Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30090 discussions

volume called 001.mgz
by Varghese Chikku 10 Jun '13

10 Jun '13

Dear All, I am getting this error message on a scan.I deleted the created subject folders and re-ran the command,but no luck.Any suggestions? Thanks in advance, CV setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni freesurfer@freesurfer-VirtualBox:~$ recon-all -i /home/freesurfer/Desktop/10035BL/T1pre/Image00001 -autorecon-all -s 10035BLFS Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/10035BLFS mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image00001 /usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image00001 /usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz file not found or unknown file type for file /home/freesurfer/Desktop/10035BL/T1pre/Image00001 #-------------------------------------------- #@# MotionCor Mon Jun 10 16:03:45 CEST 2013 ERROR: no run data found in /usr/local/freesurfer/subjects/10035BLFS/mri. Make sure to have a volume called 001.mgz in /usr/local/freesurfer/subjects/10035BLFS/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 10035BLFS exited with ERRORS at Mon Jun 10 16:03:45 CEST 2013 For more details, see the log file /usr/local/freesurfer/subjects/10035BLFS/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting freesurfer@freesurfer-VirtualBox:~$

3 2

Installation trouble on Macbook Air (no such file or directory)
by nmw 10 Jun '13

10 Jun '13

I am new to Unix and FreeSurfer, and I am having some trouble installing FreeSurfer on my Macbook Air (10.8). I've downloaded the .dmg file just fine, and when I start the installation steps, I'm instructed to add some lines to my .cshrc or .tcshrc files in my home directory. Can anyone point me to this file? Also, just below on the installation dialog, it says for sh or bash users: export FREESURFER_HOME=<freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh Can I use these instead of the first two lines of code? I tried to enter these bash lines one at a time into my terminal window. The first one ("export") did not give me any errors but for the "source" one, I received the message: bash: /freesurfer/SetUpFreeSurfer.sh: No such file or directory. Any idea as to why I am getting this error? My apologies in advance for my lack of experience. Many thanks, Nate

2 1

Coupling cortical and TRACULA results
by stdp82＠virgilio.it 10 Jun '13

10 Jun '13

Hi list, Thiebaut de Schotten et al., in an article on cortex ("Monkey to human comparative anatomy of the frontal lobe association tracts" reported that "The superior longitudinal fasciculus has three distinct branches (Petrides and Pandya, 1984). In humans, the first branch of the superior longitudinal fasciculus (SLF I) connects to the superior parietal lobule and precuneus (BA 5 and 7), to the superior frontal (BA 8, 9, 32) and perhaps to some anterior cingulate areas (BA 24). The second branch (SLF II) originatesin the anterior intraparietal sulcus and the angular gyrus (BA 39 and 40) and terminates in the posterior regions of the superior and middle frontal gyrus (BA 6, 8, 9). The third branch (SLF III) connects the intraparietal sulcus and inferior parietal lobule to the inferior frontal gyrus (BA 44, 45, 47)" By TRACULA output we have 2 output SLFp and SLFt. Having also cortical results, I wonder if possible to know which are the seed and target areas of SLF p and SLFt or al least to know which is that branch that is described by SLFp output. Thanks, Stefano

2 1

Re: [Freesurfer] CVS and group analysis
by Lilla Zollei 09 Jun '13

09 Jun '13

Do you want to compute the average intensity volume after the CVS registration steps? YOu could use mri_average with the "final_CVSmorphed_tocvs_avg35.norm.gz" files as input images. Lilla On Sun, 9 Jun 2013, Fernando Valle-Inclán wrote: > Sorry. I'm talking about "final_CVSmorphed_tocvs_avg35.norm.gz"Thanks for the very prompt reply > F > > 2013/6/9 Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > > Hi, Can you be more specific? What files / volumes do you want to compute a group average of? > > On Sun, 9 Jun 2013, Fernando Valle-Inclán wrote: > > Hi freesurfers, After doing cvs registration, how can I make a group average? Is fsaverage OK? > Thanks > > > > _______________________________________________ > 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

CVS and group analysis
by Fernando Valle-Inclán 09 Jun '13

09 Jun '13

Hi freesurfers, After doing cvs registration, how can I make a group average? Is fsaverage OK? Thanks

2 1

Morphological operations on surface labels
by Michael Waskom 09 Jun '13

09 Jun '13

Hi, Are there any utilities for performing basic morphological operations on surface-based label files buried somewhere within Freesurfer? Specifically I am hoping to perform a closing. Thanks! mw

3 6

Announcement: ESMRMB Lectures on MR: Educational on Resting State fMRI Vienna – September 2-4, 2013
by leemon albert 09 Jun '13

