RE: [Freesurfer] Repeated-measures in mris_glm
I craeted the average using make_average_surface. An average/mri/T1 directory gets created, but nothing is in there. There is no T1 volume at all. Is this because I'm using an older version of recon-all (v 1.104 2005/09/07)? Could this also explain my trouble creating scatterplots? Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Wed 4/12/2006 2:42 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm How did you create the average subject? Is there a T1.mgz in the mri dir? If so, you might have an old version of tksurfer that is looking for COR files instead of mgz. Fornito, Alexander wrote: >That did the trick, but I'm having trouble displaying the results. >First issue is that I can't seem to load my average surface in tksurfer from >the command line.I get the following: > >tksurfer average rh inflated >surfer: current subjects dir: /data/nelson/work/alex/freesurfer/subjects_twins >surfer: not in "scripts" dir ==> using cwd for session root >surfer: session root data dir ($session) set to: >surfer: /data/nelson/work/alex/freesurfer/subjects_twins >ERROR: cound not stat >/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1/COR-.info. >Does it exist? >mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgh, >-1): could not open file >zcat: /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz.gz: >No such file or directory >mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz, >-1): read error >surfer: ### Could not find anatomical header information. > >What I do instead is load a subject's surface and then click load > Surface, >and select the average one. >When I load the sigt file as an overlay, what should I specify as the >registration matrix? >Clicking "calculate identity matrix" seems to work, so I'm assuming this is ok? > >After doing this, I can visualize the SPM ok, but have trouble when I try to >obtain scatterplots for a gven vertex. tksurfer closes and I get the error >below.(I've tried specifying markers and colors in the FSGD but it doesn't >seem to make a difference) >I'm using recon-all-nmr,v 1.104 2005/09/07. > > gdfReadHeader: reading > /data/nelson/work/alex/freesurfer/subjects_twins/stats/twin_qualcheck_fsgd.txt >WARNING: Marker for class class_subj1 was invalid. >WARNING: Color for class class_subj1 was invalid. >WARNING: Marker for class class_subj2 was invalid. >WARNING: Color for class class_subj2 was invalid. >WARNING: Marker for class class_subj3 was invalid. >WARNING: Color for class class_subj3 was invalid. >WARNING: Marker for class class_subj4 was invalid. >WARNING: Color for class class_subj4 was invalid. >WARNING: Marker for class class_subj5 was invalid. >WARNING: Color for class class_subj5 was invalid. >surfer: dmin=0.8701, vno=132952, x=14.6850, y=-30.1178, z=47.7694 >% surfer: curv=0.00, fs=0.00 >% surfer: val=2.132707, val2=0.00 >% surfer: amp=2.132707, angle=0.00 deg (0.00) > >Thanks again, >A > > >Oh, I'm sorry. I see the problem now. When I said to create a class >for each subject, I meant for each person, not for each FreeSurfer >subject. So there should only be 5 classes, not 10. > >So do something like this: > >Class class_subj1 >Class class_subj2 >Class class_subj3 >Class class_subj4 >Class class_subj5 > >Variables Time >Input time1_subj1 class_subj1 -1 >Input time2_subj1 class_subj1 +1 >... > >doug > >On Tue, 11 Apr 2006, Fornito, Alexander wrote: > > > >>I still get the same error message. Maybe I've coded the variable wrong? >> >>gdfReadHeader: reading ./test_fsgd.txt >>INFO: gd2mtx_method is doss >>ERROR: Design Matrix: nrows (10) <= ncols (11) >> >> >> >>Alex Fornito >>M.Psych/PhD (clin. neuro.) candidate >>Melbourne Neuropsychiatry Centre and Department of Psychology >>National Neuroscience Facility >>The University of Melbourne >>Levels 2 & 3, Alan Gilbert Building >>161 Barry St >>Carlton South Vic 3053 Australia >>Ph:+61 3 8344 1624 >>Fax: +61 3 9348 0469 >>email: [EMAIL PROTECTED] >> >> >> >>-Original Message- >>From: Doug Greve [mailto:[EMAIL PROTECTED] >>Sent: Tue 4/11/2006 11:43 AM >>To: Fornito, Alexander >>Cc: freesurfer@nmr.mgh.harvard.edu >>Subject: RE: [Freesurfer] Repeated-measures in mris_glm >> >> >>Yes, mris_preproc is new with stable. In your FSGD file, try >>specifying the title as a single string without spaces. >> >>doug >> >> >> >>On Tue, 11 Apr 2006, Fornito, Alexander wrote: >> >> >> >>>Hi Doug, >>>Is mri_preproc a new addition to the stable version? I'm using >>>r
Re: [Freesurfer] color scale bar
