Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

Regarding: Surface projection of WMHs volume
by Dr Sampada Sinha 09 Jun '16

09 Jun '16

Dear freesurfer expert, I don't know if this question make any sense but is there a way to project white matter hypointensities volume onto the surface? Thanks and kind regards, Sampada -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India

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Segmentation Fault with mri_convert
by Christopher Finuf 09 Jun '16

09 Jun '16

I'm trying to convert the dicom to the original 001.mgz file using the following command on a Mac OSX Yosemite version 10.10.5. My SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/ . My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/ . The following is the output and error that I get. I'm running the latest version v 5.3.0 of freesurfer. Any suggestions on what the problem is? What is strange that it works with half my data set but the other has this error. I've run this command in the exact way many times before and have never had this issue. bash-3.2$ recon-all -i /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm -subjid Bigler_Repeatability_0005Ad_M1 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin NS112201PSY2.byu.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1 \n mri_convert /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz \n mri_convert /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm... Getting Series No INFO: Found 178 files in /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1 INFO: Scanning for Series Number 2 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. INFO: (224 256 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Bigler_Repeatability_AD_M Date and time StudyDate 20160512 StudyTime 075942.531000 SeriesTime 081401.859000 AcqTime 080647.620000 Acquisition parameters PulseSeq *tfl3d1_ns Protocol t1_mpr_sag_iso_ave2_ipat2_(mprage) PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.26 InversionTime 900 RepetitionTime 1900 PhEncFOV 218.75 ReadoutFOV 250 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 224 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 75.8389 136.8499 125.0000 VolRes 0.9766 0.9766 1.0000 VolDim 224 256 176 Vc 0.0767 -0.9971 0.0000 Vr -0.0000 0.0000 -1.0000 Vs -0.9971 -0.0767 0.0000 VolCenter -3.5106 21.0460 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault Darwin NS112201PSY2.byu.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed Jun 8 13:39:08 MDT 2016 For more details, see the log file /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] Longitudinal Studies Question
by Carolyn Drobak 09 Jun '16

09 Jun '16

Hello, I have six scans for a single subject. I have performed "group analysis," but wish to use longitudinal data analysis. In particular, I was able to get a base for the subjects, so can view in freeview and all of that. My issue arises when I try to use QDEC. Because QDEC can't use my long.qdec.table.dat file, nor does it like my cross.qdec.table.dat file. The problem seems to be that I only have one base, i.e. one subject. Is there some way to run analysis on this so I can still get all the statistics I want (mostly interested in cortical thickness) using just my one subject? I'm still fairly new to FS, but have done the large majority of the tutorials, so am pretty sure I'm not just messing up my files here. Thanks, CMD On Mon, Jun 6, 2016 at 9:40 AM, Carolyn Drobak <carolyn.drobak28(a)gmail.com> wrote: > Hello, > > I have six scans for a single subject. I have performed "group analysis," > but wish to use longitudinal data analysis. In particular, I was able to > get a base for the subjects, so can view in freeview and all of that. My > issue arises when I try to use QDEC. Because QDEC can't use my > long.qdec.table.dat file, nor does it like my cross.qdec.table.dat file. > The problem seems to be that I only have one base, i.e. one subject. Is > there some way to run analysis on this so I can still get all the > statistics I want (mostly interested in cortical thickness) using just my > one subject? > > I'm still fairly new to FS, but have done the large majority of the > tutorials, so am pretty sure I'm not just messing up my files here. > > Thanks, > CD >

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tutorial data
by Arkadiy Maksimovskiy 09 Jun '16

09 Jun '16

Hello, I am trying to download the light tutorial dataset from this page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data The file link is titled: tutorial_data.tar.gz <ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz> I have tried clicking on the link as well as using terminal and neither method is working. Might these data be available elsewhere? Thank you for your help, Arkadiy

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Brainmask edit error
by Sabrina Yu 09 Jun '16

09 Jun '16

Hello, I'm having problems with regenerating the surfaces for stroke cases after editing the brainmask.mgz file. In the aseg.mgz file, the brain matter around lesion area is correctly classified as brain matter. In the pial surface, this brain matter is not included. I've tried to edit the brainmask.mgz file to include this region, but when I run: recon-all -subjid <SUBJECT> -autorecon2-pial, the surfaces generated are not changed at all. I have attached some images to this email. I'm new to Freesurfer, so any help would be greatly appreciated. Thank you.

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Older Freesurfer Version with Freesurfer v. 6 HSF & Brainstem Modules
by Douglas Merkitch 08 Jun '16

08 Jun '16

Hello Freesurfer experts, I have two questions regarding the use of old (version 5.1) processed Freesurfer data with the new hippocampal subfields (HSF) and brainstem modules in Freesurfer version 6: 1) Is it possible to use data processed in Freesurfer v. 5.1 and run it directly though the new v. 6 HSF and brainstem modules? 2) Our data was acquired using a 1.5 T scanner (~1mm isotropic). Would this be an issue for either the new v. 6 HSF or brainstem modules? Any answers and/or comments as to your thought process behind your response would be appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

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FS volume estimates
by Otília 08 Jun '16

08 Jun '16

Greetings, I have two questions regarding FS volume measurements. I intend to use the volume information of .stats files but I got some doubts regarding the methods used. 1) I read that eTIV estimation is based on the TAL transformation, but what about the volumes of cortical and subcortical areas? Is it a simple voxel count? 2) In some studies the authors normalize the volumes to eTIV. In others the authors don't do any normalization. Some of them use it as co-variate. What's your opinion regarding this matter? Thank you in advance! Best regards,

2 1

latest freeview
by Jason Tourville 08 Jun '16

08 Jun '16

Hi there, Looking over the freeview development page, it looks like there are some (relatively) new features that would come in handy. Could I get a link to download the latest freeview beta? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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cespct in FS 5.3
by S.V.Shepherd [work] 08 Jun '16

08 Jun '16

Hi all, I ran an analysis on data after dividing each voxel mean across the run, and then multiplying by 100. (My intuition was that the percent signal change should be more consistent across varying SNR that the non-normalized betas). I had naively expected ces.nii and cespct.nii to be equivalent in this case, but in fact, cespct.nii is steeply larger and only imperfectly correlated with ces.nii. What am I missing? stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699

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aseg.stats and aparc.stats reliability
by Greenberg, Jonathan 08 Jun '16

08 Jun '16

Hello Are the volume and thickness measures in FreeSurfer's aseg.stats and aparc.stats accurate and reliable enough to assess changes in volume and thickness longitudinally? I have heard there have been some accuracy/reliability issues in these files in older versions of FreeSurfer. Is the data in these files strong enough to base a publication on? Thanks! Jonathan

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