Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

control points
by Don Hagler 13 Jul '07

13 Jul '07

In recon-all, it says you are supposed to use -autorecon2-cp if you use control points. So I wonder why earlier normalization steps also use control points, such as Norm1 and CANormalize. What effect do the control points have in those steps? _________________________________________________________________ http://newlivehotmail.com

3 4

Problems with surfaces
by Alexander Fornito 12 Jul '07

12 Jul '07

Hi all, I'm trying to run some 3T data through freesurfer and encouter a consistent problem in the cuneus/occiptal lobes where the pial surface fails to extend the the grey/CSF boundary and instead follows the white surface. I have attached an example. This problem happens in the same area across a substantial proportion of my images. I've tried control points, but they don't seem to help. Any suggestions would be greatly appreciated. Thanks, Alex

2 1

Image scaling in the MGZ file format
by Jerry Yeou-Wei Chen 12 Jul '07

12 Jul '07

Hello Freesurfer Forum, We have a question about the M matrix, found in the .mgz file header. We loaded an .mgz file into Matlab and took a look at the affine transform matrix M from the header: M(1,:) = [-1 0 0 132.7486]; M(2,:) = [ 0 0 1 -105.7281]; M(3,:) = [ 0 -1 0 131.7424]; M(4,:) = [ 0 0 0 1 ]; Let's call these numbers: M(1,:) = [ a 0 0 xt ]; M(2,:) = [ 0 0 c yt ]; M(3,:) = [ 0 b 0 zt ]; M(4,:) = [ 0 0 0 1 ]; We interpret a b and c as controlling rotation. xt yt zt govern translation. However, we cannot see how this matrix controls scaling. We were expecting to see the following: M(1,:) = [ xs 0 0 xt ]; M(2,:) = [ 0 ys 0 yt ]; M(3,:) = [ 0 0 zs zt ]; M(4,:) = [ 0 0 0 1 ]; ...where xs yx zs control scaling. In our empirical matrix they do not seem to be serving that function. (xs appears to be used for rotation only, ys and zs are zero). So the first question is: does the matrix control scaling, and if so, how? The second question: Is the scaling built into the image, such that each voxel is 1mm by 1mm by 1mm? If so, how can the program tell when this is the case, and when it is not? Does ndim1 represent the number of voxels in that dimension, or the distance across that dimension in millimeters? Does ras_good_flag simply indicate that the image is in the proper orientation, or does it also indicate that each voxel in the image measures 1mm x 1mm x 1mm? Thanks for your help. Jerry Chen and Geoff Pope

3 2

few oasis question
by Martin Kavec 12 Jul '07

12 Jul '07

Hi. I have few questions regarding the recently published OASIS data analyzed using Freesurfer: 1. How did you produce $SUBJECT_ID/mri/wmparc.mgz. I am running recon-all -all on my subjects, but I don't get this file. 2. How did you produce segmentation of the corpus callosum. I am running recon-all -all on my subjects, but I don't get this file. 3. Why do the structure volumes differ between $SUBJECT_ID/stats/wmparc.stat and $SUBJECT_ID/stats/aseg.stat Thanks, Martin

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flip functional using tkregister2?
by Stacy Chu 12 Jul '07

12 Jul '07

Hi all, I used reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1 and then reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1 --manual to register and edit the registration of a functional to its anatomical volume. The initial registration came out pretty bad and I think I need to do a left-right flip. I see that I can rotate/translate/resize using tkregister2, but I can't figure out how to make a flip. Does anyone know the best way to do that? If the registration looks so bad do I need to change something in the command for my initial registration process? Thanks! Best, Stacy ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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registering .gfeat
by Stacy Chu 12 Jul '07

