Re: [Freesurfer] Freesurfer QDEC Buckner Data

download the file wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz -c thanks in advance cheers Saurabh Thakur, On Mon, Apr 7, 2014 at 9:42 PM, Louis Nicholas Vinke < vi...@nmr.mgh.harvard.edu> wrote: > Hi Saurabh, > Did the wget command fail

[Freesurfer] QDEC tutorial data- problem in downloading

Hello Freesurfer , I am looking forward for alternative mirror link to download the QDEC data. i.e Buckner_data_tutorial_subj Since link provided is not working. I have tried many times. Thanks in advance, cheers Saurabh Thakur, ___ Freesurfer

[Freesurfer] Freesurfer QDEC Buckner Data

. cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@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

Re: [Freesurfer] Cortical thickness measurement using Freesurfer v 5.3

Hello Everyone, I got the answer in mri_annotation2label. I new to freesurfer and trying to learn as fast as possible. Thanks for patience and cooperation. cheers Saurabh Thakur, On Wed, Apr 2, 2014 at 10:58 AM, Saurabh Thakur wrote: > Hello Freesurfer Expert, > > I am t

[Freesurfer] Cortical thickness measurement using Freesurfer v 5.3

occipital lobe, and not very specific region wise value. Is is possible to get avg thickness value for all lobes? and If possible how to get that..? Thanks in advanced, Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Tksurfer + Histogram

get complete information.Thanks again for your advice. cheers Saurabh Thakur, On Wed, Mar 26, 2014 at 5:59 PM, Bruce Fischl wrote: > Hi Saurabh > > I'm not sure I understand. This is the purpose of recon-all - to generate > morphomological models, including the thick

Re: [Freesurfer] Tksurfer + Histogram

On Wed, Mar 26, 2014 at 2:39 PM, Saurabh Thakur wrote: > Hello Bruce, > I am referring to link > http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness > to calculate the cortical thickness of particular area such as Left > hippocampus for our own data set. > Bu

Re: [Freesurfer] Tksurfer + Histogram

set which can be used as overlay. (Used for surface to surface overlay) Can u suggest how to generate lh.thickness file for my own data using freesurfer...? Thanks in advanced. cheers Saurabh Thakur, On Tue, Mar 11, 2014 at 10:28 PM, Bruce Fischl wrote: > try configure->functional over

Re: [Freesurfer] Sample bert information

Just to get some comparative result with subject which we have. At least this can be made available for public domain. cheers Saurabh Thakur, On Thu, Mar 20, 2014 at 8:11 PM, Douglas N Greve wrote: > > why do you need to know this? bert, and the rest of the distributed > data

[Freesurfer] Sample bert information

Hello Freesurfer Expert, Can you share the freesurfer sample named *bert* information such as age,M/F and other details. Thanks in advance, cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Tksurfer + Histogram

Hello Freesurfer Expert, Can anyone help me with histogram plotting of different surfaces in tksurfer. I looking to calculate the thickness of cortex. Thanks in advance, Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Cortical thickness measuring algo

Hello Freesurfer, Laplacian based method for measuring Cortical thickness Can u anyone help me to understand how freesurfer has implemented this algo and where to find this algo for better understanding. Thanks, Saurabh Thakur, ___ Freesurfer

[Freesurfer] Looking for cortical thickness procedure

the tesselated surface and automatic topology correction* Can u help me to step no 5 and 6. How to do this steps. Thanks, Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

[Freesurfer] Difference in Volumetric measure of Hippocampus Segmentation

lysis: Lh Hippo Rh Hippo *Command used * *17* *53* asegstats2table 4563 4502 EstimatedTotalIntraCranialVol 1594882.91136 mri_label_volume 4645 4545 eTIV volume (1594796) Thanks for timely reply. cheers Saurabh Thakur, ___ Freesurfer mailing

Re: [Freesurfer] Hippocampus segmented file in tkmedit.

Thakur, On Tue, Mar 4, 2014 at 2:49 PM, Saurabh Thakur wrote: > How to create only Hippocampus segmented file in tkmedit. > > aseg.mgz. for Hippocampus file. > > Please > > cheers > Saurabh Thakur, > > > > > ___

[Freesurfer] Hippocampus segmented file in tkmedit.