> if you are using the overlay color display how can you configure the scale? > In the paper "Measuring the thickness of the human cerebral cortex from > magnetic resonance images" the images show the overlay color bar in many > different scales. Thanks What do you mean by the scale of the color, and what program are you talking about? Both tkmedit and tksurfer have dialog boxes for this, opened by choosing View -> Configure -> (Functional) Overlay... from the menu bar. There are details on how these dialogs work in the relevant wiki pages: https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide_2fTkMeditWorkingWithData_2fTkMeditFunctionalVolumes https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide_2fTkSurferWorkingWithData_2fTkSurferOverlay -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Translating labels created from aseg to DTI bfloats
Hi, is there a way to translate a label created from the aseg segmentations to DTI bfloat data? I know I asked this before, but can't find the answer in my e-mails. Thanks. -- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th St. Charlestown, MA 02129 E-mail: [EMAIL PROTECTED] Tel: 617-851-8492 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Recommendation for Linux machine
Valentina, Don't use csurf, try opening it directly in tkmedit. Here is a sample command line, please modify it depending on what it is you want to look at. tkmedit brain rh.white Jenni On Tue, 11 Apr 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote: I used the old command (csurf) to open freesurfer and then I tried to open the volume from that! It works but don't show me the segmentation lines on the brain volume (even if it show the lines on the wm volume) thanks Valentina -Original Message- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Tuesday, April 11, 2006 2:21 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: Bruce Fischl; Chunchun Ni; Freesurfer Mailing List Subject: RE: [Freesurfer] Recommendation for Linux machine what is the command-line that was typed? On Tue, 2006-04-11 at 15:13 -0400, Durastanti, Valentina (NIH/NINDS) [F] wrote: Dear Bruce, I'm trying to open some images that I analyzed with the old version of Freesurfer but when I charge the brain volume on tkmedit it doesn't show me the red and green line! Have you any suggestion? Thanks Valentina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Recommendation for Linux machine
I used the old command (csurf) to open freesurfer and then I tried to open the volume from that! It works but don't show me the segmentation lines on the brain volume (even if it show the lines on the wm volume) thanks Valentina -Original Message- From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Tuesday, April 11, 2006 2:21 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: Bruce Fischl; Chunchun Ni; Freesurfer Mailing List Subject: RE: [Freesurfer] Recommendation for Linux machine what is the command-line that was typed? On Tue, 2006-04-11 at 15:13 -0400, Durastanti, Valentina (NIH/NINDS) [F] wrote: > > Dear Bruce, > I'm trying to open some images that I analyzed with the old version of > Freesurfer but when I charge the brain volume on tkmedit it doesn't show > me the red and green line! Have you any suggestion? > Thanks > Valentina > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Recommendation for Linux machine
what is the command-line that was typed? On Tue, 2006-04-11 at 15:13 -0400, Durastanti, Valentina (NIH/NINDS) [F] wrote: > > Dear Bruce, > I'm trying to open some images that I analyzed with the old version of > Freesurfer but when I charge the brain volume on tkmedit it doesn't show > me the red and green line! Have you any suggestion? > Thanks > Valentina > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Recommendation for Linux machine
Dear Bruce, I'm trying to open some images that I analyzed with the old version of Freesurfer but when I charge the brain volume on tkmedit it doesn't show me the red and green line! Have you any suggestion? Thanks Valentina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] color scale bar
if you are using the overlay color display how can you configure the scale? In the paper "Measuring the thickness of the human cerebral cortex from magnetic resonance images" the images show the overlay color bar in many different scales. Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Converting .annot into volume
