Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

130 participants
204 discussions

Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)
by Erik Lindberg 25 Jan '16

25 Jan '16

Dear Bruce and Freesurfers, I probably then go about this in the wrong way. My aim is to create a binary mask for regions that I found differences in - in a group-comparison. I then want to export the mask so I can use it as seed area in an fMRI analysis. Can this be done Thanks Eric Hi Erik what is the dimensionality of sig.cluster.mgh? You can tell this with mri_info. It is problaby a surface overlay (so nvertices in one dimension), and can't be viewed in the volume but only on the surface. cheers Bruce

2 1

hippocampal subfields - multispectral segmentation with FLAIR
by Luigi Antelmi 25 Jan '16

25 Jan '16

Dear members, in our center we are evaluating whether to introduce a T2 into a protocol that, among others, already includes a T1 and a FLAIR sequences. Our main concern is to to maximize the information-to-duration ratio of the entire protocol. In order to improve the subfields' segmentation we read that it is better to add a T2 or "other" sequences. Will the FLAIR alone (+T1) can work well as the T2? If instead the T2 is preferable, what is the coarsest-but-still-informative resolution you suggest? Thank you for sharing your experience! Have a nice day, Luigi.

2 1

Processing .mnc files
by Ankita Chatterjee 24 Jan '16

24 Jan '16

I ran the command recon-all -all -s t2 -i t1xxxxx.mnc as Bruce suggested and the process took off but has been running for more than 6 hours and seems to be not doing anything after the step which reads MRISunfold() max_passes = 1 ----------- it has a few steps after that, but doesn't say that it completed. The last line reads - randomSeed 1234. Is it hung? Should I exit the program? Thank you for your help! Ankita

2 3

mritotal failed - help with manual registration
by will brown 24 Jan '16

24 Jan '16

Hi all, After attempting recon-all I received the error "mritotal failed, see transforms/talairach.log" etc which I understand may have something to do with bad output from registration. I've checked orig.mgz which does look out of line - the orientation is off so that it appears the subject has their head tilted off to one side (see Image1.jpg). I have tried to fix this manually with the help of this tutorial: http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview Hovever, the "movable" blurry image that I'm trying to line up with my subjects image does not match the coronal, sagittal or horizontal views, e.g. when I click "coronal" my subject is displayed correctly but the movable image is displayed horizontally (see Image2.jpg and Image3.jpg). Am I missing something obvious? (and am I even on the right track given this error?) Thanks in advance for any help. Cheers, Will

2 1

freeview on ubuntu
by Neda Mohammadi 24 Jan '16

24 Jan '16

Dear experts, I installed FreeSurfer on Ubuntu with these commands: sudo apt-get install tcsh cd /usr/local/ sudo tar -xzvf ~/freesurfer-*.tar.gz echo "FREESURFER_HOME=/usr/local/freesurfer" >> ~/.bashrc echo 'source $FREESURFER_HOME/SetUpFreeSurfer.sh' >> ~/.bashrc sudo gedit /usr/local/freesurfer/.license sudo ln -s /usr/lib/libtiff.so.{4,3} Every thing is Ok except freeview. When I load freeview this error is appeared. freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Any guidance on this would most appreciated. Thanks in advance, -- *Best Regards,* *Neda*

1 0

Processing .mnc files {Disarmed}
by Arindam Chatterjee 23 Jan '16

23 Jan '16

Hello Freesurfer experts, I am still learning various aspects of Freesurfer, so pardon my questions. I am trying to run recon-all on a mnc file. It is in a folder such as /Sample1/subjects/t1/t1xxxx.mnc. I am pointing my SUBJECTS_DIR to /Sample1/subjects. But when I run recon-all -s t1, I get and error - ERROR: nothing to do. Should I be storing the .mnc file in a different location? So it looks like it is not finding the .mnc file or can Freesurfer not process a .mnc file and I have to convert it to another format like .dcm? Also, if I am able to run recon-all, what output should I analyze to determine the gyrification index? Thanks in advance for any pointers. Ankita -- Arindam Chatterjee (515) 419-7384 www.linkedin.com/in/chatterjeea

2 2

Re: [Freesurfer] QDEC. Error in Analyze: command failed: mri_glmfit
by BAUTISTA-PERPINYA Maximilià 23 Jan '16

