Freesurfer July 2007

freesurfer@nmr.mgh.harvard.edu

61 participants
99 discussions

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

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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...

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Re: [Freesurfer] FreeSurfer relevance for studying structures other than the bra
by Greg Soltis 11 Jul '07

11 Jul '07

Howdie Doug, We are interested in studying not the ventricles, per say, but the actual cells and components of the cells that comprise these ventricles. For example, cells from a heart, spleen, sperm, or cochlea. Since we are not using an MRI machine to obtain the images, is FreeSurfer of no use to us? (You said it handles only TI-weighted MRI data). Additionally, you mentioned in a previous correspondence that as our files traverse along the data stream in FreeSurfer, they will ultimately be converted into 8-bit format. However, since we need the files in 16-bit format, would this be a deal-breaker as well? Thanks. Greg _________________________________________________________________ http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migrati…

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FreeSurfer relevance for studying structures other than the brain
by Greg Soltis 10 Jul '07

10 Jul '07

Greetings, I am attempting to use FreeSurfer/Slicer to study data from a mass sprectrometer. To be of use, the segmentation capability of FreeSurfer/Slicer has to be based on quantitative data, not morphology. It appears as if FreeSurfer uses a generic mapping of the brain's structure as a starting point for the model it generates. However, for one seeking to study a structure other than the brain, this can be a concern. Can FreeSurfer/Slicer accommodate data whose source is not an MRI and or of the brain? This concern also stems from the file entitled "SlicerTraining06_vtkFreeSurferReaders.ppt" provided on a Slicer site that has about a dozen tutorials for Slicer 2.6 (this is one of them). On Slide #25, entitled 'Determining label numbers in an ASEG file', there is a list of the first 30 sections created and various parameters. The names of these sections seem to be predetermined (i.e., Left Cerebral-Exterior, Left Cerebral-White-Matter, Left Cerebral-Cortex, etc.). This seems to imply that FreeSurfer/Slicer know what to look for from the onset and thus the segementation is not based solely on quantitative data. Please let me know if these conclusions are warranted. If I am mistaken, please advise as to why. Thanks for your time and advice, Greg _________________________________________________________________ Need a brain boost? Recharge with a stimulating game. Play now! http://club.live.com/home.aspx?icid=club_hotmailtextlink1

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smoothing and monte carlo sim
by Robert Levy 10 Jul '07

10 Jul '07

Hi Doug, As you suggested, I ran mc simulation data with a threshold taken from fwhm.dat so that the smoothing on the simulation matches the smoothing on the real data. What I was wondering is, if I use the same simulation data for several contrasts (they have the same fsgd, so this seems like a valid thing to do), it becomes less clear how to choose the smoothing. Or maybe it is not possible to use the same mc simulation data, because the smoothing turns out to be different. Should I instead use an average of the smoothing values, or maybe use the lowest one? Conceptually it seems like this might make the results less accurate, but in practice is there a certain level of slack in smoothing without sacrificing accuracy? If not, it makes a big difference, because the full simulation will take 6 days instead of 2. The z simulation, which at at least with the level of smoothing we have applied, showed results being much less significant, which is why I'm trying the full mc simulation. Thanks, Rob Just to give you an idea of the variance in the smoothing reported in fwhm.dat for the three contrasts: lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 17.128043 rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 16.675573 lh.ASevASc_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 15.202638 rh.ASevASc_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 15.771982 lh.ASevfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 14.438915 rh.ASevfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 15.766636 -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2656 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Freesurfer July 2007