Freesurfer September 2012

freesurfer@nmr.mgh.harvard.edu

89 participants
154 discussions

qdec.table.dat file
by Fidel Vila 10 Sep '12

10 Sep '12

Hi Freesurfer experts, A newbie question regarding working with QDEC. When I try to upload the qdec.table.dat file (attached) an error messages pops up "Error loading the data table". To the best of my knowledge I've followed the guidelines on the tutorial in terms of formatting. What would be your suggestions to troubleshoot this? Thanks! Fidel

6 17

mri_vol2surf problem
by Garikoitz Lerma Usabiaga 10 Sep '12

10 Sep '12

Dear freesurfers, I am trying to create .mgh labels in order to obtain CT averages from several subjects. I register the ROI-s with bbregister and I get the .nii which renders nicely in tksurfer: tksurfer Surfrend_Colin127 lh inflated -overlay /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii -overlay-reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat -fthresh 1 The problem arises when I try to use mri_vol2surf. I've been trying with many different options, for example: mri_vol2surf --mov /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii --reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat --projfrac 0.5 --projfrac-max 0 1 .01 --hemi lh --out /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh or mri_vol2surf --mov /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii --reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat --projdist-max 0 1 0.1 --projfrac 1 --interp nearest --hemi lh --out /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh When I try to visualize it with tksurfer, it gives me nothing: tksurfer Surfrend_Colin27 lh inflated -label /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh -fthresh 1 How should I use mri_vol2surf in order to obtain results? What are the alternatives in order to have surface labels? Creating a label tracing the border of the .nii label in tksurfer is a posible solution? Thank you very much for your attention, Gari [iMacGari:~] garikoitz% mri_vol2surf --mov /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii --reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat --projfrac 0.5 --projfrac-max 0 1 .01 --hemi lh --out /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh srcvol = /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii srcreg = /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume Reading surface /Applications/freesurfer/subjects/Surfrend_Colin127/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/Surfrend_Colin127/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.01 0 1 using old 3 0.02 0 1 [...] 99 0.979999 0 1 using old 100 0.989999 0 1 using old 101 0.999999 0 1 using old Done mapping volume to surface Number of source voxels hit = 32875 Writing to /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh Dim: 165607 1 1

2 3

Running @SUMA_Make_Spec_FS after FreeSurfer.
by Hye Young Heo 10 Sep '12

10 Sep '12

Hello, I successfully finished making the cortical surface using the " recon-all " command. For functional analysis, I tried to used the AFNI and SUMA. To create the spec files and AFNI files, I used the @SUMA_Make_Spec_FS. but I got the error. Warning: Found COR files and mri/orig.mgz ******** Will use COR files. echo: No match. grep: COR-.info: No such file or directory grep: COR-.info: No such file or directory grep: COR-.info: No such file or directory set: No match. I think the SUMA script tried to used the COR files to create AFNI file or convert COR file if there is a *.mgz file. After Freesurfer, I found the mgz file, but no COR files in the freesurfer directory. Thanks.

2 1

Re: [Freesurfer] scanner to RAS reslicing artifact?
by Andrew R. Dykstra 10 Sep '12

10 Sep '12

Thanks Doug. Is the same true of Freeview? And is it just coincidence that I haven't seen this with the 12-channel coil? Andy On Sep 10, 2012 5:16 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > > This is just a display issue in tkmedit. tkmedit does not display an > image slice. Instead, it reslices the image so that the slices are > aligned with the scanner coordinates. This can lead to the lines you > see. They are nothing to worry about. > doug > > > > On 09/10/2012 10:54 AM, Andrew R. Dykstra wrote: > > Hi all, > > > > I've sometimes noticed a strange reslicing artifact with MPRAGE data > > collected from a Tim Trio using the 32-channel coil. The volume looks > > normal in Freeview before applying the RAS resampling, and I've never > > noticed it with data collected using the 12-channel coil. Has anyone > > else seen this? > > > > Thanks, > > Andy > > > > -- > > Andrew R. Dykstra, PhD > > Auditory Cognition Lab > > Neurologie und Poliklinik > > Universitätsklinikum Heidelberg > > Im Neuenheimer Feld 400 > > 69120 Heidelberg > > > > "How small the cosmos. How paltry and puny compared to human > > consciousness . . . to a single individual recollection." - Vladimir > > Nabokov > > > > > > > > _______________________________________________ > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > 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

mri_vol2surf
by Tuomas Tolvanen 10 Sep '12

10 Sep '12

We need the description of sampling from 3D data on the surface (mri_vol2surf). We are specifically interested how the position is determined in 3D, when the fraction/distance from wm surface is announced. Is it e.g. the normal from one node (resulting in some overlap of 3D projections at the bottom of sulci), or is the neigbourhood somehow interpolated to get a better approximation of the normal direction. Is the projection always a point projection (nearest neighbour or symmetrical interpolation)? Is mri_vol2surf using the voxels only once or is it possible that voxels are used multiple times? If the method has been described in any publication, that would be helpful. -Tuomas

