Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

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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normalized SPGR as an input for inflation
by Vadim Axel 29 Mar '10

29 Mar '10

Dear experts, I run my statistical analysis in SPM, while after coregistration I normalize my data (SPGR and EPI). Since my models and activations images are based on normalized data it's natural for me to use the normalized SPGR as an input for freesurfer inflation. Is it a good enough? Since I run inflation for each individual brain, I basically can do it for non-normalized anatomy, which is preferable, I think. However, then the coordinates are not MNI / Talariach. Attached the comparison of activations for normalized (left side) vs. non-normalized. It looks pretty similar, though the brains look of different shape. So, am I OK to do it on normalized brain? Thanks for help, Vadim

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recon-all error
by ythomas 29 Mar '10

29 Mar '10

Hi, good morning. I encountered a recon-all error in one subject: ERROR: _FindFacePath: could not find path! Linux compute-0-117.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux Interestingly, the error does not show up in the recon-all.error file but does so in the recon-all.log file. You can find the failed subject here: /autofs/space/terrier_002/users/ythomas/GSP/failed_FS_subjects/ 090620_JG49ZK_FS Thanks, Thomas

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tksurfer: more than one overlay with "-overlay" switch?
by John Gelburg 27 Mar '10

27 Mar '10

Hi, I would like to load from the command prompt several overlays, each one for separate layer. I tried just to use twice -overlay switch, but only the last overlay was loaded. Is it feasible? Thanks, John

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calculate the average thickness of a ROI around PCC
by Guang Zeng 26 Mar '10

26 Mar '10

Hi, there, I'd like to measure the average thickness of a ROI around PCC (posterior cingulate cortex). I only have its MNI152 coordinate (-2, -45, 34). How can I calculate its corresponding RAS and Talaraich coordinate, is there an equation? Thanks! Guang _________________________________________________________________ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:…

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