Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

tracula failure
by Alena Piovar 21 Nov '14

21 Nov '14

Dear freesurfer experts, I am trying to run tracula but it fails on mri conversion of the data, it creates the nifty files from dicoms, but fails to produce bvec file where the problem could be? The terminal info as well as configuration file used for preprocessing is attached. Looking forward to your answer best regards Alena

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Linear Mixed Effects Models
by franziska baier 21 Nov '14

21 Nov '14

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Re: [Freesurfer] Odd thing about mris_convert? Position changed from freesurfer format to .stl
by ting xu 21 Nov '14

21 Nov '14

Hi Bruce, Thank you for your reply! Would you please give me a hint how does it work, save ras2vox or ras xform into to FS surface file? I searched the archive, googled, did not figure out yet. All the function such as read_susrf.m and write_surf.m only deal with coordinates and faces information. Thank you! Ting On Fri, Nov 21, 2014 05:21 Hi Ting STL may not contain the info for ras2vox transform as it is not a medicalimaging format. We've only supported it in the past for 3D printing and such. You might need to keep track of the ras2vox and restore it when you convert back (e.g. in matlab) cheers Bruce On Fri, Nov 21, 2014 at 12:18 AM, ting xu <xutingxt(a)gmail.com> wrote: > Hi there, > > In my understanding, mris_convert does not change any information > (vertices coordinates and triangles) during converting, right? However, I > observed odd thing as bellow, > > Command I used:* mris_convert subjid/surf/lh.white > subjid/surf/lh.white.stl* > > I convert the white surface to .stl format, then load original white > surface and .stl file in freeview, with subjid/mri/brainmask.mgz as volume > underlay. The shape of lh.white.stl mesh looks the same as original one, > but the position of lh.white.stl was displaced. I attached a screenshot > (yellow one is original white surface, red one is .stl format one). > > I also used freesurfer_read_surf function to read the coordinates and the > faces in matlab, then compare it to .stl coordinate, they are the same. > > I need to use .stl format for my analysis outside freesurfer, then convert > result back to freesurfer format. I am worried whether this would cause any > problems? > > PS, if it is fsaverage template surface, no position shift after format > transform. > > Many thanks if anyone help with this, > > Ting > > >

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qdec and recon-all crashes
by Jon Alan Wieser 21 Nov '14

21 Nov '14

hi freesurfer folks, when I try to run qdec or recon-all, they crash recon-all -s MJ0001 -qcache if: Expression Syntax. qdec cd: Too many arguments. we have determined that because the subjects_directory name has spaces and ()'s in it, it is causing the two programs to crash echo $SUBJECTS_DIR /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001 I know that linux doesn't like spaces and ()'s in the directory name, and I usually avoid them, but we have recently started using dropbox to backup our data, in Dropbox is causing the spaces and ()'s to be in the directory name. Is there any way to make recon-all and qdec run in directories that have these characters in the directory name thanks Jon

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repost: recon-all failure due to header
by Ashley Stillman 21 Nov '14

21 Nov '14

Hi Freesurfer team, Any ideas for the below issue we are having? We are having issues running recon-all on our dicom files, as they are saved as a mosaic. When we open the original dicom file (attached) it lists out the rows, columns and slices. However, when we run mriparsesdcmdir, it just posts 0’s for the rows and columns (screen shot attached). We are able to recreate the output file necessary to run recon-all (basically fill in the missing 0’s). Is there a way to tell recon-all to call on this file to retrieve the missing data manually? Thank you, Ashley Ashley N. Stillman Clinical Psychology Graduate Research Assistant University of Tulsa, T.R.A.P.T. Lab Laureate Institute for Brain Research email: anstillman(a)laureateinstitute.org<mailto:anstillman@laureateinstitute.org> | ashley-stillman(a)utulsa.edu<mailto:ashley-stillman@utulsa.edu>

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Odd thing about mris_convert? Position changed from freesurfer format to .stl
by ting xu 21 Nov '14

21 Nov '14

Hi there, In my understanding, mris_convert does not change any information (vertices coordinates and triangles) during converting, right? However, I observed odd thing as bellow, Command I used:* mris_convert subjid/surf/lh.white subjid/surf/lh.white.stl* I convert the white surface to .stl format, then load original white surface and .stl file in freeview, with subjid/mri/brainmask.mgz as volume underlay. The shape of lh.white.stl mesh looks the same as original one, but the position of lh.white.stl was displaced. I attached a screenshot (yellow one is original white surface, red one is .stl format one). I also used freesurfer_read_surf function to read the coordinates and the faces in matlab, then compare it to .stl coordinate, they are the same. I need to use .stl format for my analysis outside freesurfer, then convert result back to freesurfer format. I am worried whether this would cause any problems? PS, if it is fsaverage template surface, no position shift after format transform. Many thanks if anyone help with this, Ting