2 1

scanner to RAS reslicing artifact?
by Andrew R. Dykstra 10 Sep '12

10 Sep '12

Hi all, I've sometimes noticed a strange reslicing artifact with MPRAGE data collected from a Tim Trio using the 32-channel coil. The volume looks normal in Freeview before applying the RAS resampling, and I've never noticed it with data collected using the 12-channel coil. Has anyone else seen this? Thanks, Andy -- Andrew R. Dykstra, PhD Auditory Cognition Lab Neurologie und Poliklinik Universitätsklinikum Heidelberg Im Neuenheimer Feld 400 69120 Heidelberg "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov

2 1

ico4 parcellation and mri_segstats
by Linda Douw 10 Sep '12

10 Sep '12

Hi Doug, Output and sumfile are attached. Any ideas? Linda > Message: 10 > Date: Mon, 13 Aug 2012 15:55:13 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10 > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <50295BA1.8090307(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Linda, can you send the terminal output for mri_segstats? Can you also send the summary file? > doug > > On 08/13/2012 10:59 AM, Linda Douw wrote: >> Hi Doug, >> >> I first parcellate fsaverage5 using ico4 (all my functional data are morphed to fsaverage5 surface): >> >> mris_make_face_parcellation /fsaverage5/rh.inflated >> $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot >> >> Then I extract the waveforms using mri_segstats >> >> mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot fsaverage5c rh ico4 --sum ico4_rh.sum >> >> Hope this clarifies the problem! >> Linda >> >>> ------------------------------ >>> >>> Message: 25 >>> Date: Fri, 10 Aug 2012 11:18:38 -0400 >>> From: Douglas N Greve<greve(a)nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats >>> To: freesurfer(a)nmr.mgh.harvard.edu >>> Message-ID:<5025264E.3030801(a)nmr.mgh.harvard.edu> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> what are your command lines? >>> doug >>> >>> On 08/09/2012 01:21 PM, Linda Douw wrote: >>>> Dear Freesurfers, >>>> >>>> I'm trying to extract the average waveforms from all 2562 ROIs in an annotation constructed using mris_make_face_parcellation with ico4. However, I get only 2460 waveforms after doing mri_segstats, and the summary files show that several ROIs are 'skipped' for some reason. Am I >>>> missing something? >>>> >>>> Thanks, >>>> -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129

1 0

Re: [Freesurfer] FDR Correction of NHP Surface Data
by Clark Fisher 10 Sep '12

10 Sep '12

Per Bruce's suggestion, I'm reposting this now. A synopsis: I'm looking for a way to correct painted statistical maps for multiple comparisons using Freesurfer's tools, without having segmentation or any .xfm files. Thanks, Clark On Aug 23, 2012, at 10:09 AM, Clark Fisher wrote: > Hi Freesurfers, > > I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: > 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and > 2) Without segmentation, I don't have a good mask to use for the cortex only. > > My first attempts at work-arounds would be: > 1)Try to create an identity .xfm file > 2)Use the cortical ribbons from mris_volmask as a cortex mask > > Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? > > Thanks, > Clark

1 0

Differences between BrainSuite and FreeSurfer
by Patterson, James 09 Sep '12

09 Sep '12

Hello, I'm trying to figure out why I am getting differences in apparent cortical thickness between BrainSuite11a and Freesurfer. I have a patient scan - high res SPGR BRAVO off a GE 1.5T scanner. In BrainSuite, their are marked decreases in cortical thickness that is consistent with the patients TBI. In FreeSurfer, the changes are quite bit more subtle, and when I compare this one image to a group of normal images (the feature that is very attractive about freesurfer), I do not get anything close to what I would expect. Is there a way to post images? Or perhaps links to images on another site? I am not sure where to begin to search for answers as to why I am getting these differences. I would be happy to answer more questions - I likely have not provided enough information. James Patterson

2 4

RB*2008-03-26.gca vs. RB*2011-10-25.gca files
by Irwin, William 09 Sep '12

09 Sep '12

Hello- The 'RB_all_2008-03-26.gca' and 'RB_all_withskull_2008-03-26.gca' files are packaged with the 5.1 release. Is there any reason the 2011 versions ('RB_all_2011-10-25.gca' & 'RB_all_withskull_2011-10-25.gca ')are not included in the 5.1 release or users should not update to these newer versions? Thanks, Wil

3 3

← Newer
1
...
9
10
11
12
13
14
15
16
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 September 2012