Hi Doug, Yes, that's the file I referred to in my previous mail, I should have made that more clear. I'll take a look at the new label2vol, fortunately, I haven't run into the 999 limit yet. If you're re-coding it, it would be great if you could include an option to output the embedded colour table to a file, which would be less error-prone than hand-matching the correct colour tables (and would also work for files where you don't have the .ctab output, but only the embedded table). Thanks again, Johannes Doug Greve schrieb: There should be color tables in the stats directory, eg, stats/aparc.annot.a2005s.ctab Also, there's a bug in label2vol that makes it fail on any segment with id > 999 (as the cortical ones in aparc+aseg are). I've put a new version at ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol (already live in the NMR center). You can also use mri_aparc2aseg to map the a2005s annot into the aseg volume (like aparc+aseg). I'm not sure what version you have, so I copied the most recent one into ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_aparc2aseg Finally, mri_label2vol can be very slow. I'm almost finished with a version that is much faster. doug Johannes Klein wrote: Hi Doug, Thanks for the file. Unfortunately, it doesn't do the trick. I went back to the log file which reads colortable with 82 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2005.txt) Saving annotation colortable ../stats/aparc.annot.a2005s.ctab D'uh ... should have read this more patiently before - I had just looked for simple_surface_labels2005.txt and not read on ;) Out of curiosity, is there a way to extract a colour table from an annot file? Thanks again, Johannes Doug Greve schrieb: Try using the one in: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/FreeSurferColorLUT.txt doug Johannes Klein wrote: Hi folks, I'd like to create a volume segmentation from Freesurfer's .annot output. I can get it back into volume land with something like mri_label2vol --subject sub1 --annot ../label/lh.aparc.a2005s.annot --o sub1_parcellated.mgz --hemi lh --temp norm.mgz --proj frac 0 1 0.1 The thing I'm missing, though, is the appropriate colour table - I don't know how to extract the embedded one from lh.aparc.a2005s.annot I loaded the result into tkmedit and tried the different colour tables (my best bet being surface_labels.txt) provided, but none of them gives correct anatomical labels. Thanks for your help everyone, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert in 4D
I am viewing it with tkmedit. For the timeseries, it only displayed some of it. I also tried viewing it with fslview. There it was a single dashed line in the coronal view. Here is the output:mri_convert -it dicom -ot nii i6757552.MRDC.1 run.nii.gz reading from i6757552.MRDC.1...1260 DICOM 3.0 files in listFound 1260 DICOM FilesWARNING: NumberOfFrames 0 != Found Count of slices 1260.reading DICOM image...- DICOM meta-headerfile name /data/Cued_Recall/CR_ds7/s6757551/i6757552.MRDC.1Date and time study date 20050601 study time 183408 series time 190627 acquisition time 190627Identification patient name ds060105 manufacturer GE MEDICAL SYSTEMSDimensions number of rows 64 number of columns 64 number of frames 1260 pixel width 3.43752 pixel height 3.4375 slice thickness 7 field of view 220.001 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1Acquisition parameters echo time 30 repetition time 720 inversion time 0 echo number 1 flip angle 1.5708 bits allocated 16Spatial information first image position -108.281 -113.295 54.3301 last image position -108.281 -60.2276 88.2841 image orientation 1 -0 0 -0 0.538953 -0.842336 -TR=720.00, TE=30.00, TI=0.00, flip angle=90.00i_ras = (-1, 0, 0)j_ras = (0, -0.538953 , - 0.842336)k_ras = (0, -0.842337, 0.538951)writing to run.nii.gz...thanks~julia On 4/8/06, Bruce Fischl < [EMAIL PROTECTED]> wrote:how are you displaying it? And can you send the entire output? On Fri, 7 Apr2006, Julia Hamstra wrote:> Hi,> I am getting two errors when creating NIFTI files from dicoms using> mri_convert.> The first is that the 4D images are being spatially contactonated. It does > not seem to be treating it as a timeseries. This is the command:>> mri_convert -it dicom -ot nii s6761334/i6761335.MRDC.1 run.nii.gz>> Additionally it is an oblique acquizition so the coronal view is not > displaying the plane of acquizition (as intended), but an orthogonal cut> through multiple slices. Am I missing an option or additional information? I> searched the options and couldn't figure out anything that helped. The > problem applies to the co-planar oblique structural scan too.>> I'm guessing there is something simple that I am overlooking. What may that> be?> thanks> ~julia> -- Human Memory Lab8950 Villa La Jolla DriveSuite C212La Jolla, CA 92093phone: (858)534-1227fax: (858)534-1240[EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Converting .annot into volume