How to create only Hippocampus segmented file in tkmedit. aseg.mgz. for Hippocampus file. Please cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] Matlab help

Thanks Sebastian. Will take a note of it. cheers Saurabh Thakur, On Tue, Mar 4, 2014 at 1:20 PM, Sebastian Moeller < sebastian.moell...@rwth-aachen.de> wrote: > Hi Saurabh, > > > On Mar 4, 2014, at 07:56 , Saurabh Thakur wrote: > > > Hi Markus Gschwind

Re: [Freesurfer] Matlab help

efined function or variable 'IM_0001'.* 2nd example : *>> MRIread(brain.mgz,brainMRI.hdr) ??? Undefined variable "brain" or function "brain.mgz".* I looking forward to work on matlab along with freesurfer. Looking for your reply asap. Thanks for reply. cheers Saura

[Freesurfer] Matlab help

Hello Freesurfer, I am trying to runs MRIread.m file in matlab. But it is not reading the brain.mgz or any other format. Can u help in this regards. Thanks in advance, cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] Extracting only hippo campus volume

; > cheers > Bruce > > On Fri, 28 Feb 2014, Saurabh Thakur wrote: > > Hello Freesurfer expert, >> >> I have done Hippo campus segmentation using Freesurfer. >> >> Can u tell me how to extract the only Hippo campus volume from nu.mgz >> >&g

[Freesurfer] Extracting only hippo campus volume

Hello Freesurfer expert, I have done Hippo campus segmentation using Freesurfer. Can u tell me how to extract the only Hippo campus volume from nu.mgz Why only nu.mgz is used for the main volume--is there some specific reason to use? Thanks in advance , Saurabh Thakur

[Freesurfer] Volumetric data for GM,WM,CSF.

ing *wmparc.stats* *Total cortical white matter volume, 484479.305031, mm^3* mri_segstats-> giving me vol of grey matter by using* aseg.stats* *Total gray matter volume, 655593.521190, mm^3* *If i wanted to have all the value in one single window/file.* cheers Saurabh

[Freesurfer] Segmentation process

. Thanks in advance. cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@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

Re: [Freesurfer] Error mric-convert

Hello Doug, I am working as R&D engg in National Brain research Center,India. here we have our own setup, Due to which i have access to DICOM images. So Doug, what is requiredapart from images. cheers Saurabh Thakur, On Wed, Feb 19, 2014 at 8:41 PM, Douglas Greve wrote: >

Re: [Freesurfer] Error mric-convert

command i m using is :mri_convert -i /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 -o $SUBJECTS_DIR/bert/mri/orig/005.mgz cheers Saurabh Thakur, On Wed, Feb 19, 2014 at 12:22 PM, Saurabh Thakur wrote: > Hello Everyone, > > I am facing small problem to create my

[Freesurfer] Error mric-convert

MRIalloc(0, 0, 151): bad parmNo such file or directoryERROR: mri alloc failed* //===// Please reply asapi m waiting for the solution. Thanks in advanced. cheers Saurabh Thakur

Re: [Freesurfer] Number of pixel count

Hi Bruce, That means i should use mri_segstats for the same? Thanks, cheers Saurabh Thakur, On Wed, Feb 12, 2014 at 6:52 PM, Bruce Fischl wrote: > Hi Saurabh > > we don't measure sulcal CSF as it's really not visible on only a T1. The > other measures should

[Freesurfer] Segmentation using Free Surfer.

. Please suggest what the best way/ Algorithm to so get MRI image segmentation using Freesurfer. Thanks in advance. cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

[Freesurfer] Number of pixel count

Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@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

Re: [Freesurfer] Freeview not working

Hello Zeke, There was some packages missing. I have updated it,so now its working. Really thanks for the your help. cheers Saurabh Thakur, On Mon, Feb 10, 2014 at 8:50 PM, Z K wrote: > Saurabh, > > What is the output when you type "locate libXss.so.1" (without quote

Re: [Freesurfer] scuba running problem.

Oh...is it so Bruce Thanks a lot for info. cheers Saurabh Thakur, On Mon, Feb 10, 2014 at 6:55 PM, Bruce Fischl wrote: > Hi Saurabh > > scuba is deprecated - we haven't used it in years. Ruopeng or someone will > answer your freeview question when they get a chance. &

[Freesurfer] scuba running problem.

is set. //==// Thanks in advance. cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

[Freesurfer] Freeview not working

directory saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ /=// please suggest wht is going wrong. Thanks in advance, cheers Saurabh Thakur, ___ Freesurfer mailing list

[Freesurfer] Segmentation Algo

Hello Freesurfer expert, I am new to freesurfer. I wanted to know which algorithm is used for segmentation in freesurfer. Thanks in advanced, cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Freeview

while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory* can anyone help me in this regards, Thanks in advance. cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Installation error

Hi Sebastian ,Bruce and Markus. I got the freesurfer running using freesurfer-x86_64-unknown-linux-gnu-stable5-20130513 Thanks for all your help. cheers Saurabh Thakur, On Tue, Feb 4, 2014 at 9:18 PM, Sebastian Moeller < sebastian.moell...@rwth-aachen.de> wrote: > Hi Saurabh,

Re: [Freesurfer] Installation error

-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$* sudo tkmedit2 subject1 rawavg.mgz* sudo: tkmedit2: command not found saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer/tktools$ Am i doing it right...? cheers Saurabh Thakur, On Tue, Feb 4, 2014 at 8:28 PM, Sebastian Moeller

Re: [Freesurfer] Installation error

reesurfer$ //===// Still error is present...? cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in th

Re: [Freesurfer] tkmedit is not working

it one more time. and get back to you. cheers Saurabh Thakur, On Tue, Feb 4, 2014 at 7:26 PM, Bruce Fischl wrote: > yes, particularly since 5.2 was deprecated. Thanks for pointing this out > Sebastian > > Bruce > > On Tue, 4 Feb 2014, Sebastian Moeller wrote: > >

Re: [Freesurfer] Installation error

orking on laptop where as in other desktop in our lab its working fine. What should be the problem...? cheers Saurabh Thakur ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The infor

Re: [Freesurfer] tkmedit is not working

not found* //==// cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@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 w

Re: [Freesurfer] Installation error

tkUtils.tcl saurabh@saurabh-Dell-System-XPS-L502X:~$ tkedit subject1 orig.mgz tkedit: command not found saurabh@saurabh-Dell-System-XPS-L502X:~$ //==// cheers Saurabh Thakur, On Tue, Feb 4, 2014 at 6:11 PM, Markus Gschwind wrote: >

Re: [Freesurfer] Installation error

ponse asap. Thanks in advance. Saurabh Thakur, On Tue, Feb 4, 2014 at 2:09 PM, Markus Gschwind wrote: > Hi Saurabh, > > I recently installed FS un ubuntu 12.04, and it was not difficult. > > I would recommend that you again download the file from here > http://surfer.nmr.mgh

[Freesurfer] Installation error

Hello everyone, Can u anyone help me in simplest and best way to install freesurfer on *i m not able to run command : * *1. tkmedit 2. tksurfer.System specification: * Dell laptop Ubuntu 12.04 LTS RAM 8Gb Graphics cards: Nvidia cards 1 Gb Thanks in advance. Saurabh Thakur

[Freesurfer] FreeSurfer build stamps do not match

advance. Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@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

[Freesurfer] tkmedit is not working

Hi Everyone, Terminal output is: ///--// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$* tkmedit* /usr/local/freesurfer/tktools*/tkmedit.bin: Command not found.* saurabh@saurabh-D

Re: [Freesurfer] tkmedit.bin: Command not found

there is problem with tkmediteven i can physically see binary file tkmedit.bin present in tktools folder. Saurabh Thakur, Senior Research Fellow, Electronics Dept, DIAT,Pune Mobile No.:+91-9850595447 On Mon, Feb 3, 2014 at 8:30 PM, Bruce Fischl wrote: > Hi Saurabh > > can you ru

[Freesurfer] tkmedit.bin: Command not found

Hello, I have just installed freesurfer in my linux ubuntu12.04 machine. I am getting error such as : *tkmedit.bin: Command not found* but the recon-all --help is working perfectly. My environment variable is working. Please help me where i m going wrong asap. Saurabh T. ___