Freesurfer

freesurfer@nmr.mgh.harvard.edu

30088 discussions

Re: [Freesurfer] [FREESURFER] atlas applicability. (fwd)
by Lilla Zollei 29 Mar '12

29 Mar '12

Hi Cheol, > I am using freesurfer for patients with various neural disease. I wonder the > the > freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB), > epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies > already > used freesurfer for some of the diseases in the list,) I believe epilepsy > patients with lobectomy cannot be applicable. If the malformation or the difference between normal control acquisitions and your scans is significant the FS pipeline, using the FS atlas is not going to be successful. Withuot seeing your data I cannot tell which population from the above is going to be affected, but if in doubt just try processing one or two representative samples from the different populations and assess how successful the processing is. > Also is there age limit for the freesurfer atlas? How young can the atlas > work > for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper > bound? 80 year-old? The lower bound, in our experience, is about 4-5 yrs. Of course, it depends on your data quality but we had success all the way down to that age. I am not aware of any upper limits. Again, if you are processing these kind of "extreme" populations, make sure that you inspect the outcome of the FS recon pipeline carefully before proceeding with any type of analysis. Lilla

2 3

About the sample data
by bowang21＠mail.ustc.edu.cn 29 Mar '12

29 Mar '12

Dear All, I can't uncompress the data long-tutorial.tar.gz with command tar xzvf /mnt/workplace/long-tutorial.tar.gz /mnt/workplace. How can I uncompress the data?

1 0

method for detecting neighboring labels?
by David Grayson 29 Mar '12

29 Mar '12

Is there a way to output a list of all the labels within a given annotation file which share a border with another specified label? Thank you very much, David

2 1

sulci problem
by LAOUCHEDI MAKHLOUF 29 Mar '12

29 Mar '12

hi all i use mri_anot2label to extract sulci, is there a tool allowing to keep just the deepest line of the sulcus and if possible get the list of talairach coordinates of that line's points. thanks a lot for your help

2 1

TRACULA and CVS space
by Antonella Kis 29 Mar '12

29 Mar '12

Hi, I would like to know if for a probabilistic tractrography using TRACULA I can use the CVS space as a common template to register the diffusion data instead of MNI template. How I should change for the CVS space the following: set doregmni = 1 which is the default for the MNI space. If I want to use both MNI template and CVS template for comparison purposeshow this can be done? THANKS. Antonella

3 2

fsaverage
by Ahmed, F, Me <fahmed＠sun.ac.za> 29 Mar '12

29 Mar '12

Hello, I'm trying to run qdec on my own data and I'm trying to create fsaverage. Following the wiki tutorial, I copied the command: if (! -e fsaverage) ln -s $FREESURFER_HOME/subjects/fsaverage but I got the following error: bash: syntax error near unexpected token `ln' Can anyone help me in understanding why this happened? Thanks very much, Fatima ________________________________ E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige l?ers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.

2 1

[FREESURFER] atlas applicability.
by Cheol Han 29 Mar '12

29 Mar '12

Hello freesurfers I am using freesurfer for patients with various neural disease. I wonder the the freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB), epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies already used freesurfer for some of the diseases in the list,) I believe epilepsy patients with lobectomy cannot be applicable. Also is there age limit for the freesurfer atlas? How young can the atlas work for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper bound? 80 year-old? Thanks for reading and your time! Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea

1 0

V1_average missing lh.white rh.white
by dgw 28 Mar '12

28 Mar '12

Hello, I am using FreeSurfer 5.1.0. When running recon-all -label_v1 -s $SUBJECT It could not find the rh.white and lh.white surfaces. Subsequently, there was no data in the rh.v1.predict.label. % tksurfer.bin: no data in label file /cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.predict.label Additionally, no <subjid>/label/?h.v1.prob.label was created. I am using the V1_average found on the NMR servers (see output of ls -l below run in $SUBJECTS_DIR): V1_average -> /usr/local/freesurfer/stable5_1_0/subjects/V1_average Am I using the wrong V1_average? Do I need to provide any further details? Thanks, Dan Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 INFO: SUBJECTS_DIR is /autofs/cluster/haru/uni/1/users/nap_study/struct Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5_1_0 -rw-rw-r-- 1 dwakeman pls 385906 Mar 28 16:00 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/scripts/recon-all.log Linux gobo 2.6.18-238.9.1.el5 #1 SMP Tue Apr 12 18:10:13 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux #----------------------------------------- #@# Label V1 lh Wed Mar 28 17:05:43 EDT 2012 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label predict_v1.sh -h lh nap_01 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.inflated.H already exists, skipping. mris_register -inflated -a 4096 -dist 10.0 -parea 1.0 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.sphere /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/label/lh.v1.invivo.tif /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.v1.invivo.reg using inflated surface for initial alignment using n_averages = 4096 l_dist = 10.000 using l_parea = 1.000 $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.sphere... reading template parameterization from /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/label/lh.v1.invivo.tif... curvature mean = 0.000, std = 1.000 curvature mean = 0.018, std = 0.041 curvature mean = 0.006, std = 0.891 curvature mean = 0.018, std = 0.043 curvature mean = 0.002, std = 0.959 curvature mean = 0.018, std = 0.045 curvature mean = 0.001, std = 0.981 curvature mean = 0.018, std = 0.049 curvature mean = 0.000, std = 0.991 writing registered surface to /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/lh.v1.invivo.reg... curvature mean = 0.000, std = 0.604 curvature mean = 0.004, std = 0.952 curvature mean = 0.037, std = 0.807 curvature mean = -0.011, std = 0.957 curvature mean = 0.012, std = 0.930 curvature mean = -0.020, std = 0.961 curvature mean = 0.006, std = 0.967 curvature mean = -0.024, std = 0.961 curvature mean = 0.002, std = 0.985 curvature mean = -0.026, std = 0.286 curvature mean = 0.002, std = 0.068 curvature mean = 0.065, std = 0.336 curvature mean = 0.002, std = 0.081 curvature mean = 0.039, std = 0.522 curvature mean = 0.002, std = 0.087 curvature mean = 0.019, std = 0.665 curvature mean = 0.002, std = 0.090 curvature mean = 0.007, std = 0.771 expanding nbhd size to 1 mris_spherical_average -osurf v1.invivo.reg -n -o nap_01 label lh.v1.invivo.label lh v1.invivo.reg V1_average /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/lh.v1.prob.label output surface = v1.invivo.reg painting output onto subject nap_01. processing subject V1_average... MRISreadVertexPosition(white): could not open file /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/surf/lh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory threshold_labelfile_at_0p8 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/lh.v1.prob.label /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/lh.v1.predict.label thresholding the label...cat: /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/lh.v1.prob.label: No such file or directory done #----------------------------------------- #@# Label V1 rh Wed Mar 28 18:47:58 EDT 2012 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label predict_v1.sh -h rh nap_01 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.inflated.H already exists, skipping. mris_register -inflated -a 4096 -dist 10.0 -parea 0.4 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.sphere /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/label/rh.v1.invivo.tif /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.v1.invivo.reg using inflated surface for initial alignment using n_averages = 4096 l_dist = 10.000 using l_parea = 0.400 $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.sphere... reading template parameterization from /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/label/rh.v1.invivo.tif... curvature mean = -0.000, std = 1.000 curvature mean = 0.014, std = 0.039 curvature mean = 0.007, std = 0.894 curvature mean = 0.015, std = 0.037 curvature mean = 0.003, std = 0.935 curvature mean = 0.015, std = 0.039 curvature mean = 0.001, std = 0.966 curvature mean = 0.015, std = 0.042 curvature mean = 0.000, std = 0.984 writing registered surface to /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/surf/rh.v1.invivo.reg... curvature mean = 0.000, std = 0.598 curvature mean = -0.003, std = 0.935 curvature mean = 0.032, std = 0.805 curvature mean = -0.004, std = 0.942 curvature mean = 0.012, std = 0.925 curvature mean = -0.008, std = 0.944 curvature mean = 0.005, std = 0.965 curvature mean = -0.010, std = 0.943 curvature mean = 0.001, std = 0.984 curvature mean = -0.027, std = 0.279 curvature mean = 0.004, std = 0.070 curvature mean = 0.065, std = 0.345 curvature mean = 0.004, std = 0.084 curvature mean = 0.041, std = 0.531 curvature mean = 0.004, std = 0.090 curvature mean = 0.021, std = 0.675 curvature mean = 0.004, std = 0.093 curvature mean = 0.006, std = 0.787 mris_spherical_average -osurf v1.invivo.reg -n -o nap_01 label rh.v1.invivo.label rh v1.invivo.reg V1_average /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.prob.label output surface = v1.invivo.reg painting output onto subject nap_01. processing subject V1_average... MRISreadVertexPosition(white): could not open file /autofs/cluster/haru/uni/1/users/nap_study/struct/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory threshold_labelfile_at_0p8 /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.prob.label /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.predict.label thresholding the label...cat: /autofs/cluster/haru/uni/1/users/nap_study/struct/nap_01/label/rh.v1.prob.label: No such file or directory done #------------------------------------------ recon-all -s nap_01 finished without error at Wed Mar 28 20:28:12 EDT 2012 done

