Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Re: [Freesurfer] Fw: Aw: Re: Problem with uploading Cluster Simulation data
by Douglas N Greve 14 Jul '14

14 Jul '14

what is your command line? Or otherwise, how are you visualizing it? On 07/14/2014 08:09 AM, carina(a)van-vlodrop.de wrote: > *Gesendet:* Sonntag, 06. Juli 2014 um 22:48 Uhr > *Von:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de> > *An:* "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> > *Betreff:* Aw: Re: [Freesurfer] Fw: Problem with uploading Cluster > Simulation data > Hi Doug, > I have already uploaded a text file of my corrected results from the > Monte Carlo Cluster Simulation which reports 15 Clusters (attached > picture). > There is another file ending with .mgh and the tutorial identifies it > to be the overlay (clusterwise corrected map) which I can upload in > freeview. > In freeview there are the alternatives of uploading a surface or a > volume. If I upload the file ending with .mgh as a volume I just > recieve a black image with a few numbers on the coordinate plane > (attached picture). There is no brain visible. > Is it correct to upload the overlay (file ending with .mgh) as a > volume or how should I proceed? Do I have to upload a template first > and which is the right template? > Thank you so much. > Yours sincerely, > Carina > *Gesendet:* Montag, 16. Juni 2014 um 12:45 Uhr > *Von:* "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> > *An:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de>, "free surfer" > <freesurfer(a)nmr.mgh.harvard.edu> > *Betreff:* Re: [Freesurfer] Fw: Problem with uploading Cluster > Simulation data > > You should be able to view the map results in freeview just as you > would any other map. > doug > > > > > > On 6/12/14 12:19 PM, carina(a)van-vlodrop.de wrote: > > *Gesendet:* Dienstag, 10. Juni 2014 um 11:18 Uhr > *Von:* "carina(a)van-vlodrop.de" <carina(a)van-vlodrop.de> > *An:* freesurfer(a)nmr.mgh.harvard.edu > *Betreff:* Problem with uploading Cluster Simulation data > Dear freesurfer experts, > we are conducting cortical-thickness analysis using > freesurfer-4.4.0 and the final analysis with qdec. I have a > question concerning the Clusterwise Correction for Multiple > Comparison. > Is it correct that I have to visualize the results of the Monte > Carlo Simulation in freeview? > Do I have to upload a special model in freeview before uploading > the Cluster Simulation data? > Yours sincerely, > Carina > > > _______________________________________________ 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/

1 0

Question about LGI
by pfotiad＠nmr.mgh.harvard.edu 14 Jul '14

14 Jul '14

Hi FS Community, I was wondering whether LGI and Surface Area need to be corrected for total Intracranial Volume. Thanks in advance, Panos

5 10

trac-all -prep error field map error
by Eileen Moore 14 Jul '14

14 Jul '14

Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring to run tracula on some images acquired from a GE scanner. I am running into problems when I try to perform the registration-based B0-inhomogeneity compensation, getting an error in the terminal output: "ERROR: Unrecognized format of phase map". However, trac-all -prep runs fine when I skip the B0-inhomogeneity compensation step. Is there something else I need to do to use field map correction? I've attached the trac-all.log and a copy of the terminal output. Thanks, Eileen.

2 1

LME Longitudinal QDEC Table
by Elijah Mak 14 Jul '14

14 Jul '14

Hello Freesurfer Experts, I am performing a mass-univariate analyses using the LME toolbox for longitudinal studies. After running both mris_preproc and mri_surf2surf , I load the lh.thickness_sm10.mgh file using *[Y,mri] = fs_read_Y('lh.thickness_sm10.mgh');* Next, I run the following command: *Qdec = fReadQdec('qdec.table.dat');* However, it seems that the output is entirely in string format "166 x 1 cell". The first row reads as "'fsid fsid-base years group gender age'" in a single column. Because of this, I am running into problems when I try to execute the following steps: *Qdec = rmQdecCol(Qdec,1);* (removes first column) *sID = Qdec(2:end,1); (grabs the subjects' IDs)* *Qdec = rmQdecCol(Qdec,1);* (removes the subjects'ID column) *M = Qdec2num(Qdec);* (converts to a numeric matrix) *[M,Y,ni] = sortData(M,1,Y,sID);* (sorts the data) Your help will be greatly appreciated! Many thanks. Best Regards, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

2 5

Re: [Freesurfer] Patch that adds parapool support to lme_mass_F, lme_mass_fit_EMinit, lme_mass_fit, lme_mass_fit_init. lme_mass_fit_Rgw
by jorge luis 14 Jul '14

14 Jul '14

Hi Knut Thank you very much for your contribution. I'll take a look at it and apply the patches as soon as I have time (probably next weekend) on github: https://github.com/NeuroStats Best -Jorge >________________________________ > De: Knut J Bjuland <knut.j.bjuland(a)ntnu.no> >Para: jorge luis <jbernal0019(a)yahoo.es> >Enviado: Jueves 26 de junio de 2014 5:16 >Asunto: Patch that adds parapool support to lme_mass_F,lme_mass_fit_EMinit, lme_mass_fit,lme_mass_fit_init. lme_mass_fit_Rgw > > >Dear Dr Rusiel > >Matlabpool is deprecated in Matlab 2014a. I have therefore written a >patch, which adds parapool support when Matlab 2013B and above is used >vertex wise linear mixed model is used. >Please review the patch? Is the patch sound? Please apply the patch. > >Your sincerly > >Knut J Bjuland > > > >

