Re: [Freesurfer] Using FSL matrix for Talairach transform
Hi Doug, Thanks! I've tried that now, but it didn't help. Looking at the output, I get the impression that some of the axes might be swapped over. I've done a manual registration now to process my subject. Maybe it's worth following this up for future use of FSL-supplied matrices - however, the problem only applies to XFM-style output, and e.g. mri_vol2vol works fine, so I guess there aren't many other users affected. If you like, I can send you a few volumes and the associated registration matrix. Thanks for your help! Cheers, Johannes Douglas N Greve Wed, 08 May 2013 12:16:36 -0700 Hi Johannes, as a quick fix can you try inverting the matrix? doug On 05/08/2013 01:31 PM, Johannes Klein wrote: Hi Doug, Thanks for your reply! I'm getting closer to a solution now, with tkregister2's display showing a correctly transformed mni305 file, but I still cannot get a valid talairach.xfm file out of this. Here's what I tried: tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg works fine. Next, to obtain a suitable .xfm file, I ran tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg --xfmout testtal.xfm --noedit and copied the output (testtal.xfm) into mri/transforms/talairach.xfm Now, when I view the result with tkregister2 --s test --fstal --mgz the transform is way off again. Apparently, tkregister2 reads and interprets the FSL matrix correctly, but the output transform that I get is not in the right format for transforms/talairach.xfm. I wonder if I'm using the wrong output switch now - but looking at tkregister2's documentation, it seems to be the one to use? Thanks, Johannes Date: Tue, 07 May 2013 14:11:27 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using FSL matrix for Talairach transform To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 518943cf.7050...@nmr.mgh.harvard.edu mailto:518943cf.7050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Johannes, try using the --xfmout option of tkregister2. I'm not sure what regdat2xfm is doing. doug On 05/07/2013 12:42 PM, Johannes Klein wrote: Dear all, I have some tricky subjects that I cannot get to register properly with the standard Talairach process, or even the use-mritotal option. However, with some fiddling, I've produced a reasonable registration matrix with FSL's FLIRT. I'm now looking to convert my FSL registration matrix, and use it as Freesurfer's Talairach transform. From the documentation, I gathered that I need to get it into Freesurfer's xfm format, and I suppose this is a two step process. I converted the FLIRT-provided matrix cor2raw.xfm like so: tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --fslreg cor2raw.xfm --s mysubject --noedit --reg register.dat I then converted register.dat to the xfm data format: regdat2xfm /usr/local/freesurfer/average/mni305.cor.mgz rawavg.mgz register.dat tal.xfm and finally replaced talairach.xfm in the transforms directory with the output of the last command. Unfortunately, this doesn't work, and the transform is very much off target when I view it in tkregister2. Obviously, I've made a mistake when converting between the different transforms - could anybody point me in the right direction? Thanks all, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing
Re: [Freesurfer] Using FSL matrix for Talairach transform
Hi Doug, Thanks for your reply! I'm getting closer to a solution now, with tkregister2's display showing a correctly transformed mni305 file, but I still cannot get a valid talairach.xfm file out of this. Here's what I tried: tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg works fine. Next, to obtain a suitable .xfm file, I ran tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --targ orig.mgz --fsl mni2sub.mat --reg test_mni.mgz.reg --xfmout testtal.xfm --noedit and copied the output (testtal.xfm) into mri/transforms/talairach.xfm Now, when I view the result with tkregister2 --s test --fstal --mgz the transform is way off again. Apparently, tkregister2 reads and interprets the FSL matrix correctly, but the output transform that I get is not in the right format for transforms/talairach.xfm. I wonder if I'm using the wrong output switch now - but looking at tkregister2's documentation, it seems to be the one to use? Thanks, Johannes Date: Tue, 07 May 2013 14:11:27 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using FSL matrix for Talairach transform To: freesurfer@nmr.mgh.harvard.edu Message-ID: 518943cf.7050...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Johannes, try using the --xfmout option of tkregister2. I'm not sure what regdat2xfm is doing. doug On 05/07/2013 12:42 PM, Johannes Klein wrote: Dear all, I have some tricky subjects that I cannot get to register properly with the standard Talairach process, or even the use-mritotal option. However, with some fiddling, I've produced a reasonable registration matrix with FSL's FLIRT. I'm now looking to convert my FSL registration matrix, and use it as Freesurfer's Talairach transform. From the documentation, I gathered that I need to get it into Freesurfer's xfm format, and I suppose this is a two step process. I converted the FLIRT-provided matrix cor2raw.xfm like so: tkregister2 --mov /usr/local/freesurfer/average/mni305.cor.mgz --fslreg cor2raw.xfm --s mysubject --noedit --reg register.dat I then converted register.dat to the xfm data format: regdat2xfm /usr/local/freesurfer/average/mni305.cor.mgz rawavg.mgz register.dat tal.xfm and finally replaced talairach.xfm in the transforms directory with the output of the last command. Unfortunately, this doesn't work, and the transform is very much off target when I view it in tkregister2. Obviously, I've made a mistake when converting between the different transforms - could anybody point me in the right direction? Thanks all, 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Trouble with flip angle map when computing T1 maps
Dear all, I've had some trouble feeding a flip angle map into mri_ms_fitparms. If I don't provide it, the estimates look fine; with the FA map however, all brain voxels in the resultant T1.mgz are set to 5. I've checked that all images are registered, and the nominal values in the FA map look good to me. I'm running Freesurfer 5.1.0 Here's the output: johannes$ mri_ms_fitparms -afi B1Map_in_degrees.mgz DESPOT_FA_18.mgz DESPOT_FA_4.mgz t1_fs using flip angle map DESPOT1HIFI_B1Map_in_degrees.mgz with nominal value 60.0 degrees reading DESPOT_FA_18.mgz...TE = 3.70, TR = 8.00, flip angle = 18.00 reading DESPOT_FA_4.mgz...TE = 3.70, TR = 8.00, flip angle = 4.00 using 2 FLASH volumes to estimate tissue parameters. parameter rms = 77.083 non-equal flip_angle found for the volume 1. Flip_angle is set to zero. TR = 8.00, TE = 3.70, Flip_angle = 0.00 are used writing PD estimates to t1_fs/PD.mgz... writing T1 estimates to t1_fs/T1.mgz... writing residual sse to t1_fs/sse.mgz... writing faf map to t1_fs/faf.mgz... writing synthetic images to t1_fs/flash18.mgz... writing registration matrix to t1_fs/flash18.lta... writing synthetic images to t1_fs/flash4.mgz... writing registration matrix to t1_fs/flash4.lta... parameter estimation took 1 minutes and 18 seconds. Any thoughts on what I'm doing wrong? Thanks for your help, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Scripting: Feeding arguments and variables to script?