09 Jun '13

ESMRMB Lectures on MR: Educational on Resting State fMRI Vienna – September 2-4, 2013 After the big success of last year’s workshop in Magdeburg, we are proud to announce the 2013 Resting State Educational Workshop taking place in Vienna, September 2-4. The 3-day educational workshop, organized together with the ESMRMB – Lectures on MR Series, will feature the most relevant topics related to resting state imaging, including physiology, data analysis, and applications. The target audience, researchers with existing knowledge on fMRI with an interest to broaden and substantiate their knowledge on resting state fMRI, will get to experience in-depth lectures and hands-on analysis sessions by international experts in the field. Faculty: Christian Beckmann (Donders, NL) Fahmeed Hyder (Yale University, US) Catie Chang (NIH, US) Peter Fransson (Karolinska, Sweden) Mika Rubinov (Cambridge, UK) Sepideh Sadaghiani (Berkeley, US) Lucina Uddin (Stanford, US) Vesa Kiviniemi (Oulu, Finnland) Bharat Biswal (UMDNJ, US) Christian Windischberger (Vienna, Aus) Ilya Veer (Charité, Germany) Martin Walter (Magdeburg, Germany) For more information on the course program and speakers, or to simply register, please visit www.restingstate.com or www.esmrmb.org. The registration fee for PhD students and physicians in training is € 240 for ESMRMB members and € 335 for non-members, which includes access to the workshop, a course syllabus, full catering of lunches and coffee breaks, and a welcome dinner. After the workshop, a 2-day scientific mountain event will complement the course and provide the opportunity to present own work and get together with peers and colleagues. We are looking forward to see you in Vienna! Christian Windischberger Martin Walter Ilya Veer

1 0

subfield algorithm and subject intensity differences
by Joshua Lee 08 Jun '13

08 Jun '13

I'm trying to understand Leemput's subfield algorithm better as implemented in Freesurfer. Does the algorithm make use of intensity differences in the internal hippocampal lamina from the subject's T1 image to warp meshes and assign subfield probabilities? Or does it depend only on outward boundaries of the hippocampus and probability priors to determine the inner boundaries between CAs and dentate gyrus? - Josh