12 Jul '07

Hi Doug, I am trying to use reg-feat2anat to project FEAT results onto the FS surface. This works ok (except for some registration problems discussed earlier) for 1st level .feat directories. However, my study consists of two consecutive runs per subject (to allow the subject to take a break), so preprocessing for each run is first done seperately on the 1st level. Then at the second level the two runs are averaged together using FEATS fixed effects analysis. Now I have one .gfeat folder which combines both runs. It seems that not all files that reg-feat2anat requires are in the .gfeat folder. So I copied the .1stlevel.feat/reg/example_func2standard.mat to 2ndlevel.gfeat/reg/example_func2standard.mat. Now I get an error that the .../freesurfer/tmp/exfbet file can't be found. I have attached the log file. Your help would be much appreciated. Thanks, Stacy ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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export mgz+label to dicom files
by T. Song 12 Jul '07

12 Jul '07

Hi All: After imposing labels to a T1.mgz files in tkmedit, is it possible to write out dicom files with the label? Thanks in advance! Tao

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Fwd: [Freesurfer] doesn't find .dcm-files for "mri_convert -it dicom ..."
by Birte Schrader 12 Jul '07

12 Jul '07

> Hi Bruce, > > thanks for replying so fast. But somehow I still don't get this > running. When I say: > > "mri_convert avant/IM-0001-0001.dcm avant.mgz" > > I get: > > "mri_convert avant/IM-0001-0001.dcm avant.mgz > unknown file type for file avant/IM-0001-0001.dcm" > > when saying: > > "mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz" > > I get: > > "mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz > reading from avant/IM-0001-0001.dcm... > no DICOM files found. Exit" > > I don't have any idea what's wrong there. > > Cheers, > Birte > > > > > On Jul 12, 2007, at 9:02 PM, Bruce Fischl wrote: > >> Hi Birte, >> you need to specify the name of a single DICOM file that is in the >> series you want to use for building anatomical models, not just >> the directory name. >> cheers, >> Bruce >> On Thu, 12 Jul 2007, Birte Schrader wrote: >>> Hello, >>> I just downloaded and installed the freesurfer and got up the >>> step where I tested it by trying "recon-all -s bert -autorecon1". >>> This works fine :-) >>> Now I (thoroughly) followed the instructions "Getting started >>> with your own data" in of https://surfer.nmr.mgh.harvard.edu/ >>> fswiki/ TestingFreeSurfer. But unfortunately the mri_convert >>> command does not work on (my?) dicom-files: >>> "mri_convert -it dicom -ot mgz avant/ avant.mgz" >>> is what I type in. I am really in mri/orig/ and in mri/orig/avant >>> are 120 .dcm-files so I don't see what's wrong. I get the error >>> message: >>> "reading from avant/... >>> no DICOM files found. Exit" >>> Do you know if there are different types if dicom-files and not >>> all of them are supported? Or do you see anything else that might >>> be wrong? >>> Thanks in advance. >>> Birte >>> PS: The FreeSurfer software was highly recommended to me by a >>> friend of a friend of mine, so I am really looking forward to >>> trying it on my data... >>> PPS: tkmedit and tksurfer do not work yet for me. But that is >>> some problem with displaying the windows. I get "GLUT: Fatal >>> Error in tksurfer.bin: could not open display:". But this >>> shouldn't alter the no-display-functions of freesurfer, no? >>> Visualization I can do otherwise if I cannot fix it... >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Re: [Freesurfer] doesn't find .dcm-files for "mri_convert -it dicom ..."
by Birte Schrader 12 Jul '07

