Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Re: [Freesurfer] fixing bad tal registrations
by Garth Coombs 31 Mar '10

31 Mar '10

Hi, To run bbregister outside of the recon stream, I tried: setenv SUBJECTS_DIR /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR cd $SUBJECTS_DIR bbregister --mov mri/nu.mgz --int ../mni305.cor.mgz --reg mri/transforms/talairachTEST.xfm --init-spm --t1 --s amac_TEST --tmp ./TEMP but when I tried to view it with: tkregister2 --mov amac_TEST/mri/nu.mgz --fstal --reg amac_TEST/mri/transforms/talairachTEST.xfm --surf orig --s amac_TEST It looks the same as it did before, and I am concerned that the bad tal registration will affect the localization of fMRI data and ICV measurements. Does anyone have any advice on how to fix the registration? Thanks, Garth > > -- > > On Tue, 16 Mar 2010, Garth Coombs wrote: > >> Hi, >> >> I recently ran into a problem with some of my tal registrations during the recon-all process (see below message to Martino's Tech). In order to fix the problem, it was suggested that we run bbregister outside of the recon-all stream and then feed that registration into the subsequent recon stages. Does this make sense, and how would I go about doing this? I'm not sure what the --mov file should be, or if there is a way to specify fstal as the reference structural. >> >> Thanks for your help! >> >> -Garth >> >> Hi Doug & FreeSurfers, >> >> I recently re-ran a large number of recons and have been checking to make sure >> they all ran correctly, and I have come up with a couple of questions about the >> talairach transform/recon checking. >> >> For some of my recons, the green line outlining the white matter on the >> individual brain extends slightly further than the cortex surface of the fstal >> brain. While it looks relatively well aligned (e.g. ventricles, brain stem), the >> fstal brain looks slightly too small for the subject's brain. Additionally, the >> green outline tends to extend into the skull of fstal in the sagittal plane. An >> example is: >> >> setenv SUBJECTS_DIR /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/ >> tkregister2 --mgz --fstal --surf orig --s amac_anat >> >> or >> >> tkregister2 --mgz --fstal --surf orig --s amra_anat >> >> In order to fix these talairach transforms, it seems like the best option would >> be to scale the brain; however, we will be doing a cortical thickness analysis >> on this group, and we do not want to scale the brain if it will somehow affect >> the outcomes. Is this something we should worry about? >> >> Another question we have is about general recon quality control: when checking >> that the recons ran smoothly, what should we look for? I look to make sure that >> the pial and white matter surface lines don't include dura or any other matter >> and that they follow the structures correctly, skull stripping, and intensity >> normalization, but is there anything else that is particularly important? >> >> Any advice would be greatly appreciated! >> >> Thanks, >> Garth >> > >

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mri_label_volume
by Rebecca Dautoff 31 Mar '10

31 Mar '10

I have hand drawn labels that I want to find volumes for. I used mri_label2vol to create a .mgz mask of the label and am now using mri_label_volume to extract the volumes. it looks like the -s flag should output in a spreadsheet (I am assuming similar to asegstats2table) but i cant seem to get an output other than what i get in my terminal window example command line mri_label_volume mri/test/mgz 1 2 -s HRDEVtest.txt thanks, becca

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how to use own brainmask.mgz
by Guang Zeng 31 Mar '10

31 Mar '10

Hi, there, I have a scan which FreeSurfer skull-stripping gave me a bad brainmask (see fig. 1). I created a brainmask by using SPM segmentation results, then converted it to FreeSurfer format with --conform flag on. Finally, I masked T1.mgz using this brainmask, and I used it as my brainmask.mgz (see fig. 2) to run the rest part (-autorecon2 -autorecon3) However, when I loaded the new aseg.mgz, I found that lots of boundary voxel were not labled (see fig. 3) Anyone can give me some suggestions to fix this problem? Thanks a lot! Guang _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:…

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qcache for multiple subjects
by Hui J Yu 31 Mar '10

31 Mar '10

Dear freesurfer users, After running recon-all for all subjects, I started running qcache using the following commands: (in the subject directory) foreach i (*) recon-all -s $i -qcache end However, the process was terminated/stopped. Is there a way to resume the process (like what you will have with -make all). Thank you.

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Error: Loading Segmentation
by Janani Dhinakaran 30 Mar '10

30 Mar '10

Hello, With reference to this mail- Re: [Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgzI tried introducing segments to my image ERROR: Loading Segmentation aparc.a2005s+aseg.mgz Couldn't import the segmentation volume. Tkmedit wouldn't read the segmentation you specified. This could be because the segmentation volume wasn't a valid COR volume directory. The following is what happened in the text shell. s0964091@CRIC-0012:~$ tkmedit jan orig.mgz -segmentation aparc.a2005s+aseg.mgz ERROR: cannot find /home/s0964091/Desktop/jan/mri/aparc.a2005s+aseg.mgz LoadSegmentationVolume main aparc.a2005s+aseg.mgz /usr/local/freesurfer/FreeSurferColorLUT.txt Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl % So it loaded Orig but without segments. How do I rectify this? Thank you.

