> > *Betreff:* Re: Fw: Aw: Re: [Freesurfer] Problem with uploading Cluster > Simulation data > > what is your command line? Or otherwise, how are you visualizing it? > > > > On 07/14/2014 08:09 AM, carina(a)van-vlodrop.de wrote: > > *Gesendet:* Sonntag, 06. Juli 2014 um 22:48 Uhr > > *Von:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de> > > *An:* "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> > > *Betreff:* Aw: Re: [Freesurfer] Fw: Problem with uploading Cluster > > Simulation data > > Hi Doug, > > I have already uploaded a text file of my corrected results from the > > Monte Carlo Cluster Simulation which reports 15 Clusters (attached > > picture). > > There is another file ending with .mgh and the tutorial identifies it > > to be the overlay (clusterwise corrected map) which I can upload in > > freeview. > > In freeview there are the alternatives of uploading a surface or a > > volume. If I upload the file ending with .mgh as a volume I just > > recieve a black image with a few numbers on the coordinate plane > > (attached picture). There is no brain visible. > > Is it correct to upload the overlay (file ending with .mgh) as a > > volume or how should I proceed? Do I have to upload a template first > > and which is the right template? > > Thank you so much. > > Yours sincerely, > > Carina > > *Gesendet:* Montag, 16. Juni 2014 um 12:45 Uhr > > *Von:* "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> > > *An:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de>, "free surfer" > > <freesurfer(a)nmr.mgh.harvard.edu> > > *Betreff:* Re: [Freesurfer] Fw: Problem with uploading Cluster > > Simulation data > > > > You should be able to view the map results in freeview just as you > > would any other map. > > doug > > > > > > > > > > > > On 6/12/14 12:19 PM, carina(a)van-vlodrop.de wrote: > > > > *Gesendet:* Dienstag, 10. Juni 2014 um 11:18 Uhr > > *Von:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de> > > *An:* freesurfer(a)nmr.mgh.harvard.edu > > *Betreff:* Problem with uploading Cluster Simulation data > > Dear freesurfer experts, > > we are conducting cortical-thickness analysis using > > freesurfer-4.4.0 and the final analysis with qdec. I have a > > question concerning the Clusterwise Correction for Multiple > > Comparison. > > Is it correct that I have to visualize the results of the Monte > > Carlo Simulation in freeview? > > Do I have to upload a special model in freeview before uploading > > the Cluster Simulation data? > > Yours sincerely, > > Carina > > > > > > _______________________________________________ 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. > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Temporal lobe reconstruction problem
by james pardon 15 Jul '14

15 Jul '14

Hi all, On a few subjects with a specific pathology (MS) I cannot easily reconstruct temporal lobes. I think this issue comes up quite regularly on the mailing list, and I have tried to trouble shoot using control points, WM edits, even getting back to orig/001.mgz to correct areas that may seem the culprit for breaking surface reconstruction. Some subjects have gone through 7-8 runs of recon-all with different edits but still the problem persists in a few subjects in my study. I have also tried to use -mprage and -3T flags along the way to allow more liberal control point growing, despite an improvement in my results some of subjects still have very bad surface constructions. I have attached two snapshots to this email and I am happy to upload the complete subject folder if you need to take a look at them. As far as the SNR is concerned, I have designed my study based on recommended Freesurfer parameters a couple of years ago on 3T Siemens Trio with 32-channel receiver coil. A huge thank you for your previous helps, and thanks in advance for helping me with this new issue. James

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Freesurfer