Hi Graham,
Another way is to generate your TCL on the fly, see below for a simple
example:
- snip -
#!/bin/sh
outdir=/usr/people/johannes/scratch/fssubjects/pictures
mkdir -p $outdir
cd $SUBJECTS_DIR
# put your subjects here
for f in CONTROL*; do
for hemi in lh rh; do
echo scale_brain 1.05
redraw
save_tiff ${outdir}/${f}_thickness_${hemi}.tiff
exit /tmp/prettypic_$$.tcl
tksurfer $f $hemi inflated -overlay $f/surf/${hemi}.thickness -tcl
/tmp/prettypic_$$.tcl
done
done
rm /tmp/prettypic_$$.tcl
- snap -
Cheers,
Johannes
___
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Re: [Freesurfer] mris_anatomical_stats error
Sure, my command would look something like this: mris_anatomical_stats -b average_subject lh white -l lh.mylabel Works on individual subjects, but not on the averaged one. The latter was created with make_average_subject --subjects STRU_1 STRU_2 [...] --out average_subject Thanks for your help, Johannes Doug Greve schrieb: The problem is that this is being done an the average subject, which does not have a wm.mgz file. Should be easy to fix. Johannes, can you send your cmd line? doug Nick Schmansky wrote: Johannes, wm.mgz is produced in the -autorecon2 stage of recon-all. A handy table to consult is: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable or http://grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.htm Nick On Tue, 2006-10-31 at 11:49 +, Johannes Klein wrote: Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir contains T1, brain, mni305.cor and orig.mgz, but no wm.mgz. Is there a way to create this file from the data I've got? Thanks for your help, 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 -- 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] mris_anatomical_stats error
Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir contains T1, brain, mni305.cor and orig.mgz, but no wm.mgz. Is there a way to create this file from the data I've got? Thanks for your help, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer marking nodes on opposite side of brain
Hi everyone, I'm currently hand-drawing some labels using tksurfer. Unfortunately, quite often a node that I try to click will not be selected. Instead, the mark is placed on the surface behind the one I'm viewing, e.g. when trying to outline calcarine structures, the node mark will appear somewhere on the lateral surface. I wonder if anyone else has run into this? Is it possible to constrain tksurfer's node selection to the currently visible part of the cortex only? Alternatively, an undo feature to de-select the last point clicked would save me re-drawing the whole outline, but in my Edit menu, tksurfer consistently says Nothing to Undo. Do I need to enalbe the Undo feature somewhere? I'm running FS 3.0.3 centos4. Thank you very much, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cannot view average curvature after make_average_subject
Hi Doug, Thanks for your answer. I've processed my data as you suggested, and it seems to work fine now. If I may, I would like to ask some follow-up questions to you and the list. The data I'm analysing comprises a group of healthy controls and patients with increased cortical thickness. When I compare the stats tables generated from these groups, it is obvious that there is a thickness difference in almost all of the regions studied (in eg. lh.aparc.a2005.stats). After glmfit, however, there are only a few regions of significant difference, and I suspect that this is due to the DOSS option to glmfit. If I understand correctly, then this would remove the difference of mean cortical thickness, which I am interested in here. I wonder what the best way around this is. If I test for significant difference in overall thickness seperately, can I assume that the changes displayed are those that occur over and above what the difference in mean thickness explains? More generally, I wonder if the different offset approach I've been running so far is correct for comparison of thickness measurements (since the difference of the mean is meaningful here). Your input is very much appreciated. Thanks a lot, Johannes Doug Greve wrote: Use lh.curv instead of lh.avg_curv. For lh.thickness, there is a bug in make_average_subject (resamples the avg thickness to the first or last subject instead of the average subject). If you are going to be doing a group stat analysis, you will usually get the mean thickness. Otherwise, you can just run mris_preproc with the --mean option. doug Johannes Klein wrote: Hi all, I'm setting up a small study where I want to compare a subject to some matched controls. I've been following the Group analysis tutorial and I've run make_average_subject on my controls. Now, I'd like to check my data and view averaged curvature and thickness measurements. When I try to load the lh.avg_curv onto lh white in tksurfer, I get the following error: ERROR: number of vertices in XX/lh.avg_curv does not match surface (173612,163842)surfer: error reading curvature file The same applies to lh.avg_thickness However, there is a file called lh.curv that I can load. What am I doing wrong here? How can I view the average curvature and thickness measurements? Thanks a lot 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] Cannot view average curvature after make_average_subject
