Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

R: Re: convert size
by Andrea Tateo 10 Dec '12

10 Dec '12

Soory if I bother you again, actually I would like to convert from 256,128,256 to 256,256,256 and from 181,145,181 to 256,256,256. Can you tell me the complete command and not just the option. thanks immensely Andrea ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 10-dic-2012 14.36 A: "Andrea Tateo"<andrea.tateo(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] convert size Hi Andrea I think there is a typo in your email as your sizes are the same. If you have a volume you would like to reslice it like you can use the -rl <volume> option to do what you want. cheers Bruce On Mon, 10 Dec 2012, Andrea Tateo wrote: > Hello FS experts, > I would like to to convert binary images from size 256,256,256 voxels to > size 256, 256, 256. > > Is there any FreeSurfer's module to make it? > > Thank you very much > > Andrea > > 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

Re: [Freesurfer] question retinotopic mapping
by Douglas N Greve 10 Dec '12

10 Dec '12

Hi Julia, that command is fine. It will not use the fieldsign or eccen. doug On 12/10/2012 10:17 AM, Julia Foecker wrote: > Dear Doug, > > I tried version 5 with the commands suggested on the webside and this is > working > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis) > > > However, I have only polar angle runs and I am not sure if the rtview commands > is only referring to polar angle maps (because the field signs are included and > I think that they consist of eccentricity maps as well which do not have a > meaning in my analysis). > How do I have to change the command below so that it is just referring to polar > maps? > > rtview --s VGP01 --lh --polar --real polar/real.nii.gz --imag polar/imag.nii.gz > --fsig polar/fsig.nii.gz > > > Many thanks for further suggestions, > Julia > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

Detrending timeseries with yhat.mgh from mri_glmfit
by Chris McNorgan 10 Dec '12

10 Dec '12

Hello, I have a question regarding the yhat.mgh file generated from some resting-state functional data after running: mri_glmfit --y fmcpr.siemens.sm0.self.?h.nii.gz --glmdir $dest_dirname --qa --save-yhat I had assumed that the yhat file was the detrended data, but after plotting it in matlab and seeing perfectly smooth lines, I came to believe that the yhat.mgh file represents the trendline for each timeseries in the source .nii.gz? In this case, if I use mri_segstats to pull out the timeseries data from an ROI, is it then valid to calculate roi_timeseries/roi_trendline in order to arrive at a detrended timeseries for that ROI? Thanks, Chris

2 1

winkler surf data with qdec ?
by Gregory Kirk 10 Dec '12

10 Dec '12

Hi , I have winkler variety surface area data that is already smoothed and converted to vertex wise data on my average subject. Each subject has a file rh.ico7.fwhm10.mgh, lh... and Doug gave me a way with mri_concat to assemble the data into a single file so i can run command line mri_glmfit type analysis and that worked out fine. I would like if i can to use qdec so our non command line unix oriented postdoc could easily run a lot of models of interest. the LGI page says you can do recon-all -s my_subject_id -qcache -measure pial_lgi and then add a file .Qdecrc with MEASURE1 = pial_lgi but recon-all -qcache will do smoothing and smoothing has already been done by his fancy specially designed method for the surface interpolated data and also my data is in .mgh format and not curv format like thickness or lgi. is there a way i can cook this goose ? thanks greg

3 2

.licence problem
by Eva Hilland 10 Dec '12

10 Dec '12

Hi, I am setting up freesurfer on a pc laptop for a colleague. I have installed Oracle VM virtual box, Neurodebian, and FreeSurfer. Freesurfer is now running, but when I try doing recon-all I get the error message: ERROR: FreeSurfer license file /usr/local/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. This is very strange because the .licence file is actually in the freesurfer directory. Has anyone encountered this problem before? Any tips? Thanks in advance! Eva

3 2

convert size
by Andrea Tateo 10 Dec '12

10 Dec '12

Hello FS experts, I would like to to convert binary images from size 256,256,256 voxels to size 256, 256, 256. Is there any FreeSurfer's module to make it? Thank you very much Andrea

