Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

skullstrip eats brain and leaves skull
by Anne Uhlmann 23 May '12

23 May '12

Hi Freesurfers, I have problems with the troubleshoot of a scan that didn't run at all within autorecon (while the scan actually looks good). So I ran the skullstrip manually and came across the following phenomenon: -when using waterthreshold 25 it gives me an error message and no brainmask.mgz file gets created -when using waterthreshold 24 or lower big chunks of the brain go missing and most of the skull stays I am not sure the manual editing will be a good approach as I would have to remove the complete skull Any suggestions how I could get the skullstrip work? Thank you, Anne ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ###

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Vermis of cerebellum segmentation
by Rafa x 23 May '12

23 May '12

Hi Freesurfers, There is avaliable a cerebelum mask in "http://surfer.nmr.mgh.harvard.edu/fswiki/CerebellumParcellation_Buckner2011" however the corregistration from MNI152 space to subject space produces a few deformation that introduce an error in the fit of the mask into the real vermis of the subject. For that reason I would like to know if it is possible to use freesurfer to segmentate the vermis of cerebellum directly in my subject. Thank you all in advance.

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Couldn't download FsFast tutorial data
by Michael Bannert 23 May '12

23 May '12

Dear freesurfer community, I seem to be unable to download the FsFast tutorial data. ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialData ) I tried each of the two links and I tried "curl -O" as well as wget but nothing worked. Any ideas? Thanks for your help! Michael -- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab CIN Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany

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insula overlabelling
by Alana Shepherd 22 May '12

22 May '12

Dear Nick and Freesurfers, I spoke to Nick at the recent course in Boston regarding this issue. I've been running a recon-all on a 1.5T MPRAGE data set using FS version 5.1, and I've been finding on a number of participants that the aparc segment is substantially over-labelling the insula (on the Desikan atlas only), extending medially to accumbens. I've attached a screen shot of one example. Am appreciative of any suggestions. Thanks, Alana

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Re: [Freesurfer] Surface Area aparc from pial surface
by Douglas N Greve 22 May '12

22 May '12

Hi Ines, this is a good thing to post to the list since there are others that might know better than me. Also, please include the full terminal output. thanks doug On 05/18/2012 11:51 AM, Inês Violante wrote: > Thanks a lot! > > Just another question: > I get this message for one of my subjects using the previous command: > > ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray! > > I must have done something wrong. Is there a way to correct this > without having to run the whole recon-all again? > > All the best, > > ines > > > On Fri, May 18, 2012 at 4:46 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu> wrote: >> yes, but you might want to change the name of the stats file so that you >> don't overwrite the one that is there >> doug >> >> >> On 05/18/2012 11:39 AM, Inęs Violante wrote: >>> Thank you. >>> >>> I've tried this command: >>> >>> mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a >>> AC/label/lh.aparc.annot -c ./aparc.annot.ctab AC lh pial >>> >>> Would this be appropriate? >>> >>> >>> ines >>> >>> On Fri, May 18, 2012 at 4:32 PM, Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu> wrote: >>>> And you can get the full command line from the >>>> $subject/scripts/recon-all.log file >>>> doug >>>> >>>> On 05/18/2012 10:41 AM, Michael Harms wrote: >>>>> The last argument of mris_anatomical_stats allows you to specify the >>>>> surface to use (pial in your case) >>>>> >>>>> cheers, >>>>> -MH >>>>> >>>>> >>>>> NAME >>>>> mris_anatomical_stats >>>>> >>>>> SYNOPSIS >>>>> mris_anatomical_stats [options]<subjectname> <hemi> >>>>> [<surfacename>] >>>>> >>>>> >>>>> On Fri, 2012-05-18 at 15:18 +0100, Inęs Violante wrote: >>>>>> Hi, >>>>>> >>>>>> I need to know the surface area of the structures in the aparc file >>>>>> but I want to obtain this measurement from the pial surface and not >>>>>> the white matter surface. >>>>>> How can I do that? >>>>>> >>>>>> Thank you a lot for your help. >>>>>> >>>>>> ines >>>>>> _______________________________________________ >>>>>> 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. >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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area, and other dependent measures
by Mahinda Yogarajah 22 May '12

22 May '12

Dear Experts, I have some related questions: 1) Am I right in thinking that the default settings for recon-all produce aparc files where the areas are based on white matter and not pia ? 2) Therefore am I right in assuming that when I use aparcstats2table across my subjects using "--meas area", the area is also going to be based on white matter unless I redo the processing using mris_anatomical with a "pial" flag 3) If the above is correct, why is the default to measure areas based on white matter - intuitively this does not make sense to me or seem as useful as gray matter ROI areas (particularly as from my understanding there are further assumptions made in the algorithsm that does the labelling of underlying white matter from the cortex) - are their papers where white matter areas are being reportted ? 4) In a vertex wise analysis of area (using newer version of mris_preproc) what nuisance factors are people using - does it make sense to use total brain surface area (rather than say ICV as one might use in thickness) and in which case does it make a difference to use total pial or white matter area ? 5) Finally what do the dependent measures - intensity_deep/intensity_superficial, intensity_deep.mgz/intensity_superficial.mgz and white K/H measure in qdec ... Thanks. Mahinda