1 0

Hippocampal Subsectioning
by Joshua S 13 Jul '14

13 Jul '14

Hi, I was doing a hippocampal subsectioning <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation> on a data set. Previously recon-all -all was used, and then I did recon-all -hippo-subfields. I then used the script kvlQuantifyHippocampalSubfieldSegmentations.sh to find the volume of the hippocampus and its sub parts. I was confused as to the data I was getting out. The hippocampus seems to large. The voxel size is 0.5 mm * 0.5 mm * 0.5 mm so the hippocampal areas seem to large. Also the subunits of the hippocampus are larger than the actual hippocampus which again does not make sense. I attached one of the output files Thank you for any replies, From Joshua Segaran

3 2

Understanding Hippocampal volume stats
by Zia, Mohammad 13 Jul '14

13 Jul '14

Hi, Freesurfer reported the following hippocampal volumes for a subject volumeInVoxels: right_CA1: 2652.3 right_CA2_3: 7245.11 right_CA4_DG: 3967.28 right_fimbria: 423.555 right_hippocampal_fissure: 191.897 right_presubiculum: 3598.99 right_subiculum: 4868.1 Right-Hippocampus: 3258.77 I have two questions about it 1. I don’t understand why the right_subiculum volume is more than the Right-Hippocampus volume. 2. Since the voxel size for the volumes is 0.5^mm, do we have to divide these volumes by 8 to convert them to voxel size 1^mm so that we can do direct comparison with other freesurfer stats volume (for example the volumes in rh.aparc.stats)? Thanks --Mohammad Zia This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original.

2 1

Re: [Freesurfer] Correlation coeffecient
by Lars M. Rimol 13 Jul '14

13 Jul '14

Hi Doug, A naive question in regard to the issue brought up by Chris (see below): Could one simply use this formula (with the F from the GLM for a given contrast): r² = F/(F+df) ? LMR try this oneftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_p… On 07/11/2014 01:51 PM, Chris Wertz wrote: > Hi Freesurfer experts > > I am trying to obtain correlation coefficients for significant > clusters and found a previous post about this, > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/023616.html > > > but the MATLAB function link within this post is dead? > > any help is greatly appreciated > > thanks, > Chris -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

2 1

Re: [Freesurfer] create label from binary .mgh file {Disarmed}
by Lars M. Rimol 12 Jul '14

12 Jul '14

Hi Doug, That works! Thanks! I don't know why it didn't the first time (I can't find the old command line). But this command line works (in case anybody else wants to do the same thing): [LMR in ~ ] mri_cor2label --i /home/lmr/ANALYSIS/binary_pmaps/lh_binarymap_area_covar8.mgh --id 1 --l /home/lmr/ANALYSIS/binary_pmaps/lh_binarymap_area_covar8 --surf fsaverage lh LMR Douglas N Greve <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Fri, 11 Jul 2014 11:02:38 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> use mri_cor2label with the --surf option On 07/11/2014 01:36 PM, Bruce Fischl wrote: > Hi Lars > > this would be pretty simple to do in matlab, but I'm not sure if we > have anything do to it otherwise (Doug might) > > cheers > Bruce > On Fri, 11 Jul 2014, Lars M. Rimol wrote: > >> Hi, >> >> Is there a way to take a binary .mgh file (surface file with 163842 >> vertices containing 1 or >> 0) and create a label such that the ones in the input file == the >> label? For instance, to >> create a label from a p-map. >> >> I tried using mri_cor2label based on previous responses on the >> mailing list, but that seems >> to produce volumes and I'm not really sure what it does anyway... >> >> >> Thank you! >> >> >> >> -- >> yours, >> Lars M. Rimol, PhD >> St. Olavs Hospital >> Trondheim, >> Norway >> >> > > > _______________________________________________ > 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 Centergr...(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/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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. - Previous message <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36914.html> - View by thread <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/index.html#36917> - View by date <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/maillist.html#36…> - Next message <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36915.html> - [Freesurfer] create label from binary .mgh file <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36913.html> Lars M. Rimol - - Re: [Freesurfer] create label from binary .mgh file <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36914.html> Bruce Fischl - - Re: [Freesurfer] create label from binary .mgh fi... Douglas N Greve Reply via email to [image: The Mail Archive] <http://www.mail-archive.com/> - The Mail Archive home <http://www.mail-archive.com/> - freesurfer - all messages <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/> - freesurfer - about the list <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/info.html> - Previous message <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36914.html> - Next message <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36915.html> -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

1 0

Segmentation fault with mri_ca_train
by Mark Plantz 11 Jul '14

11 Jul '14

Hello freesurfers, I am running into some sort of memory allocation issue when running mri_ca_train. I am simply using an intensity volume and a segmentation volume to create a GCA atlas. I keep getting this "segmentation fault: 11", which is data allocation error. I have tried using all different environments and can't avoid it. The output is below: sh-3.2# mri_ca_train -T1 withSkull.mgz -seg seg_edited.mgz atlas_test /hearingbrain/Desktop/atlas_withSkull.gca reading T1 data from subject's mri/withSkull.mgz directory reading segmentation from subject's mri/seg_edited.mgz directory training on 1 subject and writing results to /Volumes/Macintosh HD/Users/hearingbrain/Desktop/atlas_withSkull.gca *************************************************************************** processing subject atlas_test, 1 of 1... reading input 0: /Applications/freesurfer/subjects/atlas_test/mri/withSkull.mgz gca width modified from 256 to 181 gca height modified from 256 to 217 gca depth modified from 256 to 181 Segmentation fault: 11 Any ideas? -MP

2 2

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