Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

qdec with custom paths?
by Mishkin Derakhshan 09 Nov '10

09 Nov '10

Hi, My data is not in the usual SUBJECTS_DIR/fsid structure. 1. Is it possible to run qdec so that it loads each subject from a full path instead of expecting them all to be under the same SUBJECTS_DIR? ie. with something like this: qdec.table.dat path_to_fsid gender age /full/path/fsid1 Male 23 /full/otherpath/fsid2 Female 27 2. If not, do you think creating a new common subjects dir and then using symbolic links will work? 3. If not, would I have to copy the entirety of the <fsid> directory, or do I only need a select few subdirs like the surf/ and stats/ ? thanks, mishkin

2 1

posible error in BrainSegVol (aseg.stats) ?...
by Gonzalo Rojas Costa 09 Nov '10

09 Nov '10

Hi: There could be an error in the computation of BrainSegVol (aseg.stats) ?... How can I check it ?... Sincerely, Gonzalo Rojas Costa

1 0

A question about VirtualBox version of FreeSurfer Ver 5.0
by Guang Zeng 09 Nov '10

09 Nov '10

Hi, there, I tried to use the VirtualBox version of FreeSurfer Ver 5.0 (I downloaded freesurfer-Virtualbox-linux-x86-stable-pub-v5.0.0-full.vdi) My system is Windows 7 64-bits, the VirtualBox I am using is Version 3.2.10 r66523, I tried to select Ubuntu and Ubuntu 64-bits as the guest OS, but after I added freesurfer-Virtualbox-linux-x86-stable-pub-v5.0.0-full.vdi, and ran it, a black window poped up, and says: "GRUB Loading stage1.5.. GRUB loading, please wait...." Then it stayed there for almost an hour, and nothing happen, Anyone can help me fix this problem? Thanks alot! Guang

2 1

Re: [Freesurfer] Select surface vertices
by Bruce Fischl 09 Nov '10

09 Nov '10

Hi Alexander this is probably best done by running tksurfer and tkmedit simultaneously. You can save point in tkmedit and goto point in tksurfer to find the vertex. Or you can do it in freeview, which will display the vertex directly (or you can use tkmedit->tools->find nearest vertex) cheers Bruce On Tue, 9 Nov 2010, Alexander Hunold wrote: > Hello all, > > > > I segmented a brain with FreeSurfer and I am very satisfied about the > result. > After that I visualized the T1.mgz together with the white surface in > TkMedit. > Now I am looking for interesting anatomical structures. My goal is to assign > vertices in the white surface at the corresponding points and save the > coordinates or better the index of the vertices. > Later I will use the selected vertices in Matlab. I already read the surface > with <freesurfer_read_surf.m>. > > Do you have a good procedure to do that? > I appreciate any hint. > > Thank you so much in advance. > > > > Sincerely, > > Alexander > > > >

1 0

Select surface vertices
by Alexander Hunold 09 Nov '10

09 Nov '10

Hello all, I segmented a brain with FreeSurfer and I am very satisfied about the result. After that I visualized the T1.mgz together with the white surface in TkMedit. Now I am looking for interesting anatomical structures. My goal is to assign vertices in the white surface at the corresponding points and save the coordinates or better the index of the vertices. Later I will use the selected vertices in Matlab. I already read the surface with <freesurfer_read_surf.m>. Do you have a good procedure to do that? I appreciate any hint. Thank you so much in advance. Sincerely, Alexander

1 0

selxavg3-sess in OSX
by Jason Webster 09 Nov '10

09 Nov '10

I'm trying to run a retinotopic analysis with the following commands: mkanalysis-sess -analysis retino-lh -TR 2 -retinotopy 40 -paradigm rtopy.para -funcstem fmcpr.sm5.self -surface self lh -mcextreg -runlistfile retRuns -fwhm 0 selxavg3-sess -analysis retino-lh -s somesubject -df sessdir and am getting the error: >> >> >> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.88.2.2 2010/07/16 15:31:24 greve Exp $ outtop = /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data Extension format = nii ERROR: cannot determine format of /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data/nsLGHa/bold/001/fmcpr.sm5.self ERROR: attempting to read /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data/nsLGHa/bold/001/fmcpr.sm5.self ------------------------------------------ ERROR: fast_selxavg3() failed\n It looks like this might have something to do with analysis.info ... funcstem fmcpr.sm5.self ... RawSpace surface self lh ... Should the funcstem have gotten '.lh' or should this be worked out by getana or selxavg3-sess? Thanks, ~Jason

2 2

Question about reorienting images
by Timour Al-Khindi 09 Nov '10

09 Nov '10

Hello, We are looking for a way to reorient the orig.mgz files and the segmentation (aseg.mgz) into a different plane, and we have a couple of questions. We've used tkregister2 to reorient the orig image: tkregister2 –mov orig.mgz –tar orig.mgz –regheader –reg myregister.dat myregister.dat is created by this command line. We rotate the brain in the tkregister2 gui, then save the registration. Finally, we use the mri_vol2vol command line to rotate the orig and the aseg images. For aseg.mgz: mri_vol2vol --mov aseg.mgz --targ orig.mgz --reg myregister.dat --interp nearest --o rotaseg.mgz For orig.mgz: mri_vol2vol --mov orig.mgz --targ aseg.mgz --reg myregister.dat --o rotorig.mgz This seems to look decent when we load it up in tkmedit, but we have two questions about the use of mri_vol2vol 1) Why does the algorithm need a target (won't run without it), since the transformation info is saved in myregister.dat? Also, how does it manage to work (which it does), given than neither of the targets entered are in the reoriented space? Should we use a different target? What is the role of the target? 2) A previous post specifies that "interp nearest" should be used to rotate the aseg.mgz file. What is the function played by that command? Should we also use it when rotating the orig.mgz file? It works without it, but do we risk distorting the image? Thanks in advance! Tim Al-Khindi

3 2

longitudinal base error
by Guang Zeng 09 Nov '10

09 Nov '10

Hi, there, %% After running this command with FS v4.5 : recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force %% I get the following error: mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity.nofile 005_S_0221BASE_to_005_S_0221_45_20070321.105506_1.lta invert the first LTA before applying it MatrixInverse: NULL input matrix! Read individual LTAs %%%%%%%%%% Any one can help me? Thanks a lot!uang

2 6

Talairach registration
by Leatherday, Chris 08 Nov '10

08 Nov '10

Hello, I am a new freesurfer user and am interested in the subcortical volumetric segmentation procedure that is used, particularly relating to the hippocampus. I am finding it difficult to decipher exactly what freesurfer does in relation to Talairach registration, I've read that there is an affine registration and a detailed non-linear warping procedure, as well as registration to a brain atlas template. Could you please point me in the right direction so that I can understand the exact procedure that the program follows in terms of warping to a standard space? Thank you Chris Leatherday

1 0

How to get the Talairach coordinate of labels
by Jin Li 08 Nov '10

08 Nov '10

Hi, Freesurfers, As the *.label file provide the vertex number and R,A,S positions. How could I get the corresponding position in Talairach coordinates for each vertex? That is, how could I convert the label in a subject's space into that in talairach space, considering the label is generated from a surface, like shown in the attachment? I tried to use mri_label2label to convert the label into fsaverage space, but when shown in tksurfer, the RAS position was not similar to Talairach position in fsaverage. Any help would be appreciated. Best! Jin

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