1 0

Re: [Freesurfer] dt_recon and tractography
by Antonella Kis 28 Mar '12

28 Mar '12

Hi Anastasia, Many thanks for your reply and help. I was wondering that instead to redo all the preprocessing and registration steps s mentioned on FSTutorial/Running Tracula: * Eddy-current correction * Intra-subject registration (diffusion data to T1) * Inter-subject registration (individual subject to a common space) * Creation of cortical and white-matter masks from FreeSurfer recons I can use all this results from my DTI Data Analysis Preprocessing Stream as mentioned on the FSTutorial/Diffusion, by runningfirst the dt_recon (this is performing an Eddy-current correction) and then I resampled structural data in the Diffusion space (aparc+aseg2diff.mgz, wm2diff.mgz), then I applyed the mask to the diffusion data and removed the unwanted "noise", using the 'mri_mask' command to get the masked fractional anisotropy volume (fa-masked.mgz), adc-masked.mgz and then doing individual subject registration on the CVA space and get resampled int CVS space (fa-masked.ANAT+CVS-to-avg35.mgz) using the using mri_cvs_register. I also have all the outputs mentioned under FSL's dtifit since I got them by running dt_recon. So I wonder if is possible to perform a DTI probabilistic tractography using TRACULA by starting only from the last two steps mentioned in trac-all -prep: * Computing anatomical priors for WM pathways, Recontructing WM Pathways, then visualizing the WM pathways, and then doing only statistics. This is what I meant by my previous results. Thank you for your time and help. Antonella ________________________________ From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Wednesday, March 28, 2012 2:07 PM Subject: Re: [Freesurfer] dt_recon and tractography Trackvis does deterministic tractography, not probabilistic. Which previous results do you want to use and why? On Wed, 28 Mar 2012, Antonella Kis wrote: > Dear FS experts, > > I would like to know if for a Diffusion tensor imaging (DTI) tractography study > with TRACULA I can use my previous results from FSTutorial/Diffusion more > exactly my results after running dt_recon and registrations on the CVS space. > If not can you please advise me if for a DTI probabilistic tractography using > my previous results as mentioned above I can use TracVis. > > > Thank you. > Antonella > > > > _______________________________________________ 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.

2 1

dt_recon and tractography
by Antonella Kis 28 Mar '12

28 Mar '12

Dear FS experts, I would like to know if for a Diffusion tensor imaging (DTI) tractography study with TRACULA I can use my previous results from FSTutorial/Diffusion more exactly my results after running dt_recon and registrations on the CVS space. If not can you please advise me if for a DTI probabilistic tractography using my previous results as mentioned above I can use TracVis. Thank you. Antonella

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer