Freesurfer May 2010

freesurfer@nmr.mgh.harvard.edu

98 participants
145 discussions

Reporting coordinates from Group analysis
by Rajagopalan, Venkateswaran 21 May '10

21 May '10

Dear All, I checked the archives but couldn't get a complete answer. I performed group analysis of cortical thickness using mri_glmfit. I am wondering how to report the coordinates of regions where cortical thickness is significantly different, i used FDR for multiple comparisons in tksurfer. So how to get these coordinates after FDR where is this file stored. Thanks venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Re: [Freesurfer] tksurfer tcl scripting: Environment variables for hemisphere and subject
by Andreas Schindler 21 May '10

21 May '10

Thanks! :-) btw: Is there a tcl interface for View -> Configure -> Phase Encoded Data Display: Angle Cycles ? bw Andreas Bruce Fischl wrote: > Hi Andreas, > > the tcl variables $subject and $hemi should be set properly by tksurfer, so > you can use them generically. > > cheers > Bruce > > On Fri, 21 May 2010, Andreas Schindler wrote: > > >> Hello >> >> I am currently writing a tcl script for tksurfer which I am using for >> several subjects. >> That's why I am wondering if it is possible to avoid adapting this tcl >> script for every subject by >> reading out tksurfer's variables for hemisphere and subject as they are >> committed by the shell, anyway. >> >> Many thanks >> >> bw >> >> Andreas >> _______________________________________________ >> 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 > > > 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. > >

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tksurfer tcl scripting: Environment variables for hemisphere and subject
by Andreas Schindler 21 May '10

21 May '10

Hello I am currently writing a tcl script for tksurfer which I am using for several subjects. That's why I am wondering if it is possible to avoid adapting this tcl script for every subject by reading out tksurfer's variables for hemisphere and subject as they are committed by the shell, anyway. Many thanks bw Andreas

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transform ribbon to FSL-diffusion space
by Theodor R?ber 20 May '10

20 May '10

Dear Freesurfers, I am trying to transform a Freesurfer-generated white matter mask (ribbon) to FSL diffusion space in order to use it as a stop-mask in fibertracking. I have tried to coregister and reslice it to the normalized dti_FA with SPM and I also tried to transform it with FSL-FLIRT and FSL-FNIRT as described on http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html. Unfortunately, neither approach yielded satisfying results. What steps would you recommend to turn the Freesurfer output into a FSL-FDT compatible white matter mask? Thank you very much in advance. Your help will be greatly appreciated. Best, Theodor

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how to QC hippocampal measurement
by Guang Zeng 20 May '10

20 May '10

Hi, there, I have used FreeSurfer to measure the hippocampal size of 200 ADNI subjects, and now I'd like to QC the hippocampal measurement. Anyone can give me some suggestion to do this, instead of loading they one-by-one ? Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/

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Changing roi label display color in tkmedit
by Lena Palaniyappan 20 May '10

20 May '10

I want to show a group of 5 labels ach with a different color in tkmedit (Orig.mgz) display can I manipulate the colors of these lables I am able to do this in tksurfer: not tkmedit. Am I missing something? Cheers Lena _______________________________________________________ Lena Palaniyappan PhD Student & 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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No green line in tkregister2...
by Gonzalo Rojas Costa 19 May '10

19 May '10

Hi: No green line appears in tkregister2 over the fuzzy volume... Why ?... Sincerely, Gonzalo Rojas Costa

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Number of Time points
by Tadimeti, Usha 19 May '10

19 May '10

Hi , I am basically trying to get an output with 300 lines and the events "one", "two"..."seven" and "null" to be distributed in those 300 points. But when I get the output, I get more than 300 lines and the number of "null" lines in the output is variable(i.e., the 2 output files ex-001.par and ex-002.par both show different number of lines of output with variable number of "null" lines). I slightly changed the code and still I don't get the desired output. So, in a nutshell, I need 300 lines of output with all the events and "null" in those 300 lines. Can you let me know what I should be doing now? The code is as follows: optseq2 --ntp 300 --tr 2 \ >>> --psdwin 0 20 \ >>> --ev one 2 20 \ >>> --ev two 2 15 \ >>> --ev three 2 15 \ >>> --ev four 2 50 \ >>> --ev five 2 50 \ >>> --ev six 2 50 \ >>> --ev seven 2 50 \ >>> --nkeep 2 \ >>> --o ex \ >>> --nsearch 10 Usha

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OASIS database difference aseg volumetry...
by Gonzalo Rojas Costa 19 May '10

19 May '10

Hi: I downloaded a dataset image from OASIS (OAS1_0068_MR1)... I reprocessed with Freesurfer v4.5.0 (recon-all -legacy command).... But, there are differences between the old and new aseg.stats file... for example, the ICV: 1433107.255467 (old), 1328556.632821 (new)... left Hippocampus: 4130.0 (old), 3900.0 (new), etc... Why ?... Sincerely, Gonzalo Rojas Costa

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Freesurfer for stroke subjects?
by Cheol Han 19 May '10

19 May '10

Hello Freesurfers We are going to handle some subjects with stroke or subjects who receives a surgery to remove brain tumors. I just wonder whether it is possible to use freesurfer for those subjects and how the surface registration is affected. Best, Han

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Freesurfer May 2010