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Repost: estimating lesion size on surface
by Timothy Meier 20 Nov '14

20 Nov '14

Hello, I just wanted to repost this to see if anyone had any thoughts on an appropriate 'lesion' size for a pothole analysis performed on the surface. We want to compare the average number of small surface lesions (estimated from cortical thickness) across single subjects for a control group relative to our patient group. We have done similar analyses in the volume for white matter, so one thought was to use that same lesion size. However, that requires estimating a surface area from our previously used volume. Any thoughts on how to approach this, or thoughts on an appropriate lesion size to use would be appreciated. Thanks, -Tim ---------------------------------------------------------------------- > > Message: 3 > Date: Thu, 30 Oct 2014 15:03:53 -0500 > From: Timothy Meier <tmeier(a)mrn.org> > Subject: [Freesurfer] Converting lesion volume to surface area > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAGXOw+14YO4VBWUAA4YfzE7Gerxo-PG33FPCEmpm8PxpTpW= > CA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > Previously we have used a lesion of 128 microliters and have filtered out > anything smaller in volume than that for analyses (single subject "pothole" > analysis). Now we want to do something similar on the surface. So we need > to approximate the surface area of that 128 microliters when translated to > group analysis surface (fsaverage). > > 128 microliters is 128 data points in 1x1x1 resolution. Let's say those > data points only exist in the cortical ribbon volume. > > Question 1: How many of the 128 data points from cortical ribbon volume get > translated into surface space? What is the volume to surface translation > ratio? > > Question 2: Because we want to filter clusters with mri_surfcluster, we are > interested in the resulting area of our original 128 lesion. Therefore, how > much area is represented by each data point when translated onto the > surface? > > Is this simply "AvgVtxArea" of the inflated surface multiplied by the > number of data points that get translated from volume to surface? > > And what is the best way to answer these two questions from standard > Freesurfer output: > e.g. Should we calculate from the ("NumVert" "SurfArea" "GrayVol") columns > of the lh.aparc.stats file, get the mean of all SurfArea/GrayVol from > aparc.stats, and then multiple by our 128? > > Any thoughts or suggestions would be appreciated. > > Thanks, > Tim >

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Odd thing about mris_convert? Position changed from freesurfer format to .stl
by ting xu 20 Nov '14

20 Nov '14

Hi there, In my understanding, mris_convert does not change any information (vertices coordinates and triangles) during converting, right? However, I observed odd thing as bellow, Command I used:* mris_convert subjid/surf/lh.white subjid/surf/lh.white.stl* I convert the white surface to .stl format, then load original white surface and .stl file in freeview, with subjid/mri/brainmask.mgz as volume underlay. The shape of lh.white.stl mesh looks the same as original one, but the position of lh.white.stl has totally been displaced. I attached a screenshot (yellow one is original white surface, red one is .stl format one). I also used freesurfer_read_surf function to read the coordinates and the faces in matlab, then compare it to .stl coordinate, they are the same. I need to use .stl format for my analysis outside freesurfer, then convert result back to freesurfer format. I am worried whether this odd thing cause any problems? [image: Inline image 2] PS, if it is fsaverage template surface, no position shift after format transform. Many thanks if anyone help with this, Ting

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Re: [Freesurfer] FreeSurfer GUI tutorial
by Lilla Zollei 20 Nov '14

20 Nov '14

Hi Piotr, There are several tutorials that describe our standard data processing pipeline. You can start by looking at: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial with "Introduction to Freesurfer" and "Analyzing the Individual Subject". If you have any further questions, please, send them to the freesurfer mailing list. Lilla On Thu, 20 Nov 2014, Piotr Konrad Chlebda wrote: > Hello, > I have downloaded and installed freesurfer(as VM for Windows), but I can not find any simple gui tutorial for it. I need to extract corpus callosum from DICOM pictures. I thought that freesurfer provide me with simple way to do that, but actually did not.Could you send me any easy step by step guide to perform > what I need, please ? > > Best regards, > > Piotr > > >

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mri_convert : no output & infinite loop
by Nooshin Zadeh 20 Nov '14

20 Nov '14

Dear FreeSurfer experts, I get a new message when I use "mri_convert" command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file, and goes to infinite loop. *mri_convert "/M1/t1_se_ax_5/IM-0004-0001.dcm" "/FS/M1/mri/orig/001.mgz"* mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards Nooshin PhD Candidate Departments of Electrical & Computer Engineering University of Miami Email: n.zadeh(a)miami.edu

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