2 1

Parcellation of cerebellum.
by charles laidi 10 Dec '12

10 Dec '12

Dear freesurfer, I'm trying to perform parcellation on the cerebellum. After reading closely freesurfer wiki and the questions related to this topic on the mailing list, my understanding is that there is no way to perform fully automted cerebellar parcellation on structural mri with freesurfer. Could you tell me if I'm right ? Thanks a lot for your attention Charles

2 1

VOI
by octavian lie 09 Dec '12

09 Dec '12

Dear All, I have 2 coregistered MR volume (pre and postresective MRI) sets for several epilepsy patients. I need to extract the resection volume (VOI= pre - postresection volume) as a set of voxel coordinates. Can I do this in freesurfer? Ideally I would avoid manual delineation slice by slice as in MRImicro and if possible I would do it automatically by thresholding, for example. If not, manual is fine if it can be done in FS. Please advise. Thank you, Octavian.

2 3

Re: [Freesurfer] regarding longitudinal segmentations
by Martin Reuter 08 Dec '12

08 Dec '12

Hi Prasanna, yes, simply looking at the label in aseg.mgz is fine. I don't think pretess is part of recon-all and it may happen, that these labels are not very smooth. Pretess helps a little (but this is mainly important for people who generate a surface mesh from the label). For you it is probably not necessary. best Martin p.s please always reply to the list so that others can answer. On Dec 8, 2012, at 3:18 PM, Prasanna M <prasanna(a)sci.utah.edu> wrote: > Hi Martin, > > For each subject and each time-point, I did the cross-sectional processing. Then I ran the recon-all base to create templates for each subject. Then I ran the recon-all long to do the longitudinal processing. I ran each of these commands with the -all option. Isn't mri_pretess part of the recon-all stage already? Do I need to use it again to clean up voxels? > > So for each subject and each time-point, I have all the segmentations with labels for each subcortical structures, say 17 for the left hippocampus, and 53 for the right hippocampus. So would I need only to threshold each of these aseg.mgz files at these values to get an accurate segmentation of structures? Or would I need to do something more? I'm new to image processing, so I apologize if these questions seem too trivial. > > Thanks, > Prasanna > > > > > On Fri, Dec 7, 2012 at 11:45 AM, Prasanna M <prasanna(a)sci.utah.edu> wrote: > Thanks martin. My mistake. nothing to do with longitudinal processing. Wanted to be able to segment out each structure. I'll look up mri_pretess. > > Thanks. > > > On Fri, Dec 7, 2012 at 11:27 AM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: > Hi Prasanna, > > not sure what you are asking and what this has to do with longitudinal. > But generally: subcortical segmentations are stored in the aseg.mgz file > (this is true also for the longituinal stream, do not look at the > aseg.fused.mgz , it is an intermediate step). Final results are in > aseg.mgz. > > Aparc is for the parcellations of the cortex. > > Freesurfer has tools to create e.g. a hippocampus mask from the aseg. > mri_pretess can probably do it and cleans up the mask a little. > > Best, Martin > > On Fri, 2012-12-07 at 11:04 -0700, Prasanna M wrote: > > Hi, > > > > > > Do I work with aseg.fused.mgz or do I work with aparc files to get the > > most accurate segmentation of brain structures? > > > > > > > > I tried using freeview to look at segmentations. Is there a way to > > isolate mgz files of very specific structures. I mean, is there an > > inbuilt tool which can do that for me, or would I have to go image by > > image, and threshold to get, say the hippocampus? > > > > > > Thanks, > > Prasanna > > > > > > > > > > > > -- > > -- > > Let there be peace on earth... > > And let it begin with me. > > > > > > > > > > > > > > > > _______________________________________________ > > 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. > > > > -- > -- > Let there be peace on earth... > And let it begin with me. > > > > > > -- > -- > Let there be peace on earth... > And let it begin with me. > > --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

1 0

Calculating the mean intensity ratio in one specific region
by Kong, Li 08 Dec '12

08 Dec '12

Hello everyone, I got grey matter/ white matter intensity ratio at each vertex across the cortex. I would like to know the mean intensity ratio in one region (ex, superior temporal gyrus). Anyone knows how to get it? Thanks in advance! Li

3 4

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