There should be color tables in the stats directory, eg, stats/aparc.annot.a2005s.ctab Also, there's a bug in label2vol that makes it fail on any segment with id > 999 (as the cortical ones in aparc+aseg are). I've put a new version at ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol (already live in the NMR center). You can also use mri_aparc2aseg to map the a2005s annot into the aseg volume (like aparc+aseg). I'm not sure what version you have, so I copied the most recent one into ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_aparc2aseg Finally, mri_label2vol can be very slow. I'm almost finished with a version that is much faster. doug Johannes Klein wrote: Hi Doug, Thanks for the file. Unfortunately, it doesn't do the trick. I went back to the log file which reads colortable with 82 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2005.txt) Saving annotation colortable ../stats/aparc.annot.a2005s.ctab D'uh ... should have read this more patiently before - I had just looked for simple_surface_labels2005.txt and not read on ;) Out of curiosity, is there a way to extract a colour table from an annot file? Thanks again, Johannes Doug Greve schrieb: Try using the one in: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/FreeSurferColorLUT.txt doug Johannes Klein wrote: Hi folks, I'd like to create a volume segmentation from Freesurfer's .annot output. I can get it back into volume land with something like mri_label2vol --subject sub1 --annot ../label/lh.aparc.a2005s.annot --o sub1_parcellated.mgz --hemi lh --temp norm.mgz --proj frac 0 1 0.1 The thing I'm missing, though, is the appropriate colour table - I don't know how to extract the embedded one from lh.aparc.a2005s.annot I loaded the result into tkmedit and tried the different colour tables (my best bet being surface_labels.txt) provided, but none of them gives correct anatomical labels. Thanks for your help everyone, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Converting .annot into volume
Hi Doug, Thanks for the file. Unfortunately, it doesn't do the trick. I went back to the log file which reads colortable with 82 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2005.txt) Saving annotation colortable ../stats/aparc.annot.a2005s.ctab D'uh ... should have read this more patiently before - I had just looked for simple_surface_labels2005.txt and not read on ;) Out of curiosity, is there a way to extract a colour table from an annot file? Thanks again, Johannes Doug Greve schrieb: Try using the one in: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/FreeSurferColorLUT.txt doug Johannes Klein wrote: Hi folks, I'd like to create a volume segmentation from Freesurfer's .annot output. I can get it back into volume land with something like mri_label2vol --subject sub1 --annot ../label/lh.aparc.a2005s.annot --o sub1_parcellated.mgz --hemi lh --temp norm.mgz --proj frac 0 1 0.1 The thing I'm missing, though, is the appropriate colour table - I don't know how to extract the embedded one from lh.aparc.a2005s.annot I loaded the result into tkmedit and tried the different colour tables (my best bet being surface_labels.txt) provided, but none of them gives correct anatomical labels. Thanks for your help everyone, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Repeated-measures in mris_glm
How did you create the average subject? Is there a T1.mgz in the mri dir? If so, you might have an old version of tksurfer that is looking for COR files instead of mgz. Fornito, Alexander wrote: That did the trick, but I'm having trouble displaying the results. First issue is that I can't seem to load my average surface in tksurfer from the command line.I get the following: tksurfer average rh inflated surfer: current subjects dir: /data/nelson/work/alex/freesurfer/subjects_twins surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/nelson/work/alex/freesurfer/subjects_twins ERROR: cound not stat /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1/COR-.info. Does it exist? mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgh, -1): could not open file zcat: /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz.gz: No such file or directory mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz, -1): read error surfer: ### Could not find anatomical header information. What I do instead is load a subject's surface and then click load > Surface, and select the average one. When I load the sigt file as an overlay, what should I specify as the registration matrix? Clicking "calculate identity matrix" seems to work, so I'm assuming this is ok? After doing this, I can visualize the SPM ok, but have trouble when I try to obtain scatterplots for a gven vertex. tksurfer closes and I get the error below.