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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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how to map the anatomical to the diffusion space
by 李盟 22 May '12

22 May '12

Hi FreeSurfer Experts, Using the mri_surfcluster command, I got the labels of the significant regions from qdec comparisons of thickness between two groups. The diffusion data was not processed using the dt_recon, but DTI-studio. So how can I map the significant regions to the individual diffusion space? Thanks a lot. Meng Li

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Nipype connectivity workshop 2012
by Chris Filo Gorgolewski 22 May '12

22 May '12

Dear fellow neuroimagers, I am very excited to announce the second Nipype workshop which will take place on 8-9 September 2012 in Magdeburg, Germany. For those who have not heard about Nipype it is a framework which helps designing, maintaining, sharing and executing data processing workflows. It allows you to combine existing data processing solutions (such as FSL, SPM, FreeSurfer and many others), cache partial results, do parameter space exploration and run workflows in parallel (both locally and on clusters). You can read more about Nipype at http://nipy.org/nipype . This year the workshop is going to be a satellite event to the Third Biennial Conference on Resting State Brain Connectivity and therefore focus of the covered analyses will follow the theme of brain connectivity. To learn more about the workshop and register (make sure to be quick - we have limited number of spaces) go to http://nipype.blogspot.com On behalf of the Nipype team, Chris Gorgolewski

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question about reconstructing surface on monkeys
by Leon 21 May '12

21 May '12

Hi, FreeSurfer experts I have some problems reconstructing a wm surface out of a monkey template and would appreciate help from you all. Basically, I try to reconstruct a surface based on the average T1 images of a group of monkeys (see the attached figure). The original surface (?h.orig) looks fine, following the filled.mgz and wm.mgz very well. However, the wm and pial surfaces look messed up, not following the wm.mgz at all and the white matter surface and pial surface almost overlap on each other (i.e., almost zero thickness). I have reconstructed ~6 individual subjects' surfaces in which the T1 image was used to derive the template mentioned above and I have never seen this type of error. I ran the recon-all twice and the results were almost identical. So, I wonder if anyone would tell me what is causing this and possible directions for avoiding such problems. Many thanks in advanceLeon

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label shape with mris_divide_parcellation
by Linda Douw 21 May '12

21 May '12

Hi all, I would like to make a fine-grained surface parcellation from aparc - let's say 500 labels, and I would like the labels to be more or less isometric. When subdividing the parcellation with mris_divide_parcellation, the labels become very stretched instead of isometric. Is there a way to get a different result? Thanks! -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129

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