23 Jan '16

Thank you for the reply Douglas, Factor 1 (diagnosis) has 3 levels (BPD, CCP, NPC). I created using the vi editor, one line for each level. Same as factor 2. Max On dijous 14 gener 2016 22:20 CET, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > how many levels does factor 1 have? How did you make the factor file?> > On 01/14/2016 05:30 AM, BAUTISTA-PERPINYA Maximilià wrote: > > Hi there experts, > > > > I'm runing qdec to analyze my subject data. I am able to import the qdec.table.dat, but the problem comes in the Design step. I select 'Volume-based' measure, 'Diagnosis' as my discrete independent variable and 'LeftAmygdala' as the continuous variable. I don't select any nuisance factor. I then set my Design Name: 'LAmyDiagnosis' and click Analyze, but gives me the following error: > > > > --------------------------------------------------------------------------------------------------------------- > > > > ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels > > ninputs = 137 > > Checking inputs > > nframestot = 137 > > Allocing output > > Done allocing > > nframes = 137 > > Writing to /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh > > gdfReadHeader: reading /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > > Continuous Variable Means (all subjects) > > 0 LeftAmygdala 1502.65 189.974 > > Class Means of each Continuous Variable > > 1 diagnosisBPD 1497.7548 > > 2 diagnosisCCP 1540.8923 > > 3 diagnosisNPC 1488.5490 > > INFO: gd2mtx_method is dods > > Reading source surface /home/freesurfer/Desktop/test005/subjects/fsaverage/surf/lh.white > > ERROR: no contrasts specified. > > Error in Analyze: command failed: mri_glmfit --y /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/y.mgh --fsgd /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis/qdec.fsgd dods --glmdir /home/freesurfer/Desktop/test005/subjects/qdec/LAmyDiagnosis --surf fsaverage lh > > > > --------------------------------------------------------------------------------------------------------------- > > > > Any recommendations? Any help is much appreciated :) > > > > > > Best, > > > > Max > > > > _______________________________________________> > 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. -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg (+49) 015759302368 maximila.bautista-perpinya(a)etu.unistra.fr maxbauper(a)gmail.com -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg (+49) 015759302368 maximila.bautista-perpinya(a)etu.unistra.fr maxbauper(a)gmail.com

3 2

recon-all finishing without error but happens too quickly and output not present
by AMY LIN 22 Jan '16

22 Jan '16

Hi all, I'm trying to re-run subjects through recon-all for version 5.3.0 on a Mac 10.10.5 using Centos 6 but am not getting the normal output. There seems to be several strange things happening. The process ends almost instantaneously and says that it finished without error, so I don't get any errors or warnings. The correct subject directory folders are created (mri, bem, scripts, etc), but most of them are empty. The only folder that has anything in them are the scripts folder and the mri folder, which has the orig and transforms folders and are pretty much empty. It seems that the program is only running the mri_convert command on the 001.mgz file, writing the output to the folder that I've specified and then finishes without error. I've tried to run the commands on both local and remote servers to rule out an issue with the server and from different user accounts to rule out permission issues as I am a new lab member. I've also tried several different subjects to rule out problems with the scans. Also, these subjects have been run previously on an older version of FS, so the problem is likely not with the scans themselves. Any help at all would be much appreciated!

3 2

HippocampalSubfields only generates lh
by Jiook Cha 22 Jan '16

22 Jan '16

Hi Iglesias, I recently tried HippocampalSubfields in freesurfer 6.0. It only completed hippocampal segmentation for the left hemisphere, but not the right. Under scripts folder, recon-all.error says: /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/recon-all PWD /ifs/scratch/pimri/posnerlab/1anal/osa/fs2/B03/label CMD /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/segmentSF_T1.sh /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/MCRv80 /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer B03 /ifs/scratch/pimri/posnerlab/1anal/osa/fs2 left So it seems as left hippocampus failed the pipeline didn’t try the right hippocampus. Attached is hippocampal-subfields-T1.log. Do you have any idea what’s happening here? Best, Jiook

2 4

Centroid of a binary volume question
by pfotiad＠nmr.mgh.harvard.edu 22 Jan '16

22 Jan '16

Dear FS Community, I was wondering whether there is a way to create a binary volumetric file of just the centroid of a binary volume (represented maybe as a dot of 1x1x1 mm^3 voxel size). I know how to find the coordinates of the centroid (through either the fslstats command or MATLAB), but I didn't know whether there was a way to create a new binary volume of just the centroid through the terminal. (I would do it manually, but I have ~500 binary volumes that I would like to apply the same method to). Thank you in advance for your help! Best, Panos

1 0

← Newer
1
...
6
7
8
9
10
11
12
...
21
Older →

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 January 2016