(I've tried specifying markers and colors in the FSGD but it doesn't seem to make a difference) I'm using recon-all-nmr,v 1.104 2005/09/07. gdfReadHeader: reading /data/nelson/work/alex/freesurfer/subjects_twins/stats/twin_qualcheck_fsgd.txt WARNING: Marker for class class_subj1 was invalid. WARNING: Color for class class_subj1 was invalid. WARNING: Marker for class class_subj2 was invalid. WARNING: Color for class class_subj2 was invalid. WARNING: Marker for class class_subj3 was invalid. WARNING: Color for class class_subj3 was invalid. WARNING: Marker for class class_subj4 was invalid. WARNING: Color for class class_subj4 was invalid. WARNING: Marker for class class_subj5 was invalid. WARNING: Color for class class_subj5 was invalid. surfer: dmin=0.8701, vno=132952, x=14.6850, y=-30.1178, z=47.7694 % surfer: curv=0.00, fs=0.00 % surfer: val=2.132707, val2=0.00 % surfer: amp=2.132707, angle=0.00 deg (0.00) Thanks again, A Oh, I'm sorry. I see the problem now. When I said to create a class for each subject, I meant for each person, not for each FreeSurfer subject. So there should only be 5 classes, not 10. So do something like this: Class class_subj1 Class class_subj2 Class class_subj3 Class class_subj4 Class class_subj5 Variables Time Input time1_subj1 class_subj1 -1 Input time2_subj1 class_subj1 +1 ... doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: I still get the same error message. Maybe I've coded the variable wrong? gdfReadHeader: reading ./test_fsgd.txt INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) <= ncols (11) Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED]] Sent: Tue 4/11/2006 11:43 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Repeated-measures in mris_glm Yes, mris_preproc is new with stable. In your FSGD file, try specifying the title as a single string without spaces. doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: Hi Doug, Is mri_preproc a new addition to the stable version? I'm using recon-all-nmr,v 1.104 2005/09/07 and can't seem to find it. I tried running the analysis through mris_glm as per option 1 as you described, but came across a problem. Command, error, and my FSGD are below. Thanks, Alex Command: mris_glm --surfmeas thickness --hemi lh --trgsubj ../average --fsgd ./test_fsgd.txt doss --beta ./beta_doss_thickness-100_lh bfloat --var ./var_doss_thickness-100_lh.w paint --y ./y_doss_thickness-100_lh_000.bfloat --nsmooth 100 gdfReadHeader: reading ./test_fsgd.txt INFO: ignoring tag 1 INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) <= ncols (11) My FSGD: GroupDescriptorFile 1 Title Time 1 vs Time 2 Class class_time1_subj1 Class class_time1_subj2 Class class_time1_subj3 Class class_time1_subj4 Class class_time1_subj5 Class class_time2_subj1 Class class_time2_subj2 Class class_time2_subj3 Class class_time2_subj4 Class class_time2_subj5 Variables Time Input time1_subj1 class_time1_subj1 -1 Input time1_subj2 class_time1_subj2 -1 Input time1_sub
Re: [Freesurfer] Converting .annot into volume
Try using the one in: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/FreeSurferColorLUT.txt doug Johannes Klein wrote: Hi folks, I'd like to create a volume segmentation from Freesurfer's .annot output. I can get it back into volume land with something like mri_label2vol --subject sub1 --annot ../label/lh.aparc.a2005s.annot --o sub1_parcellated.mgz --hemi lh --temp norm.mgz --proj frac 0 1 0.1 The thing I'm missing, though, is the appropriate colour table - I don't know how to extract the embedded one from lh.aparc.a2005s.annot I loaded the result into tkmedit and tried the different colour tables (my best bet being surface_labels.txt) provided, but none of them gives correct anatomical labels. Thanks for your help everyone, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Converting .annot into volume
Hi folks, I'd like to create a volume segmentation from Freesurfer's .annot output. I can get it back into volume land with something like mri_label2vol --subject sub1 --annot ../label/lh.aparc.a2005s.annot --o sub1_parcellated.mgz --hemi lh --temp norm.mgz --proj frac 0 1 0.1 The thing I'm missing, though, is the appropriate colour table - I don't know how to extract the embedded one from lh.aparc.a2005s.annot I loaded the result into tkmedit and tried the different colour tables (my best bet being surface_labels.txt) provided, but none of them gives correct anatomical labels. Thanks for your help everyone, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] segmentation error.