12 Jul '07

yes, it is. PS: Birte is a girl's name... :-) On Jul 12, 2007, at 9:57 PM, Mithra wrote: > Hello Mr.Schrader, > Is is the "avant" folder saved in the path/folder from where you > are runnning this command? > > Thanks. > > > On 7/12/07, Birte Schrader <birte(a)ethz.ch> wrote: > >> Hi Bruce, >> >> >> thanks for replying so fast. But somehow I still don't get this >> running. When I say: >> >> >> "mri_convert avant/IM-0001-0001.dcm avant.mgz" >> >> >> I get: >> >> >> "mri_convert avant/IM-0001-0001.dcm avant.mgz >> unknown file type for file avant/IM-0001-0001.dcm" >> >> >> when saying: >> >> >> "mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz" >> >> >> I get: >> >> >> "mri_convert -it dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz >> reading from avant/IM-0001-0001.dcm... >> no DICOM files found. Exit" >> >> >> I don't have any idea what's wrong there. >> >> >> Cheers, >> Birte >> >> >> >> >> >> >> >> >> On Jul 12, 2007, at 9:02 PM, Bruce Fischl wrote: >> >> >>> Hi Birte, >>> you need to specify the name of a single DICOM file that is in >>> the series you want to use for building anatomical models, not >>> just the directory name. >>> cheers, >>> Bruce >>> On Thu, 12 Jul 2007, Birte Schrader wrote: >>>> Hello, >>>> I just downloaded and installed the freesurfer and got up the >>>> step where I tested it by trying "recon-all -s bert - >>>> autorecon1". This works fine :-) >>>> Now I (thoroughly) followed the instructions "Getting started >>>> with your own data" in of https://surfer.nmr.mgh.harvard.edu/ >>>> fswiki/ TestingFreeSurfer. But unfortunately the mri_convert >>>> command does not work on (my?) dicom-files: >>>> "mri_convert -it dicom -ot mgz avant/ avant.mgz" >>>> is what I type in. I am really in mri/orig/ and in mri/orig/ >>>> avant are 120 .dcm-files so I don't see what's wrong. I get the >>>> error message: >>>> "reading from avant/... >>>> no DICOM files found. Exit" >>>> Do you know if there are different types if dicom-files and not >>>> all of them are supported? Or do you see anything else that >>>> might be wrong? >>>> Thanks in advance. >>>> Birte >>>> PS: The FreeSurfer software was highly recommended to me by a >>>> friend of a friend of mine, so I am really looking forward to >>>> trying it on my data... >>>> PPS: tkmedit and tksurfer do not work yet for me. But that is >>>> some problem with displaying the windows. I get "GLUT: Fatal >>>> Error in tksurfer.bin: could not open display:". But this >>>> shouldn't alter the no-display-functions of freesurfer, no? >>>> Visualization I can do otherwise if I cannot fix it... >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > Regards, > Mithra > > Imaging Research Center > University of Texas, Austin > 3925-B W Braker Lane > Austin. TX - 78759 > Tel: (512) 232-5725 > Fax: (512) 232-4202 > > www.irc.utexas.edu

1 0

doesn't find .dcm-files for "mri_convert -it dicom ..."
by Birte Schrader 12 Jul '07

12 Jul '07

Hello, I just downloaded and installed the freesurfer and got up the step where I tested it by trying "recon-all -s bert -autorecon1". This works fine :-) Now I (thoroughly) followed the instructions "Getting started with your own data" in of https://surfer.nmr.mgh.harvard.edu/fswiki/ TestingFreeSurfer. But unfortunately the mri_convert command does not work on (my?) dicom-files: "mri_convert -it dicom -ot mgz avant/ avant.mgz" is what I type in. I am really in mri/orig/ and in mri/orig/avant are 120 .dcm-files so I don't see what's wrong. I get the error message: "reading from avant/... no DICOM files found. Exit" Do you know if there are different types if dicom-files and not all of them are supported? Or do you see anything else that might be wrong? Thanks in advance. Birte PS: The FreeSurfer software was highly recommended to me by a friend of a friend of mine, so I am really looking forward to trying it on my data... PPS: tkmedit and tksurfer do not work yet for me. But that is some problem with displaying the windows. I get "GLUT: Fatal Error in tksurfer.bin: could not open display:". But this shouldn't alter the no-display-functions of freesurfer, no? Visualization I can do otherwise if I cannot fix it...

2 1

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