3 5

Re: [Freesurfer] Cortical thickness
by Joshua deSouza 08 Jun '13

08 Jun '13

Hello Doug, Each individuals subject data has already been smoothed by 5 10 15 20 and 25 through the qache function during the initial processing. I'm a little confused now. I thought that the mri_preproc would use the non-smoothed values of the subjects and create an mgh file. After which I smooth the mgh file and then use mri_glmfit to analyse it according to the contrasts. If the above is not the case and the subject data has already been smoothed, then what should I do if I wish my final mgh file to have a smoothing value of 15 before doing a glmfit on it? Thank you, Joshua On Wed, Jun 5, 2013 at 12:40 AM, Joshua deSouza <desouzajoshua00(a)gmail.com>wrote: > Hello Doug, > > Each individuals subject data has already been smoothed by 5 10 15 20 and > 25 through the qache function during the initial processing. > > I'm a little confused now. I thought that the mri_preproc would use the > non-smoothed values of the subjects and create an mgh file. After which I > smooth the mgh file and then use mri_glmfit to analyse it according to the > contrasts. > > If the above is not the case and the subject data has already been > smoothed, then what should I do if I wish my final mgh file to have a > smoothing value of 15 before doing a glmfit on it? > > Thank you, > > Joshua > > On Mon, Jun 3, 2013 at 11:13 PM, Douglas Greve <greve(a)nmr.mgh.harvard.edu>wrote: > >> >> Hi Joshua, when you add --fwhm 15 to the command line you are instructing >> mri_glmfit to smooth by 15mm. Is this what you want? Or is the data >> already smoothed? >> doug >> >> >> >> On 6/3/13 12:26 AM, Joshua deSouza wrote: >> >> Hi Doug, >> >> The command line is mri_glmfit --y lh.t.15.mgh --fsgd t.txt dods --C >> t1.txt --surface fsaverage lh --cortex --fwhm 15 --glmdir lh.t.15.glmdir >> >> I am doing a whole hemisphere analysis and am measuring cortical >> thickness. I do not have my own mask but I have doubts about the mask that >> has been produced because from previous studies, there has been significant >> thinning in the area around the hippocampus and parts of it are being left >> out in the mask, such as the para-hippocampal region. >> >> Regards >> >> Joshua >> >> On Mon, Jun 3, 2013 at 10:54 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu >> > wrote: >> >>> >>> The residual FWHM is measured from the data itself. You apply a certain >>> amount of smoothing, but there is already some smoothness to the data, so >>> the final fwhm is a combination of what is already there and what you >>> apply. A fwhm of 47 is huge and may indicate that something is wrong. What >>> is the input? cortical thickness? Are you using your own mask or is this a >>> whole hemisphere analysis? >>> >>> doug >>> >>> >>> >>> >>> >>> >>> On 6/2/13 10:29 PM, Joshua deSouza wrote: >>> >>> Hello Doug, >>> >>> Thank you for your quick replies to my queries. Really appreciate it. >>> >>> I have found the files containing the cortical thickness values. Thank >>> you. I assume that the order in which they follow are based on the fsgd >>> file and the cluster annotation numbers. >>> >>> I was just slightly confused about the residual fwhm. I have already >>> done a smoothing of 15 on the file and have recieved a residual value of >>> 47, which I assume is extremely large. Since I'm finding out values for the >>> entire cortex I cannot do a glmfit-sim as there are no fwhm cache values of >>> 47. Could you please tell me what the residual values mean? What do you >>> recommend I do? Is there anything I can read up on to find out more about >>> this? (Please pardon my questions if they seem a little trivial) >>> >>> Thank you >>> >>> Joshua >>> >>> On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve < >>> greve(a)nmr.mgh.harvard.edu> wrote: >>> >>>> >>>> This file is always created by mri_glmfit-sim. It might be named >>>> something different depending on your parameters (should always end in >>>> y.ocn.dat) >>>> doug >>>> >>>> >>>> On 6/2/13 3:57 AM, Joshua deSouza wrote: >>>> >>>> Hi Doug, >>>> >>>> This file that your saying, will be created after glmfit-sim is done >>>> using the cache function and a threshold of 1.3 and absolute ,with y being >>>> the fsgd file? Am I understanding this correctly? >>>> >>>> Thank you >>>> >>>> Joshua >>>> >>>> On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve < >>>> greve(a)nmr.mgh.harvard.edu> wrote: >>>> >>>>> There should be a file called something like cache.th13.abs.y.ocn.dat. >>>>> This will have a column for each cluster and a row for each subject. >>>>> The >>>>> value in the row will be the input for each subject. >>>>> doug >>>>> >>>>> On 05/30/2013 11:21 PM, Joshua deSouza wrote: >>>>> > Hello everyone, >>>>> > >>>>> > Please pardon my rather simple question >>>>> > >>>>> > I have done a GLM fit anlysis and have obtained a file sig.mgh alonf >>>>> > with a few others after the analysis.As I know, I do not have to >>>>> > create ROIs in order to do this. I also understand that doing a >>>>> > multiple comparison analysis just compares the regions of importance >>>>> > and evaluates them giving the most resilient cluster depending on the >>>>> > threshold. So, this does not give a thickness estimate. I would like >>>>> > to know how do I get the cortical thickness values from the results? >>>>> > If so, can I do it after glmfit? >>>>> > >>>>> > And thanks Doug for your help in the other questions that I had prior >>>>> > to this! >>>>> > >>>>> > Thank you >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > Freesurfer mailing list >>>>> > Freesurfer(a)nmr.mgh.harvard.edu >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> -- >>>>> 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/ >>>>> >>>>> _______________________________________________ >>>>> 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 4

Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
by Douglas N Greve 07 Jun '13

07 Jun '13

Hi Pablo, please respond to the list and not to us directly. Please just cut and paste the text of the error into the email. thanks doug On 06/06/2013 12:30 PM, pablo najt wrote: > Thank you for your quick response. I have re run the installation but > I get the following erros with _tkmedit bert orig.mgz_ and _tksurfer > bert rh pial_ commands. > Please see attach for the detailed errors. > Best, > Pablo > > > > Date: Thu, 6 Jun 2013 12:01:22 -0400 > > From: greve(a)nmr.mgh.harvard.edu > > To: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed} > > > > what command is not found? > > On 06/06/2013 11:58 AM, pablo najt wrote: > > > Hello I have a question regarding the installation/running FreeSurfer. > > > I have just completed the installation and got the confirmation that > > > Free surfer was installed. Please see snapshot. > > > However when I follow the steps for testing (*MailScanner has > detected > > > a possible fraud attempt from "connect.yale.edu" claiming to be* > > > https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer > > > > <https://connect.yale.edu/owa/14.3.123.3/scripts/premium/redir.aspx?C=Alh1Yj…>), > > > > I always get "command not found". I was wondering if you would be > able > > > to help me. > > > Thanks, > > > Pablo > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > 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/ > > > > _______________________________________________ > > 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

3 5

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