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Retinotopy analysis ERROR: selfreqavg failed
by Yuhong Jiang 30 Mar '10

30 Mar '10

Hi, I've been getting "ERROR: selfreqavg failed" for my retinotopic analysis and would appreciate any suggestions about what might have gone wrong. The command I was using was sfa-sess. Here's the command and the output from freesurfer: sfa-sess -a rtopy -sf sessid -df sessdir -------------------------------------------------------------- sfa-sess logfile is /redactedout.log -------------------------------------------------------------- ------------------------------------------- /Users/JiangLabfMRI/freesurferData/SUBJECT1 Tue Mar 30 16:33:53 CDT 2010 INFO (SUBJECT1): RunList = 011 012 013 014 -------------------------------------------------- /Users/JiangLabfMRI/freesurferData/SUBJECT1/bold selfreqavg -TR 2 -o rtopy/polar/h -i 011/fmcs -i 012/fmcs -i 013/fmcs -cfg /Users/JiangLabfMRI/freesurferData/SUBJECT1/results/rtopy/analysis.cfg -parname para.para -------------------------------------------------- --- Parsing Config File: /Users/JiangLabfMRI/freesurferData/SUBJECT1/results/rtopy/analysis.cfg ---- -ncycles 8 -delay 0 -nskip 3 -fwhm 0 DirectionList: +1 +1 +1 ERROR: selfreqavg failed Thank you for your help. -- ---------------------------------------------------------- Yuhong Vanessa Jiang, PhD, Department of Psychology, Univ of Minnesota http://jianglab.psych.umn.edu/ ----------------------------------------------------------

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Caudate volume error in Huntington´s disease
by Diego Herrera 30 Mar '10

30 Mar '10

Hello I tried recon-all in a patient with Huntington´s disease with severe atrophy of caudate nucleus (visually). It seems that freesurfer subcortical segmentation failed because the volume reported is within normal limits. How can I correct this? Thanks -- Diego Herrera, M.D. Neuroradiologist Medellin, COLOMBIA

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aparc+aseg2diff.mgz files
by Esther Walton 30 Mar '10

30 Mar '10

Hi, in $SUBJECTS_DIR/any_subject_ID/mri/ there are aparc+aseg2diff.mgz files and norm2diff.mgz files. What does the -2diff- mean and where does it come from? I suspect it's the reason why we have problems with one subject that has a 90 degree turn in fslview, since it was the only one, which didn't have -2diff- files thanks, Esther _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:…

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retinotopic mapping with polar data only
by Yuhong Jiang 29 Mar '10

29 Mar '10

Hi Doug, I was running Freesurfer's retinotopic mapping command (sfa-sess<http://surfer.nmr.mgh.harvard.edu/fswiki/sfa-sess>-a rtopy -s) with only polar angle data. An error was returned saying that it expects eccentricity data. Someone else posted this question last December and you replied and said that one can "fool" the program by copying the polar data into eccen folder. What do you mean exactly by that? Should I copy the bold directory (e.g., 002) that contains the polar data into another run (e.g., 003), and modify the paradigm file (stimtype eccen)? But would that lead to incorrect interpretation by the program? Thanks for your reply. ---------------------------------------------------------- Yuhong Vanessa Jiang, PhD, Department of Psychology, Univ of Minnesota http://jianglab.psych.umn.edu/ ----------------------------------------------------------

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Displaying parcellation labels asegstats2table
by Lena Palaniyappan 29 Mar '10

29 Mar '10

I am trying to obtain mean intensities of Destrieux parcellations using the following command. asegstats2table --subjects <subjid vbms08> --meas mean --statsfile lh.aparc.a2009s.stats --tablefile somename.txt But the output text files does not contain any label names. instead it contains the following as output Measure:mean 2.184 2.442 2.307 2.755 2.869 2.632 2.360 2.073 2.901 2.617 2.186 2.890 3.070 2.748 2.759 2.777 3.201 3.737 2.801 2.376 2.893 1.964 2.967 2.928 2.886 2.778 2.426 2.316 2.805 2.567 2.320 2.522 2.809 3.307 4.177 2.774 2.732 3.128 2.232 2.691 2.258 0.737 2.148 3.682 2.066 1.856 1.972 2.999 2.651 2.521 2.978 1.969 2.207 2.443 2.369 2.455 2.099 1.856 1.821 2.293 2.698 2.386 1.973 2.096 2.393 2.129 2.122 1.981 2.359 2.276 2.645 2.204 2.382 2.379 2.709 vbms08 0.509 0.525 0.482 0.442 0.444 0.706 0.706 0.595 0.551 0.615 0.468 0.499 0.338 0.518 0.472 0.588 0.54 0.881 0.606 0.554 0.453 0.518 0.949 0.763 0.565 0.53 0.52 0.492 0.491 0.522 0.731 0.909 0.393 0.518 0.631 0.448 0.953 0.673 0.305 0.631 0.521 1.353 0.552 0.828 0.595 0.457 0.607 0.538 0.643 0.5 0.721 0.43 0.471 0.53 0.492 0.333 0.471 0.457 0.451 0.489 0.549 0.452 0.427 0.661 0.608 0.531 1.182 0.41 0.476 0.481 0.777 0.559 0.677 0.547 0.417 How can I get the parcellation labels displayed? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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