Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

negative thickness value problem
by eunkyung kim 01 Apr '10

01 Apr '10

Dear all I performed recon-all -s subjectID -qcache and obtained thickness data which was normalized to fsaverage template. I'd like to extract thickness value of the '-rh(or lh).thickness.fwhm0.fsaverage.mgh' file in each subjects, so it was transformed to the ascii file format. However, the thickness data obtained from the ascii file did have some negative values. !!! Interestingly, the thickness value that was not normalized to the fsaverage did not have negative values so I was very confused.. Please let me know how can I treat the negative value. I really THANK YOU for your reply. Sincerely, EK.

2 1

autorecon2 error
by Ahmed, F, Me <fahmed＠sun.ac.za> 01 Apr '10

01 Apr '10

Hello, I have been successfully running the recon-all process on all my subjects and have come to a problem with my last subject. I ran autorecon1 without error but when I ran autorecon2, it exited with errors and I don't know why. I have attached the recon-all log and hope someone could give me some insight into what the problem might be. I haven't changed anything so theoretically this subject should have run smoothly as did the 44 others I did previously. Any help would be greatly appreciated. Thank you, Fatima

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averaging FS-Fast retinotopy across subjects
by Lindsay Lewis 31 Mar '10

31 Mar '10

Hi, I have produced retinotopic maps using the FS-Fast retinotopy processing stream for individual subjects. I was wondering if anyone has advice regarding how to average these retinotopic maps across subjects, in order to produce a group average retinotopic map? (something surface-based would be preferable) Many thanks! Lindsay

1 0

Labels to annotation?
by Dankner, Nathan (NIH/NIMH) [F] 31 Mar '10

31 Mar '10

Hi All, I'm sure this information is on the website somewhere, but I had a hard time finding it. Is there a way to consolidate 2 or more labels into one annotation? I am attempting to load two cluster labels onto the difference map in qdec for the purposes of making a figure, but I cannot load more than one label at once, and the cluster annotation includes labels which I do not want to display. Thanks! Nathan

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FW: how to modify the wm.mgz
by Guang Zeng 31 Mar '10

31 Mar '10

Hi there, Recently, I use FreeSurfer analyze a clinic data, the result show a very thin cortex layer, (see figure. 1). I load the wm,mgz (see figure.2), and then overlay the segmentation results, (see figure. 3). As you can see, part of wm.mgz around the wm mask boundary are classified as gm, I guess this is because of partial volume. My question is if I use a better wm mask to replace freesurefer's brainmask (see figure. 4), could I get a better result? Thanks! 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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Re: [Freesurfer] Freesurfer Digest, Vol 73, Issue 76
by mcgray＠usa.com 31 Mar '10

31 Mar '10

Hey my brother .. For the love of God Let this nonsense in the Writing Well, help me .. I was stuck in Turkey .. My only wish for it from you, on that .. Harvard.edu end of an e-mail address is ending as I want .. But unfortunately I can not get such an e-mail address .. Please help me on this subject .. Regards .. McGray

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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

2 1

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:…

2 1

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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