Hi all, I'm setting up a small study where I want to compare a subject to some matched controls. I've been following the Group analysis tutorial and I've run make_average_subject on my controls. Now, I'd like to check my data and view averaged curvature and thickness measurements. When I try to load the lh.avg_curv onto lh white in tksurfer, I get the following error: ERROR: number of vertices in XX/lh.avg_curv does not match surface (173612,163842)surfer: error reading curvature file The same applies to lh.avg_thickness However, there is a file called lh.curv that I can load. What am I doing wrong here? How can I view the average curvature and thickness measurements? Thanks a lot everyone, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkmedit problem, crash on loading aseg
Hi everyone, I have a rather obscure problem. There are some subjects whose aseg subcortical parcellations will not load up in tkmedit, causing it to crash. This happens when using a Mac with X11 to view them, not on my Linux machine. Interestingly though, this does not happen for all subjects, some do get displayed correctly on the Mac, too. Here's what I do: tkmedit mysubj T1.mgz Then, use tkmedit's File-Load Segmentation There, select aseg.mgz and tkmeditColorsCMA tkmedit then crashes, producing the following log: tkmedit started: Tue Sep 5 17:26:20 2006 tkmedit PAT_ T1.mgz lh.white -aux-surface rh.white $Id: tkmedit.c,v 1.274.2.1 2006/03/06 19:52:48 kteich Exp $ $Name: stable3 $ Set user home dir to /Volumes/JalapenoSAN/Scratch/XX/fs Set subject home dir to /Scratch/XX/fs/PAT_ Using interface file /usr/local/freesurfer/lib/tcl/tkmedit.tcl Tcl: Successfully parsed tkmedit.tcl Tcl: Successfully parsed tkm_functional.tcl Error 1 in CLUT_GetLabel: Invalid pointer to object. I wonder if this is a known problem for Macs? Thanks, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all: error in topology correction step
Hi Nick, hi everyone, I just ran the 3.0.2 topology fixer on a linux machine over one of the failed surfaces, and that seems to have worked - great! The compute servers have since been upgraded to 3.0.3, so I'll feed the results into the rest of the recon-all pipeline and see how it goes. Thanks for all your help, Johannes Nick Schmansky schrieb: Johannes, In looking at your recon-all.log, it looks like you are running v3.0.1 of freesurfer, which can be confirmed by typing: cat $FREESURFER_HOME/build-stamp.txt In v3.0.2, a bug in the topology fixer was fixed (namely, the 'mrisDefectAnalysis' routine). Is it possible for you to download the latest freesurfer and rerun on the trouble subjects? It should not be necessary to re-run on the other subjects. The fixed topology fixer is likely to successfully process your subjects. I can also send you this new mris_topology_fixer binary for the Mac if you don't want to download/re-install. Nick On Wed, 2006-07-12 at 18:50 +0100, Johannes Klein wrote: Hi Nick, Thanks for your message. Unfortunately, the topology fixer did not produce a defect_labels file, it seems to have aborted before doing so. Is there a way to make mris_fix_topology produce the defect labels without actually running topology correction? I thought of trying the -correct_defect option with one of the defects that didn't cause problems. Does that make sense? Thanks, Johannes Nick Schmansky schrieb: Johannes, To visualize defect locations: tksurfer subjid lh inflated.nofix then: File-Curvature-Load Curvature select: surf/lh.defect_labels and the defects will display in red. Remember you can click on a defect vertex in tksurfer, then click 'save point' and then in tkmedit, click 'goto saved point', which is handy to see exactly where in a volume things went wrong. Nick ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all: error in topology correction step
Hi everyone, I'm using recon-all to flatten a number of scans from patients and controls. Most of them work fine, but there are 3 that do not reconstruct correctly. They all seem to share the same problem: Recon-all aborts during the automatic topology correction step, and there's a line in the log saying mrisDefectAnalysis : defect XXX overlap defect YYY. I've checked registration to talairach, skull strip and initial surfaces, the only thing I could see was that in some cases, bits of the superior sagittal sinus were wrongly included in the lh.orig.nofix, or small bits of dura, but nothing major. I'm attaching the relevant output from the topology fixer for two different cases. I would be grateful if someone could point me at other things to try. Is it possible to visualise the defects' locations, so I could find out which defect is actually causing the overlap message? Thanks for your help everyone, Johannes -- CASE 1 [EMAIL PROTECTED] Fix