Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

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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How to get deformation maps in surface-based registrations
by Xiaojing Long 18 May '10

18 May '10

Hi, all, I have a question regarding how to get the deformation map in surface-based registration. I am wanting to use mris_register to align two surfaces. Can I get the deformation maps describing the vertex-to-vertex correspondence? How can I get it? Thanks a lot. Best, Xiaojing

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Re: [Freesurfer] Number of time pointsTuesday, May 18, 2010 12:17 PM
by Tadimeti, Usha 18 May '10

18 May '10

Hi Doug, Thank you very much for the reply. The question that I have now is, how do I distribute my time points between the events and also specify a fixed number of time points for the "NULL" cases? Thanks and Regards, Usha you should not interpret each line as a time point. Each line is a stimulus presentation. You have specified that the presentations are 1 sec long and can occur at an time divisible by 1 sec (--psdwin 0 12 1), so you could have as many as 600 lines. BTW, I would probably go longer than 12 sec for the window, more like 20 would be better. doug Tadimeti, Usha wrote: > Hi, > >> I was trying out a code to generate optimal sequences using optseq2. The code is as follows: >> >> >> optseq2 --ntp 300 --tr 2 \ >> --psdwin 0 12 1 \ >> --ev one 1 20 \ >> --ev two 1 15 \ >> --ev three 1 15 \ >> --ev four 1 50 \ >> --ev five 1 50 \ >> --ev six 1 50 \ >> --ev seven 1 50 \ >> --nkeep 2 \ >> --o ex \ >> --nsearch 10 >> >> The output file for the above code displays more than 300 lines,i.e., >300 time points. How can I modify the code so as to limit the output to 300 time points. Also, the output has all the required categories(events) till the end, Hence I could not just ignore the lines above 300. >> >> Thanks, >> Usha Tadimeti >> Biomedical Engineering Student >> Marquette University >> Milwaukee, Wisconsin >> usha.tadimeti(a)marquette.edu<http://us.mc344.mail.yahoo.com/mc/compose?to=usha.tadimeti@marquette.edu>

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Number of time points
by Tadimeti, Usha 18 May '10

18 May '10

Hi, > > I was trying out a code to generate optimal sequences using optseq2. The code is as follows: > > > optseq2 --ntp 300 --tr 2 \ > --psdwin 0 12 1 \ > --ev one 1 20 \ > --ev two 1 15 \ > --ev three 1 15 \ > --ev four 1 50 \ > --ev five 1 50 \ > --ev six 1 50 \ > --ev seven 1 50 \ > --nkeep 2 \ > --o ex \ > --nsearch 10 > > The output file for the above code displays more than 300 lines,i.e., >300 time points. How can I modify the code so as to limit the output to 300 time points. Also, the output has all the required categories(events) till the end, Hence I could not just ignore the lines above 300. > > Thanks, > Usha Tadimeti > Biomedical Engineering Student > Marquette University > Milwaukee, Wisconsin > usha.tadimeti(a)marquette.edu<http://us.mc344.mail.yahoo.com/mc/compose?to=usha.tadimeti@marquette.edu>

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mri_aparc2aseg on a custom annotation
by Martin Kavec 18 May '10

18 May '10

Hi, I have a problem using mri_aparc2aseg with a custom annotations containing labels created manually in tksurfer and exported. Basically, I would like to end up with a volume file similar as aparc+aseg.mgz but containing only a strip of a cortex corresponding to a label defined using tksurfer. The command I used is following: mri_aparc2aseg --s fsaverage --o labels.mgz --anot labels The command passes fine, but what I get is 2000 for all the cortical voxels, while I expected zeros for all the cortical voxels, except for those corresponding to the label. Any help on is greatly appreciated. Thanks, Martin

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