Hi Martin, can you show the orig surface also? This is probably due to a topological defect being incorrectly fixed. You can load the ?h.orig.nofix (or inflated.nofix) surface and read in the ?h.defect_labels curvature file to see if there was a defect in these regions. Does the white matter connect across the banks of the sulcus if you go forward and back a few slices? Or is it disconnected? The wm looks extremely bright there, not sure why. Did you pick any control points? Bruce On Tue, 11 Apr 2006, Martin Ystad wrote: Hi, I'm running the stable release v 3.0.1 for centos4 and I've had some problems with the segmentation. The main surface doesn't follow the wm-surface in some of the sulci, it rather 'jumps' across to the next gyri. (see picture) I've tried to edit the wm-surface and running autorecon2 again, but it doesn't work. Any ideas? Thanks, Martin Ystad University of Bergen, Norway. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer - autorecon1 will not write to established directory
Hi Adam, you shouldn't need to use "-i orig.mgz" when running -autorecon1, this will already use orig.mgz when re-running this step. You should be able to simply use: recon-all -autorecon1 -s 13667 If you are trying to do something different, and you wish to specify a different input and re-run a subject that is already there you will need to add the flag -force to the command. (and the -i flag requires a full path to the file) So, like this: recon-all -i /full/path/to/file -autorecon1 -force -s 13667 Jenni On Tue, 11 Apr 2006, adam walczak wrote: Hi, I have been having some basic problems with regard to paths. Freesurfer doesn't seem to want to write to directories that already exist. I was wondering if there is something different I need to do (I am running the reconstruction tutorial) to make this work. freesurfer-Linux-rh9-stable-pub-v3.0.1 SUBJECTS_DIR is /cajal/public/programs/freesurfer/subjects which: recon-all / autorecon1 pwd - /cajal/public/programs/freesurfer/subjects/13667/mri command line - recon-all -i orig.mgz -autorecon1 -s 13667 error- INFO: SUBJECTS_DIR is /cajal/public/programs/freesurfer/subjects ERROR: /cajal/public/programs/freesurfer/subjects/13667 exists I am at a loss as to why this happens. Any help would be appreciated. Adam Walczak - Love cheap thrills? Enjoy PC-to-Phone calls to 30+ countries for just 2¢/min with Yahoo! Messenger with Voice.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Freesurfer - autorecon1 will not write to established directory
Hi, I have been having some basic problems with regard to paths. Freesurfer doesn't seem to want to write to directories that already exist. I was wondering if there is something different I need to do (I am running the reconstruction tutorial) to make this work. freesurfer-Linux-rh9-stable-pub-v3.0.1 SUBJECTS_DIR is /cajal/public/programs/freesurfer/subjects which: recon-all / autorecon1 pwd - /cajal/public/programs/freesurfer/subjects/13667/mri command line - recon-all -i orig.mgz -autorecon1 -s 13667 error- INFO: SUBJECTS_DIR is /cajal/public/programs/freesurfer/subjects ERROR: /cajal/public/programs/freesurfer/subjects/13667 exists I am at a loss as to why this happens. Any help would be appreciated. Adam Walczak Love cheap thrills? Enjoy PC-to-Phone calls to 30+ countries for just 2¢/min with Yahoo! Messenger with Voice.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Curvature
it's the mean curvuture, which is the average of the two principal curvatures. Look in a differential geometry book! Bruce On Mon, 10 Apr 2006, anthony gallo wrote: How should one interpret the curvature function...what is the essence of it's being...what does it mean? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Repeated-measures in mris_glm