Topology lh Wed Jun 14 04:04:29 BST 2006 \n cp ../surf/lh.orig.nofix ../surf/lh.orig \n \n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_2280/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga PAT_2280 lh \n reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters * Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations :10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices :0 ordering dependant retessellation: 0 use precomputed edge table :0 smooth retessellated patch :2 match retessellated patch : 1 verbose mode : 0 * INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ $Id: mrisurf.c,v 1.441.2.1 2006/03/06 21:12:31 greve Exp $ before topology correction, eno=-656 (nv=197397, nf=396220, ne=594273, g=329) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 30743 ambiguous faces found in tessellation segmenting defects... defect 6 : 7 vertices have been added to the surface [ ... ] defect 314 : 2 vertices have been added to the surface total of 95 vertices has been added to the surface analyzing defects... mrisDefectAnalysis : defect 277 overlap defect 272 reading input surface /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_2280/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Darwin jalapeno6.fmrib.ox.ac.uk 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Wed Jun 14 04:08:10 BST 2006 CASE 2 [EMAIL PROTECTED] Fix Topology rh Thu Jun 15 12:13:05 BST 2006 \n cp ../surf/rh.orig.nofix ../surf/rh.orig \n \n cp ../surf/rh.inflated.nofix ../surf/rh.inflated \n /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_3509/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga PAT_3509 rh \n reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters * Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations :10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices :0 ordering dependant retessellation: 0 use precomputed edge table :0 smooth retessellated patch :2 match retessellated patch : 1 verbose mode : 0 * INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ $Id: mrisurf.c,v 1.441.2.1 2006/03/06 21:12:31 greve Exp $
[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] 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] 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
Re: [Freesurfer] mri_convert documentation error
Hi Doug, Thanks for clarifying this. My data is in Nifti-Format and looks fine in FSLview, meaning that left is on the right-hand side of the screen and vice versa. There is no qform orientation information in the header. When I convert my data without --in_orientation LAS, it ends up looking the wrong way round in tkmedit. When I convert as in mri_convert --in_orientation LAS mydata.nii 001.mgz it looks alright again, i.e. left is on the right-hand side of the screen in tkmedit. Now - having changed the orientation info, does that mean that I can rely on the lh.* surfaces truly being the left hemisphere, as long as I make sure that the 001.mgz input looks correct in tkmedit? Or is there some more intricate problem with the orientation info that I am missing? Thanks again, Johannes Doug Greve schrieb: I think this has been fixed. BTW, be very careful changing the orientation describtion. Note that it is the description that is being chaanged, NOT the pixel data. If your pixel data were oriented one way and the description was correct, changing the description will make the description wrong. doug Johannes Klein wrote: Hi folks, There's a small bug in the online help for mri_convert I found when trying to get my input Nifti's left/right to match with freesurfer conventions. When run without any parameters, the last paragraph describes the use of the --in-orientation switch. That must read --in_orientation (probably same for out-/out_). Took me a while to figure that one out ;) Cheers, 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 documentation error
Hi folks, There's a small bug in the online help for mri_convert I found when trying to get my input Nifti's left/right to match with freesurfer conventions. When run without any parameters, the last paragraph describes the use of the --in-orientation switch. That must read --in_orientation (probably same for out-/out_). Took me a while to figure that one out ;) Cheers, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] converting thickess file to ascii
Hi Adam, mris_convert still wants a surface file for reference. I've succeeded doing what you want by pretending it's a curvature file as in mris_convert -c lh.thickness lh.orig lh.thickness.asc Johannes Thomas, Adam (NIH/NIMH) schrieb: Can mris_convert be used to convert thickness files to ascii? My attempts so far have resulted in segfaults: [EMAIL PROTECTED] surf]$ mris_convert lh.thickness lh.thickness.asc Segmentation fault [EMAIL PROTECTED] surf]$ Or is there another way to convert thickness files to ascii? Thanks, -Adam --- Adam Thomas [EMAIL PROTECTED] Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 ___ 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
