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freesurfer@nmr.mgh.harvard.edu

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30135 discussions

wm.mgz edits amygdala hippocampus cerebral cortex
by marco mcsweeney 09 Jun '16

09 Jun '16

Dear all Freesurfer users, I have a few questions regarding wm.mgz edits. I am very new to this area and have only recently started using Freesurfer so please excuse me if my questions appear naive or misinformed. I have managed to make most of the necessary edits needed to fix skullstrip errors, intensity normalization errors and pial errors, but I am a bit stuck when it comes to fixing topological defects. My question relates to what should or should not be included in the wm.mgz. Apart from the optic chiasm, which I have removed, is it normal to have, what appear to be, multiple specs included in the wm.mgz which when the aseg is loaded turn out to be parts of the amygdala and hippocampus. When I view the smoothwm.nofix these appear as jagged shard like shapes protruding out from the surface. In one publication I saw recently it was suggested that these should be removed but should this be done if they are parts of the amygdala and hippocampus. I am worried about this as these are the 2 main subcortical areas I will be focusing on. Also, is it normal for the wm.mgz to include parts of the cerebral cortex (labelled as such in the aseg). Also, most of the scans I am working with have numerous holes and handles and this is taking a very long time to fix. I have tried to run the automatic topology fixer again. This has helped a bit but the scans still require a lot of edits. Could this be down to the quality of the scans or could it be that I have edited too much - control points for example. I have followed the advice given and have tried not to make too many edits, but having said that it has taken me a very long time. Any advice in relation to any of these questions would be very very very much appreciated. Best wishes fuzzy

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Resampling the parametric map of brain activations onto a surface
by Zhao, Yue 09 Jun '16

09 Jun '16

Hi All, I am using a Ubuntu FreeSurfer v5.3.0 in the VirtualBox. I am trying to overlay a parametric map onto a FreeSurfer surface. Here are the tutorial codes I found: 1. To resample the paramatric map onto the individual's surface: mri_vol2surf --src spm001.img --srcreg register.dat --hemi lh --projfrac 0.5 --out ./spm001-lh.w --out_type paint 2. Visualize and overlay: qsurfer -stat spm001 -hemi lh -subject bert-brf 3. Configure the image by selecting "View -> Configure -> Overlay" and play with the histogram The image looks like this: [https://mail.google.com/mail/u/0/?ui=2&ik=fffa1c9b37&view=fimg&th=1552b8aa0…] I assigned one single value to the voxels in each cortical parcellation. So the white matter and subcortical regions (e.g. caudate, putamen, hippocampus) are 0. The contrast represents the variations of the parameter across the cortex. Everything looks good to me except that I couldn't get rid of that green "noise" appearing at the hippocampus and occipital area. Does anyone have any idea why this is happening and how to get rid of it? Another minor issue is that even though I play with the histogram in "Overlay" to get the best contrast, the colorbar looks less dynamic. Too much red but very little yellow. Any suggestion to improve that? Thanks a lot! Best, Yue

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mri_binarize --rmax option unknown
by Lakhani, Bimal 09 Jun '16

09 Jun '16

Good afternoon, I am trying to run a fairly simple mri_binarize command on FS v 5.3, Linux 64bit, but when I use the option — rmax, I am getting an error that says the —rmax option is not recognized. It is made weirded because —rmin works perfectly. Here is the command line and the following error: boydsrv01:~/Desktop/Arrowsmith/Freesurfer/Output> mri_binarize --i '/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07_MWF2Brain.mgz' --rmax 1.95 --o '/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07__MWF2Brain.bin.mgz’ ERROR: Option --rmax unknown Thanks very much! Bimal

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Command to summarize 35 cortical thickness
by shi yao wang 09 Jun '16

09 Jun '16

Dear FS expert, I am using command "mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh" to calculate cortical thickness in 35 regions. I have 50 subjects. I am wondering how can I summarize these results and export to one document? (I just need cortical thickness results) thanks Lawrence Emory University

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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 >

2 3

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

1 1

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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