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mri_convert and --out_orientation (once again)
by Clark Fisher 22 May '12

22 May '12

Hi everyone, I have looked through the mailing list, and read a number of threads on using (or rather not using) mri_convert to change the orientation of a volume, and I have read the mri_convert help, which says about the --in_orientation and --out_orientation flags: "This is only to be used when the orientation information in the input file is *wrong*. If it is correct, this will make it wrong!" This lead me to believe that using these flags will only change the header, and not the data matrix, of my nifti files. However, I had a T1 volume in LIA format (taken from a monkey in sphinx position where mri_convert --sphinx had been applied), and needed to put it into RAS format for further processing. mri_convert --out_orientation RAS seemed to work for this, which fslswapdim (which I have seen recommended on the mailing list) introduced a Left/Right switch. That is to say, when I opened the volume output by mri_convert --out_orientation RAS with tkmedit, it displayed properly (unchanged from how it was before mri_convert), and when I loaded it into Matlab with MRIread, the .vol array (and not just the headers) had been reoriented. When I tried to use fslswapdim, on the other hand, the output volume had a left-right switch when viewed in tkmedit (I can tell thanks to a fiducial marker). I'm confused by all of this: is mri_convert behaving like I would like it to, or am I just fooling myself? I'm happy to provide the volumes for other people to inspect. By the way, I'm using FreeSurfer v4.5. -Clark

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Assigning unlabeled vertices to a label
by Sam Carpenter 22 May '12

22 May '12

Hey All, I currently have a cortical parcellation with some unlabeled vertices in it. I'm wondering if anybody knows how to assign a series of unlabeled vertices to a single .label file. These vertices are copious and minute, trying to avoid several hundred 'click, save label as..' repetitions. Thanks in advance! -Sam

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About Mapping voxels from Structural Image to Functional Image
by Sinem Burcu Erdoğan 22 May '12

22 May '12

Dear Freesurfer Community; I need to find the corresponding voxel in a functional image for a specific structural image voxel after coregistering two images. My structural image has 256*256*125 voxels and the functional image has 64*64*30 voxels. I use the following command tkregister2 --s subjectname --targ structural.nii --mov functional.nii --regheader --reg directorythatyouwanttosaveregisterfile/MYregister.dat Where the target is structural image and movable is the functional image then click save to get MYregister.dat. then take the inverse of the matrix save it as invMYregister.dat, and try to use this matrix to transform from anatomical to functional. However; as an example when I try to map voxel (169 , 62 ,35) of the anatomical image to the functional space using the inverse registration matrix; i get the values below - 64.3319 -146.4394 -157.2665 as the corresponding voxels' coordinates at the functional space which is far beyond the functional volume size and is negative. It is clear I cannot manage to use the trasfer matrices appropriately. Your help will be greatly appreciated. Thank you; Sinem Burcu ERDOGAN -- Sinem Burcu ERDOĞAN Research Assistant Bogazici University Biomedical Engineering Institute Kandilli Kampüs 34684 Çengelköy / İSTANBUL TURKEY Tel :+90-216-5163433 Fax :+90-216-5163479 e-mail: burcu.erdogan(a)boun.edu.tr

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Re: [Freesurfer] Question about DODS model and DOSS model
by Douglas N Greve 22 May '12

22 May '12

If things are significant at .001, then there is probably an interaction, but you should also do a correction for multiple comparisons. doug On 05/19/2012 09:55 PM, ZhiLiangLong wrote: > Hi Doug: > Thank so much for your suggestions. Please find Freesufer Digest, Vol > 99, Issue 23, Topic 11: > Question about DODS model and DOSS model. As you suggested, I have > four regressors: Group1 > Intercept, G2 Intercept, G1 slope, G2 slope, and the contrast [0 0 1 > -1].I will test the > interactions between group and age. Is that to say to test the null > hypothesis that G1 slope is > equal with G2 slope? > In qdec, while the analysis was complete, I cliked the Display tab and > saw a list of > questions summarizing the various analyses that were completed. And i > cliked on 'Does the > thickness--age correlation differ between Male and Female?' to test > whether there is no > interactions, and the qdec displayed the statistically significant > regions. I set threshold to > 0.001 and found all regions showing decreased thickness-age > correlation in Male relative to > Female(no increased thickness-age correlation was found). So, may i > draw the conclusion that > there is no interactions between group and age? However, if i set the > threshold lower (e.g. > 0.01), both increased and decreased thickness-age correlation was > found, does that mean the > interactions exist? if so, how do i set the threshold? > Hope you can give me some suggestions. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Freesurfer May 2012