That did the trick, but I'm having trouble displaying the results. First issue is that I can't seem to load my average surface in tksurfer from the command line.I get the following: tksurfer average rh inflated surfer: current subjects dir: /data/nelson/work/alex/freesurfer/subjects_twins surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/nelson/work/alex/freesurfer/subjects_twins ERROR: cound not stat /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1/COR-.info. Does it exist? mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgh, -1): could not open file zcat: /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz.gz: No such file or directory mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz, -1): read error surfer: ### Could not find anatomical header information. What I do instead is load a subject's surface and then click load > Surface, and select the average one. When I load the sigt file as an overlay, what should I specify as the registration matrix? Clicking "calculate identity matrix" seems to work, so I'm assuming this is ok? After doing this, I can visualize the SPM ok, but have trouble when I try to obtain scatterplots for a gven vertex. tksurfer closes and I get the error below.(I've tried specifying markers and colors in the FSGD but it doesn't seem to make a difference) I'm using recon-all-nmr,v 1.104 2005/09/07. gdfReadHeader: reading /data/nelson/work/alex/freesurfer/subjects_twins/stats/twin_qualcheck_fsgd.txt WARNING: Marker for class class_subj1 was invalid. WARNING: Color for class class_subj1 was invalid. WARNING: Marker for class class_subj2 was invalid. WARNING: Color for class class_subj2 was invalid. WARNING: Marker for class class_subj3 was invalid. WARNING: Color for class class_subj3 was invalid. WARNING: Marker for class class_subj4 was invalid. WARNING: Color for class class_subj4 was invalid. WARNING: Marker for class class_subj5 was invalid. WARNING: Color for class class_subj5 was invalid. surfer: dmin=0.8701, vno=132952, x=14.6850, y=-30.1178, z=47.7694 % surfer: curv=0.00, fs=0.00 % surfer: val=2.132707, val2=0.00 % surfer: amp=2.132707, angle=0.00 deg (0.00) Thanks again, A Oh, I'm sorry. I see the problem now. When I said to create a class for each subject, I meant for each person, not for each FreeSurfer subject. So there should only be 5 classes, not 10. So do something like this: Class class_subj1 Class class_subj2 Class class_subj3 Class class_subj4 Class class_subj5 Variables Time Input time1_subj1 class_subj1 -1 Input time2_subj1 class_subj1 +1 ... doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: > I still get the same error message. Maybe I've coded the variable wrong? > > gdfReadHeader: reading ./test_fsgd.txt > INFO: gd2mtx_method is doss > ERROR: Design Matrix: nrows (10) <= ncols (11) > > > > Alex Fornito > M.Psych/PhD (clin. neuro.) candidate > Melbourne Neuropsychiatry Centre and Department of Psychology > National Neuroscience Facility > The University of Melbourne > Levels 2 & 3, Alan Gilbert Building > 161 Barry St > Carlton South Vic 3053 Australia > Ph:+61 3 8344 1624 > Fax: +61 3 9348 0469 > email: [EMAIL PROTECTED] > > > > -Original Message- > From: Doug Greve [mailto:[EMAIL PROTECTED] > Sent: Tue 4/11/2006 11:43 AM > To: Fornito, Alexander > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Repeated-measures in mris_glm > > > Yes, mris_preproc is new with stable. In your FSGD file, try > specifying the title as a single string without spaces. > > doug > > > > On Tue, 11 Apr 2006, Fornito, Alexander wrote: > >> Hi Doug, >> Is mri_preproc a new addition to the stable version? I'm using >> recon-all-nmr,v 1.104 2005/09/07 and can't seem to find it. >> I tried running the analysis through mris_glm as per option 1 as you >> described, but came across a problem. Command, error, and my FSGD are below. >> Thanks, >> Alex >> >> Command: >> >> mris_glm --surfmeas thickness --hemi lh --trgsubj ../average --fsgd >> ./test_fsgd.txt doss --beta ./beta_doss_thickness-100_lh bfloat --var >> ./var_doss_thickness-100_lh.w paint --y ./y_doss_thickness-100_lh_000.bfloat >> --nsmooth 100 >> gdfReadHeader: reading ./test_fsgd.txt >> INFO: ignoring tag 1 >> INFO: gd2mtx_method is doss >> ERROR: Design Matrix: nrows (10) <= ncols (11) >> >> My FSGD: >> >> GroupDescriptorFile 1 >> Title Time 1 vs Time 2 >> Class class_time1_subj1 >> Class class_time1_subj2 >> Class class_time1_subj3 >> Class class_time1_subj4 >> Class class_time1_subj5 >> Class class_time2_subj1 >> Class class_time2_subj2 >> Class class_time2_subj3 >> Class class_time2_subj4 >> Class class_time2_subj5 >> VariablesTime >> Input time1_subj1 class_time1_subj1 -1 >> Input time1_subj2 class_time1_subj2 -1 >> Input time1_sub
